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Difference between revisions of "Polysaccharide epimerases"

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== Introduction ==
 
== Introduction ==
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Epimerases and racemases catalyse the inversion of stereochemistry in biological molecules. Epimerases invert the stereochemistry of only one stereogenic center in a molecule that has at least two, and racemases create racemates from pure enantiomers. These functionalities makes organisms able to utilize several different stereoisomers of the same compounds. Whereas most enzymes catalyze reactions where reactants and products have only one stereochemistry, epimerases and racemases must be able to accomodate two different stereoisomers in their active site. Many epimerases and racemases break a C-H bond next to a carbonyl functional group, and then reform it with the new stereochemistry <cite>tanner2002</cite>.
  
=== Classification ===
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van Overtveldt et al. classified 39 known carbohydrate epimerase specificities into 14 different families based on sequence alignments <cite>overtveldt2015</cite>. Five different epimerization mechanisms were described: I) deprotonation/reprotonation,  II) transient keto intermediate, III) carbon-carbon bond cleavage, IV) nucleotide elimination and V) mutarotation. Members of a family share mechanism and conserved catalytic residues. Only two of the 14 families are active on polysaccharides: CEP7 containing mannuronan C5-epimerases (alginate epimerases) and CEP8 containing heparosan-N-sulfate-glucuronate 5-epimerase (heparosan epimerase). Together with the unclassified dermatan sulfate C5-epimerase (chondroitin epimerase), these enzymes perform a similar polymer level C5-epimerization on polysaccharides consisting of hexuronic acids. Both alginates and the glycosaminoglycans heparin/heparan and dermatan sulfate are block copolymers of the two monomers created by these epimerases. In alginates the epimerization is from <font style="font-feature-settings: 'smcp'">d</font>-mannuronic acid to <font style="font-feature-settings: 'smcp'">l</font>-guluronic acid, while in the glycosaminoglycans it is from <font style="font-feature-settings: 'smcp'">d</font>-glucuronic acid to <font style="font-feature-settings: 'smcp'">l</font>-iduronic acid <cite>haug1969, Lindahl1972, malmstrom1975, valla2001</cite>.
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Alginate and glucosaminoglycan epimerases share a deprotonation/reprotonation mechanism where neutralization of the sugar carboxyl group is followed by proton abstraction from one side of the sugar ring, creating an intermediate that is resonance stabilized by the carboxyl group. The pK<sub>a</sub> of the hydrogen is lowered due to this resonance stabilization <cite>valla2001, tanner2002</cite>. For the mannuronan C5-epimerase the intermediate is thought to be an enolate anion, while for the heparin epimerase it could be a neutral enol <cite>debarnot2019</cite>. For the dermatan epimerases it is proposed to be a 4,5-unsaturated residue where the glycosidic bond is cleaved and subsequently reformed <cite>pacheco2009</cite>, and this is also proposed as an alternative hypothesis for the alginate epimerases <cite>jerga2006</cite>. Addition of another proton to the opposite face of the sugar ring creates the epimer. The mechanism is probably similar to that of the corresponding polysaccharide lyases, see [[Polysaccharide Lyases]] <cite>gacesa1987</cite>. For the lyases, the intermediate created by the proton abstraction results in a &beta;-elimination where the leaving group is protonated by the enzyme instead of the C5-carbon, and 4,5-unsaturated residue is the reaction product.
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Despite performing similar reactions, the three hexuronyl C5-epimerase families share almost no sequence or structural identity <cite>overtveldt2015, qin2015</cite>.
  
 
== Mannuronan C5-epimerases ==
 
== Mannuronan C5-epimerases ==
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[[Image:Alginate structures4.png|thumb|400px|Figure 1. A. Haworth structures of <font style="font-feature-settings: 'smcp'">d</font>-mannuronic acid (M) and <font style="font-feature-settings: 'smcp'">l</font>-guluronic acid (G). B. The three different block structures found in alginate: non-epimerized M-blocks, MG-blocks and G-blocks.]]
 
[[Image:Alginate structures4.png|thumb|400px|Figure 1. A. Haworth structures of <font style="font-feature-settings: 'smcp'">d</font>-mannuronic acid (M) and <font style="font-feature-settings: 'smcp'">l</font>-guluronic acid (G). B. The three different block structures found in alginate: non-epimerized M-blocks, MG-blocks and G-blocks.]]
 
Mannuronan C5-epimerases are a group of enzymes that catalyze epimerization at the polymer-level of &beta;-<font style="font-feature-settings: 'smcp'">d</font>-mannuronic acid residues (hereafter denoted M) into &alpha;-<font style="font-feature-settings: 'smcp'">l</font>-guluronic acid residues (hereafter denoted G) in alginate <cite>haug1969, larsen1971, haug1971</cite>. Alginate is an anionic polysaccharide made by brown seaweeds, some species of red algae, and the gram-negative bacterial genera ''Pseudomonas'' and ''Azotobacter'' <cite>Stanford1883, Gorin1966, Linker1966, govan1981, okazaki1982</cite>. The function of alginate in the different organisms are various, and related to structure, protection and surface adhesion <cite>painter1983, campos1996, Pier2001, Harmsen2010 </cite>. Alginate is a copolymer of the two 1-4 linked epimers <cite> Hirst1939, fischer1955, Drummond1962 </cite>, and by changing the composition of the two monomers the epimerases fine-tune the properties of the polymer <cite> Ertesvaag1999 </cite>.
 
Mannuronan C5-epimerases are a group of enzymes that catalyze epimerization at the polymer-level of &beta;-<font style="font-feature-settings: 'smcp'">d</font>-mannuronic acid residues (hereafter denoted M) into &alpha;-<font style="font-feature-settings: 'smcp'">l</font>-guluronic acid residues (hereafter denoted G) in alginate <cite>haug1969, larsen1971, haug1971</cite>. Alginate is an anionic polysaccharide made by brown seaweeds, some species of red algae, and the gram-negative bacterial genera ''Pseudomonas'' and ''Azotobacter'' <cite>Stanford1883, Gorin1966, Linker1966, govan1981, okazaki1982</cite>. The function of alginate in the different organisms are various, and related to structure, protection and surface adhesion <cite>painter1983, campos1996, Pier2001, Harmsen2010 </cite>. Alginate is a copolymer of the two 1-4 linked epimers <cite> Hirst1939, fischer1955, Drummond1962 </cite>, and by changing the composition of the two monomers the epimerases fine-tune the properties of the polymer <cite> Ertesvaag1999 </cite>.
At first, alginate is made as a homopolymer of M in the cell. Epimerases then convert some of the M residues in the polymer into G-residues <cite> lin1966, haug1971, franklin1994 </cite>. This epimerization is not random and creates block structures of M, G or alternating MG <cite> haug1966, haug1967 </cite>, see Figure 1. Alginate residues that are oxidized or acetylated are not substrates for the epimerases, and acetylation of alginate could be a way to control epimerization in nature <cite> skjaakbrek1985, Kristiansen2009 </cite>.
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At first, alginate is made as a homopolymer of M in the cell. Epimerases then convert some of the M-residues in the polymer into G-residues <cite> lin1966, haug1971, franklin1994 </cite>. This epimerization is not random and creates block structures of M, G or alternating MG <cite> haug1966, haug1967 </cite>, see Figure 1. Alginate residues that are oxidized or acetylated are not substrates for the epimerases, and acetylation of alginate could be a way to control epimerization in nature <cite> skjaakbrek1985, Kristiansen2009 </cite>.
  
Mannuronan C5-epimerases exist both in algae and in bacteria <cite> haug1969, madgwick1973 </cite>. Gene analyses propose as many as 31 different genes encoding putative mannuronan C-5 epimerases in the brown algae ''Ectocarpus'' <cite> Fischl2016 </cite>. However, the algal epimerases are difficult to express and it is the bacterial enzymes that have been studied most extensively <cite> nyvall2003, Fischl2016 </cite>. Two categories of bacterial mannuronan C-5-epimerases have been described: the periplasmic AlgG and the extracellular and calcium dependent AlgE. AlgG creates single G residues in stretches of mannuronan, while the AlgE enzymes are processive and create MG-blocks and G-blocks. ''Pseudomonas'' is only known to produce AlgG <cite> Chitnis1990, franklin1994, morea2001 </cite>, while ''A. vinelandii'' contains seven active AlgE enzymes in addition to AlgG <cite> ertesvag1994, ertesvag1995, rehm1996, svanem1999 </cite>. A mutant strain of ''P. fluorescens'' without the ''algG'' gene creates pure mannuronan <cite> Gimmestad2003 </cite>. This strain can be used to produce unepimerized substrate, which is useful for the study of the epimerization reaction. Methods for studying this are discussed in a later section.
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Mannuronan C5-epimerases exist both in algae and in bacteria <cite> haug1969, madgwick1973 </cite>. Gene analyses propose as many as 31 different genes encoding putative mannuronan C-5 epimerases in the brown algae ''Ectocarpus'' <cite> Fischl2016 </cite>. However, the algal epimerases are difficult to express and it is the bacterial enzymes that have been studied most extensively <cite> nyvall2003, Fischl2016 </cite>. Two categories of bacterial mannuronan C-5-epimerases have been described: the periplasmic AlgG and the extracellular and calcium dependent AlgE. AlgG creates single G residues in stretches of mannuronan, while the AlgE enzymes are processive and create MG-blocks and G-blocks. ''Pseudomonas'' is only known to produce AlgG <cite> Chitnis1990, franklin1994, morea2001 </cite>, while ''A. vinelandii'' contains seven active AlgE enzymes in addition to AlgG <cite> ertesvag1994, ertesvag1995, rehm1996, svanem1999 </cite>. A mutant strain of ''P. fluorescens'' without the ''algG'' gene creates pure mannuronan <cite> Gimmestad2003 </cite>. This strain can be used to produce unepimerized substrate, which is useful for the study of the epimerization reaction. Methods for studying this are discussed in a [[#Methods to study the reaction|later section.]]
  
 
=== Product profiles ===
 
=== Product profiles ===
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The mechanism is suggested to be similar to the lyase mechanism, as illustrated in Figure 2 <cite> gacesa1987 </cite>. This is supported by several of the ''A. vinelandii'' enzymes having both lyase and epimerase activity <cite> ramstad1999, svanem1999, svanem2001, Holtan2006 </cite>. Different versions of NNHSY is a common motif in both epimerases and lyases, and it is implicated to be important for catalysis or binding <cite> yoon2001, Ertesvag1998b, Gimmestad2003 </cite>.
 
The mechanism is suggested to be similar to the lyase mechanism, as illustrated in Figure 2 <cite> gacesa1987 </cite>. This is supported by several of the ''A. vinelandii'' enzymes having both lyase and epimerase activity <cite> ramstad1999, svanem1999, svanem2001, Holtan2006 </cite>. Different versions of NNHSY is a common motif in both epimerases and lyases, and it is implicated to be important for catalysis or binding <cite> yoon2001, Ertesvag1998b, Gimmestad2003 </cite>.
  
The proposed epimerase mechanism is initiated with neutralization of the negative charge of the carboxylate group. This is followed by abstraction of H5 by a catalytic base and ends with an addition of another proton to the opposite side of the sugar ring by a catalytic acid. The conformation of the monomer flips from <sup>4</sup>C<sub>1</sub> to <sup>1</sup>C<sub>4</sub>, and changes it from &beta;-<font style="font-feature-settings: 'smcp'">d</font>-mannuronate to &alpha;-<font style="font-feature-settings: 'smcp'">l</font>-guluronate. In the lyase mechanism, the second step is a &beta;-elimination of the 4-''O''-glycosidic bond to form a 4-deoxy-<font style="font-feature-settings: 'smcp'">l</font>-''erythro''-hex-4-enepyranosyluronate, called &Delta;, at the non-reducing end.
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The proposed epimerase mechanism is initiated with neutralization of the negative charge of the carboxylate group. This is followed by abstraction of H-5 by a catalytic base and ends with an addition of another proton to the opposite side of the sugar ring by a catalytic acid. The conformation of the monomer flips from <sup>4</sup>C<sub>1</sub> to <sup>1</sup>C<sub>4</sub>, and changes it from &beta;-<font style="font-feature-settings: 'smcp'">d</font>-mannuronate to &alpha;-<font style="font-feature-settings: 'smcp'">l</font>-guluronate. In the lyase mechanism, the second step is a &beta;-elimination of the 4-''O''-glycosidic bond to form a 4-deoxy-<font style="font-feature-settings: 'smcp'">l</font>-''erythro''-hex-4-enepyranosyluronate, called &Delta;, at the non-reducing end.
 
=== Methods to study the reaction ===
 
=== Methods to study the reaction ===
 
Several methods have been used either to measure catalytic rates, or to characterize the epimerized product in terms of relative amounts of M, G and block compositions at different conditions and treatment times.
 
Several methods have been used either to measure catalytic rates, or to characterize the epimerized product in terms of relative amounts of M, G and block compositions at different conditions and treatment times.
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=== Catalytic residues ===
 
=== Catalytic residues ===
 
[[Image:binding_actsite2.png|thumb|400px|Figure 3. Electrostatic surface potential and catalytic sites of A. AlgE4 ([{{PDBlink}}2PYH PDB ID 2PYH], <cite> Rozeboom2008 </cite>) and B. AlgG ([{{PDBlink}}4NK6 PDB ID 4NK6], <cite> wolfram2014 </cite>). The maps are created using the APBS electrostatics plug-in <cite> jurrus2018 </cite> in PyMOL <cite> PyMOL </cite>. The scale is from -5 to +5 kT/e, where negative potential is colored red and positive potential is colored blue. The mannuronate trimer in the crystal strucutre of AlgE4 is shown as ball-and-stick with carbon atoms in green and oxygen atoms in red.]]
 
[[Image:binding_actsite2.png|thumb|400px|Figure 3. Electrostatic surface potential and catalytic sites of A. AlgE4 ([{{PDBlink}}2PYH PDB ID 2PYH], <cite> Rozeboom2008 </cite>) and B. AlgG ([{{PDBlink}}4NK6 PDB ID 4NK6], <cite> wolfram2014 </cite>). The maps are created using the APBS electrostatics plug-in <cite> jurrus2018 </cite> in PyMOL <cite> PyMOL </cite>. The scale is from -5 to +5 kT/e, where negative potential is colored red and positive potential is colored blue. The mannuronate trimer in the crystal strucutre of AlgE4 is shown as ball-and-stick with carbon atoms in green and oxygen atoms in red.]]
All known epimerases share a YG(F/I)DPH(D/E) motif located in the +1 subsite. In the AlgE epimerases the catalytic residues are identified as the four essential amino acids Y149, D152 and H154 of this motif, in addition to D178 that is lacking in AlgG <cite> svanem2001, nyvall2003, Douthit2005, Rozeboom2008 </cite> (See Figure 3A). A lot is still unclear about the catalytic mechanism and of the exact role of each catalytic residue. It has been suggested that tyrosine acts as the catalytic base in the reaction, marked AA2 in Figure 2, while the histidine is the catalytic acid, AA3 <cite> Rozeboom2008 </cite>. The two acidic residues might be important in maintaining the pKa of this site, as well as orienting the catalytic base. In AlgG (Figure 3B), H319 is hypothesized to be the catalytic base, water to be the catalytic acid and R345 to neutralize the carboxyl group <cite> wolfram2014 </cite>.
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All known epimerases share a YG(F/I)DPH(D/E) motif located in the +1 subsite. In the AlgE epimerases the catalytic residues are identified as the four essential amino acids Y149, D152 and H154 of this motif, in addition to D178 that is lacking in AlgG <cite> svanem2001, nyvall2003, Douthit2005, Rozeboom2008 </cite> (See Figure 3A). A lot is still unclear about the catalytic mechanism and of the exact role of each catalytic residue. It has been suggested that tyrosine acts as the catalytic base in the reaction, marked AA2 in Figure 2, while the histidine is the catalytic acid, AA3 <cite> Rozeboom2008 </cite>. The two acidic residues might be important in maintaining the pK<sub>a</sub> of this site, as well as orienting the catalytic base. In AlgG (Figure 3B), H319 is hypothesized to be the catalytic base, water to be the catalytic acid and R345 to neutralize the carboxyl group <cite> wolfram2014 </cite>.
 
=== Role of calcium ===
 
=== Role of calcium ===
The seven secreted epimerases of ''A. vinelandii'', AlgE1-AlgE7, are all calcium-dependent <cite> haug1969, ofstad1981, ertesvag1999 </cite>. Activity increases with increasing calcium concentration up to around 5 mM calcium, with the optimum depending on the enzyme <cite> haug1971, Ertesvag1998, hoidal1999, ramstad1999, svanem2001 </cite>. At the same time increased calcium concentration gives a decrease in end point conversion due to gelation of product <cite> haug1971 </cite>. It is unknown whether calcium is important for the mechanism itself or if its only role is to stabilize the structure (see next section). Early studies indicated it had a role in enzyme stability, as the temperature stability increased at higher calcium concentrations <cite> haug1971 </cite>. In the resolved crystal structure of AlgE4's A-module, a calcium ion is bound in a hairpin loop away from the active site <cite> Rozeboom2008 </cite> ([{{PDBlink}}2PYH PDB ID 2PYH]). Without the calcium ion the loop would likely change conformation, which could destabilize the active fold of the enzyme. If calcium has an additional role in the catalytic activity, it could be in neutralizing the negative charge of the carboxylic anion. This is observed in the structurally similar alginate lyases from the polysaccharide lyase family 6 <cite> huang1999, michel2004, xu2017, stender2019b </cite>. The periplasmic AlgG epimerases do not require calcium for their activity <cite> franklin1994, rehm1996 </cite>.
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The seven secreted epimerases of ''A. vinelandii'', AlgE1-AlgE7, are all calcium-dependent <cite> haug1969, ofstad1981, ertesvag1999 </cite>. Activity increases with increasing calcium concentration up to around 5 mM calcium, with the optimum depending on the enzyme <cite> haug1971, Ertesvag1998, hoidal1999, ramstad1999, svanem2001 </cite>. At the same time increased calcium concentration gives a decrease in end point conversion due to gelation of product <cite> haug1971 </cite>. It is unknown whether calcium is important for the mechanism itself or if its only role is to stabilize the structure (see the section about [[#Three-dimensional structures|three-dimensional structures]]). Early studies indicated it had a role in enzyme stability, as the temperature stability increased at higher calcium concentrations <cite> haug1971 </cite>. In the resolved crystal structure of AlgE4's A-module, a calcium ion is bound in a hairpin loop away from the active site <cite> Rozeboom2008 </cite> ([{{PDBlink}}2PYH PDB ID 2PYH]). Without the calcium ion the loop would likely change conformation, which could destabilize the active fold of the enzyme. If calcium has an additional role in the catalytic activity, it could be in neutralizing the negative charge of the carboxylic anion. This is observed in the structurally similar alginate lyases from the polysaccharide lyase family 6 <cite> huang1999, michel2004, xu2017, stender2019b </cite>. The periplasmic AlgG epimerases do not require calcium for their activity <cite> franklin1994, rehm1996 </cite>.
  
 
=== Substrate binding ===
 
=== Substrate binding ===
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The parallel &beta;-helix fold found in the active modules of the epimerases was first encountered in another enzyme active on polyanionic substrate, namely the pectate lyase C of ''Erwinia chrysanthemi'' <cite> yoder1993 </cite>. It is also called a &beta;-solenoid-type fold as it consists of repeated &beta; strands, and it is a type L &beta;-solenoid <cite> kajava2006 </cite>. In the epimerases it is found together with an N-terminal &alpha;-helix cap that shields the hydrophobic interior of the &beta;-helix from the solvent. This combination is found in several other enzyme families of glycoside hydrolases ([[GH28]], [[GH49]], [[GH55]], [[GH82]], and [[GH87]] in the CAZy database <cite> rigden2002 </cite>) and of polysaccharide lyases ([[PL1]], [[PL3]], [[PL6]], and [[PL9]] <cite> Garron2010 </cite>): alginate lyases <cite> xu2017 </cite>, dextranases <cite> Larsson2003 </cite>, rhamnogalacturonases <cite> petersen1997 </cite>, polygalacturonase <cite> pickersgill1998 </cite>, &beta;-1,3-glucanases <cite> Ishida2009 </cite>, &iota;-carrageenases <cite> michel2001 </cite>, endorhamnosidases <cite> steinbacher1994 </cite>, pectate and pectin lyases <cite> yoder1993, mayans1997, akita2001, Jenkins2004 </cite> and chondroitin B (dermatan sulfate) lyases <cite> huang1999 </cite>. Since these enzymes have a high degree of structural similarity, it is thought that at least some of them diverged from a common ancestor <cite> jenkins1998 </cite>, although convergent evolution is not unlikely <cite> kajava2006 </cite>.
 
The parallel &beta;-helix fold found in the active modules of the epimerases was first encountered in another enzyme active on polyanionic substrate, namely the pectate lyase C of ''Erwinia chrysanthemi'' <cite> yoder1993 </cite>. It is also called a &beta;-solenoid-type fold as it consists of repeated &beta; strands, and it is a type L &beta;-solenoid <cite> kajava2006 </cite>. In the epimerases it is found together with an N-terminal &alpha;-helix cap that shields the hydrophobic interior of the &beta;-helix from the solvent. This combination is found in several other enzyme families of glycoside hydrolases ([[GH28]], [[GH49]], [[GH55]], [[GH82]], and [[GH87]] in the CAZy database <cite> rigden2002 </cite>) and of polysaccharide lyases ([[PL1]], [[PL3]], [[PL6]], and [[PL9]] <cite> Garron2010 </cite>): alginate lyases <cite> xu2017 </cite>, dextranases <cite> Larsson2003 </cite>, rhamnogalacturonases <cite> petersen1997 </cite>, polygalacturonase <cite> pickersgill1998 </cite>, &beta;-1,3-glucanases <cite> Ishida2009 </cite>, &iota;-carrageenases <cite> michel2001 </cite>, endorhamnosidases <cite> steinbacher1994 </cite>, pectate and pectin lyases <cite> yoder1993, mayans1997, akita2001, Jenkins2004 </cite> and chondroitin B (dermatan sulfate) lyases <cite> huang1999 </cite>. Since these enzymes have a high degree of structural similarity, it is thought that at least some of them diverged from a common ancestor <cite> jenkins1998 </cite>, although convergent evolution is not unlikely <cite> kajava2006 </cite>.
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== Heparosan-N-sulfate-glucuronate 5-epimerase ==
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=== Substrate specificities ===
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[[Image:XXX.png|thumb|400px|Figure 5. Heparan sulfate]]
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The heparin/heparan epimerase catalyze the polymer level epimerization of &beta;-<font style="font-feature-settings: 'smcp'">d</font>-glucuronic acid (GlcA) to &alpha;-<font style="font-feature-settings: 'smcp'">l</font>-iduronic acid (IdoA) in the glycosaminoglycan heparan sulfate <cite>hook1974</cite>. Heparan sulfate consists of long chains of a repeating disaccharide motif, 1-4 linked alternating monomers of GlcA or IdoA and &alpha;-<font style="font-feature-settings: 'smcp'">d</font>-glucosamine (GlcN). GlcN monomers can be acetylated, and all three sugar units can be either ''O''-sulfated or ''N''-sulfated. While GlcA adopts a <sup>4</sup>C<sub>1</sub> chair conformation, IdoA exists in an equilibrium between <sup>1</sup>C<sub>4</sub> and the skew-boat conformation <sup>2</sup>S<sub>0</sub>  <cite>valla2001</cite>. Domains in heparan sulfate have various compositions of monomers and modifications, and long domains with high amounts of ''N''-sulfated disaccharide units are called heparin <cite>gallagher1985</cite>.
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Heparan sulfate is found in all animal cells as proteoglycans. Due to its negative charge and diverse sequence motifs, the polysaccharide is known to interact with many different proteins and affect most cellular processes mainly through electrostatic interactions. Heparin is stored in secretory granules in mast cells and released when tissue is injured. When it binds to antithrombin it aids in inhibiting blood coagulation. Heparin is produced industrially as an anticoagulant, but its roles in tissue injury and repair in cells are diverse and complex <cite>valla2001, bishop2007</cite>.
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Activity of the heparin/heparan epimerase requires that the residue to be epimerased has a deacetylated and ''N''-sulfated glucosamine linked to its C-4 (subsite -1). ''O''-sulfation of the residue in the active site or of neighbouring residues inhibits epimerization. The residue linked to C-1 of the sugar unit in the active site can be either ''N''-sulfated or ''N''-acetylated for epimerization to occur, but ''N''-sulfated is the better substrate. An octasaccharide is found to be the minimal substrate size <cite>jacobsson1984, hagner2000</cite>.
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The enzymatic reaction is reversible when the substrate has a glucosamine or sulfated glucosamine three residues away from the epimerization site towards the nonreducing end, or if this site is unoccupied. On the other hand, if the substrate has an acetylated glucosamine in the same site the enzyme irreversibly introduce <font style="font-feature-settings: 'smcp'">l</font>-iduronic acid residues to the heparin chains. The reaction is also irreversible in vivo, probably due to the structure of the biosynthetic pathway <cite>hagner2004, li2010, sheng2012</cite>.
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An enzyme with a slightly different substrate specificity has been identified from the giant African snail ''Achatina fulica'' <cite>mochizuki2015</cite>. The glycosaminoglycan acharan sulfate contains repeating units of acetylated glucosamine and ''O''-sulfated IdoA. The epimerase creating IdoA in this polymer is named heparosan-glucuronate 5-epimerase since it is active on heparosan, as opposed to the heparosan-N-sulfate-glucuronate 5-epimerase that requires a deacetylated and sulfated substrate.
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=== Catalytic reaction and mechanism ===
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The catalytic reaction is thought to follow a similar mechanism to the mannuronan C5-epimerases described in [[#Mechanism|an earlier section]], and also to that of heparin and dermatan sulfate lyases <cite>Han2009,lunin2004</cite>. A tyrosine is recognized as the proton acceptor, and a glutamate as the proton donor. Based on structural analysis of substrate and product complexes it is thought that the reaction proceeds through a neutral enol intermediate, with ring distortion to facilitate epimerization <cite>debarnot2019</cite>. Originally this intermediate was proposed to be an &alpha;-carbanion <cite>prihar1980</cite>, or an enolate as for the other polysaccharide epimerases <cite>qin2015</cite>. Two other tyrosines are shown to be essential for activity, and they are hypothesized to be part of proton relay pathways between the active site and the solvent <cite>qin2015, debarnot2019</cite>. The readdition of the proton is the rate-limiting step <cite>hagner2000b, debarnot2019</cite>. heparin/heparan epimerases do not require divalent cations for activity, unlike the alginate and dermatan sulfate epimerases <cite>malmstrom1980</cite>. However, one calcium ion is bound to each subunit in the crystal structure of human heparin/heparan epimerase <cite>debarnot2019</cite>. In the crystal structure of zebrafish heparin/heparan epimerase, a water molecule is bound in the same position <cite>qin2015</cite>.
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=== Three-dimensional structures ===
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[[Image:hglce.png|thumb|400px|Figure 6. Cartoon representation of the dimeric assembly of human glucuronyl C5-epimerase ([{{PDBlink}}6HZZ PDB ID 6HZZ]) <cite>debarnot2019</cite>. The N-terminal &beta;-hairpin domain is colored in purple, the &beta;-sandwich domain is colored in red and the (&alpha;/&alpha;)<sub>4</sub>-barrel domain is colored in green. One calcium ion is coordinated in the sandwich domain of each subunit and shown as an orange sphere. Three ''N''-glycans bound to each subunit are shown in sticks and spheres.]]
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In 2015 the first crystal structure was solved, <font style="font-feature-settings: 'smcp'">d</font>-Glucuronyl C5-epimerase from zebrafish ([{{PDBlink}}4PW2 PDB ID 4PW2]) <cite>qin2015</cite>. The protein crystallizes as a homodimer and has three domains: an &alpha;-helical transmembrane region, a &beta;-barrel domain and a flexible N-terminal loop. Enzyme complexed with an inhibiting heparin hexamer was also crystallized ([{{PDBlink}}4PXQ PDB ID 4PXQ]).
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The next structure to be solved was human <font style="font-feature-settings: 'smcp'">d</font>-Glucuronyl C5-epimerase ([{{PDBlink}}6HZZ PDB ID 6HZZ]) <cite>debarnot2019</cite>. Like the zebrafish enzyme it is a dimer where each subunit has three domains. The N-terminal domain consists of two antiparallel &beta;-hairpins connected by a helix. This is followed by a &beta;-sandwich domain, and a C-terminal (&alpha;/&alpha;)<sub>4</sub>-barrel domain containing the active site. The dimer is probably the active form of the enzyme. Figure 6 shows the dimeric structure of human glucuronyl C5-epimerase. Structures of an inactive mutant bound to a substrate and a product were also deposited (PDB IDs [{{PDBlink}}6I01 6I01] and [{{PDBlink}}6I02 6I02]) <cite>debarnot2019</cite>.
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== Dermatan sulfate C5-epimerase ==
 +
 +
=== Substrate specificities ===
 +
Just like the heparin epimerase, the two dermatan sulfate epimerases catalyze the epimerization of &beta;-<font style="font-feature-settings: 'smcp'">d</font>-glucuronic acid (GlcA) to &alpha;-<font style="font-feature-settings: 'smcp'">l</font>-iduronic acid (IdoA) in polymers of glycosaminoglycans <cite>malmstrom1982, maccarana2006, pacheco2009b</cite>. The repeating disaccharide unit of dermatan sulfate is 1-3 linked GlcA or IdoA and 1-4 linked &beta;-<font style="font-feature-settings: 'smcp'">d</font>-N-acetyl galactosamine (GalNAc). Sulfation can occur at C-2 of iduronic acid and at C-4 and/or C-6 of galactosamine. The polymer can have various length, epimerization and sulfation, and bind to a variety of proteins <cite>trowbridge2002</cite>. The unepimerized polymer is called chondroitin sulfate. Although dermatan sulfate was earlier known as chondroitin B it is no longer classified as a chondroitin sulfate <cite>NLM2020</cite>. Chondroitin/dermatan sulfate exists as proteoglycans in extracellular matrixes in mammalian tissues, especially skin. The polysaccharide is involved in many different cell processes due to its sequence variability and diverse protein partners <cite>trowbridge2002</cite>.
 +
 +
Dermatan sulfate consists of block structures of (IdoA-GalNAc)n, (GlcA-GalNAc)n and hybrid domains containing both uronic acids. Two epimerases are characterized, dermatan sulfate epimerase 1 and 2, and they have slightly different product pattern which could be important in regulating domain formation. They are found in a variety of animals, including humans <cite>pacheco2009b</cite>.
 +
 +
Dermatan is a better substrate for the epimerases than chondroitin, and the epimerases are not active on sulfated substrates <cite>malmstrom1984</cite>. However, the co-incubation of epimerases and sulfotransferases synergistically promotes formation of iduronic acid. To be able to processively form long iduronic acid containing domains, the epimerases physically interact with the sulfotransferase <cite>malmstrom1975, tykesson2018</cite>. The minimal substrate length for optimal binding has been shown to be an octamer <cite>tykesson2016</cite>.
 +
 +
=== Catalytic reaction and mechanism ===
 +
A mechanism is suggested where a proton is abstracted from one side of glucuronic acid by a histidine, the glycosidic bond is cleaved by involvement of a tyrosine and another histidine attaching a proton to the other side of the ring. This will involve a 4,5-unsaturated intermediate, similar to the end product of polysaccharide lyases. The glycosidic bond would be formed again by the tyrosinate ion or a second general acid <cite>pacheco2009</cite>. The two histidines could switch roles as acid and base, giving rise to the reversibility seen in vitro <cite>hannesson1996</cite>. The enzyme requires divalent cations, preferably Mn<sup>2+</sup>, and N-glycosylation for activity <cite>malmstrom1982, pacheco2009</cite>. It processively epimerizes four to five monomers from the reducing towards the non-reducing end, with decreased binding affinity for each processive step <cite>tykesson2016</cite>. In vivo the concomitant action of epimerase and sulfotransferase could account for a higher processivity, as well as irreversible formation of iduronic acid <cite>malmstrom1984, eklund2000, tykesson2018</cite>.
 +
 +
=== Three-dimensional structures ===
 +
The crystal structure of human dermatan sulfate epimerase 1 was deposited in PDB in 2020 ([{{PDBlink}}6HZN PDB ID 6HZN]). It contains an (&alpha;/&alpha;)6 toroid  N-terminal domain, a &beta;-sheet domain and a C-terminal domain with a long &alpha;-helix. A manganese ion is bound close to the putative active site, which is located in a groove between the two main domains.
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
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#tanner2002 Tanner, Martin E. (2002) Understanding Nature's Strategies for Enzyme-Catalyzed Racemization and Epimerization. ''Accounts of Chemical Research'' vol. 35, no. 4, pp. 237-246. [https://doi.org/10.1021/ar000056y DOI:10.1021/ar000056y]
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#overtveldt2015 pmid=26505535
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#Lindahl1972 Lindahl, Ulf and Bäckström, Gudrun and Malmström, Anders and Fransson, Lars-Åke. (1972) Biosynthesis of <font style="font-feature-settings: 'smcp'">l</font>-iduronic acid in heparin: Epimerization of <font style="font-feature-settings: 'smcp'">d</font>-glucuronic acid on the polymer level. ''Biochemical and Biophysical Research Communications'' vol. 46, no. 2, pp. 985-991. [https://doi.org/10.1016/S0006-291X(72)80238-9 DOI:10.1016/S0006-291X(72)80238-9]
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#malmstrom1975 pmid=1123348
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#valla2001 Valla, Svein and Li, Jin-ping and Ertesvåg, Helga  and Barbeyron, Tristan  and Lindahl, Ulf. (2001) Hexuronyl C5-epimerases in alginate and glycosaminoglycan biosynthesis. ''Biochimie'' vol. 83, no. 8, pp. 819-830. [https://doi.org/10.1016/S0300-9084(01)01313-X DOI:10.1016/S0300-9084(01)01313-X]
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#debarnot2019 pmid=30872481
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#pacheco2009 pmid=19004833
 +
#jerga2006 pmid=16866359
 +
#gacesa1987 Gacesa, Peter. (1987) Alginate-modifying enzymes: A proposed unified mechanism of action for the lyases and epimerases. ''FEBS Letters'' vol. 212, no. 2, pp. 199-202. [https://doi.org/10.1016/0014-5793(87)81344-3 DOI:10.1016/0014-5793(87)81344-3]
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#qin2015 pmid=25568314
 
#haug1969 pmid=5368261
 
#haug1969 pmid=5368261
 
#larsen1971 pmid=5150891
 
#larsen1971 pmid=5150891
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#Jenkins2004 pmid=14670977
 
#Jenkins2004 pmid=14670977
 
#jenkins1998 Jenkins, John and Mayans, Olga and Pickersgill, Richard. (1998) Structure and Evolution of Parallel &beta;-Helix Proteins. ''Journal of Structural Biology'', vol. 122, nos. 1-2, pp. 236–246. [https://doi.org/10.1006/jsbi.1998.3985 DOI:10.1006/JSBI.1998.3985]
 
#jenkins1998 Jenkins, John and Mayans, Olga and Pickersgill, Richard. (1998) Structure and Evolution of Parallel &beta;-Helix Proteins. ''Journal of Structural Biology'', vol. 122, nos. 1-2, pp. 236–246. [https://doi.org/10.1006/jsbi.1998.3985 DOI:10.1006/JSBI.1998.3985]
 +
#yoder19932 pmid=8081738
 +
#hook1974 pmid=4276135
 +
#gallagher1985 pmid=2933029
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#bishop2007 pmid=17460664
 +
#jacobsson1984 pmid=6420398
 +
#hagner2000 Hagner-McWhirter, Åsa and Hannesson, Helgi H. and Campbell, Patrick and Westley, John and Rodén, Lennart and Lindahl, Ulf and Li, Jin-Ping. (2000) Biosynthesis of heparin/heparan sulfate: kinetic studies of the glucuronyl C5-epimerase with N-sulfated derivatives of the ''Escherichia coli'' K5 capsular polysaccharide as substrates. ''Glycobiology'' vol. 10, no. 2, pp. 159-171. [https://doi.org/10.1093/glycob/10.2.159 DOI:10.1093/glycob/10.2.159]
 +
#hagner2004 pmid=14718527
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#li2010 pmid=20807641
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#sheng2012 pmid=22528493
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#mochizuki2015 pmid=25677302
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#Han2009 pmid=19801541
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#lunin2004 pmid=15003453
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#prihar1980 pmid=7356942
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#hagner2000b pmid=10727403
 +
#malmstrom1980 pmid=6768743
 +
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#malmstrom1982 pmid=7092807
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 +
#maccarana2006 pmid=16505484
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#pacheco2009b pmid=19188366
 +
 +
#trowbridge2002 pmid=12213784
 +
 +
#NLM2020 US National Library of Medicine. (2020) Chondroitin Sulfates MeSH Descriptor Data 2020. [https://meshb.nlm.nih.gov/record/ui?name=Chondroitin%20sulfates Unique ID: D002809]
 +
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#malmstrom1984 pmid=6706927
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#tykesson2018 pmid=29976758
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#tykesson2016 pmid=26900446
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#hannesson1996 pmid=8573097
  
#yoder19932 pmid=8081738
+
#eklund2000 pmid=11185550
  
 
</biblio>
 
</biblio>
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[[Category:Definitions and explanations]]
 
[[Category:Definitions and explanations]]

Revision as of 06:11, 29 June 2020


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Introduction

Epimerases and racemases catalyse the inversion of stereochemistry in biological molecules. Epimerases invert the stereochemistry of only one stereogenic center in a molecule that has at least two, and racemases create racemates from pure enantiomers. These functionalities makes organisms able to utilize several different stereoisomers of the same compounds. Whereas most enzymes catalyze reactions where reactants and products have only one stereochemistry, epimerases and racemases must be able to accomodate two different stereoisomers in their active site. Many epimerases and racemases break a C-H bond next to a carbonyl functional group, and then reform it with the new stereochemistry [1].

van Overtveldt et al. classified 39 known carbohydrate epimerase specificities into 14 different families based on sequence alignments [2]. Five different epimerization mechanisms were described: I) deprotonation/reprotonation, II) transient keto intermediate, III) carbon-carbon bond cleavage, IV) nucleotide elimination and V) mutarotation. Members of a family share mechanism and conserved catalytic residues. Only two of the 14 families are active on polysaccharides: CEP7 containing mannuronan C5-epimerases (alginate epimerases) and CEP8 containing heparosan-N-sulfate-glucuronate 5-epimerase (heparosan epimerase). Together with the unclassified dermatan sulfate C5-epimerase (chondroitin epimerase), these enzymes perform a similar polymer level C5-epimerization on polysaccharides consisting of hexuronic acids. Both alginates and the glycosaminoglycans heparin/heparan and dermatan sulfate are block copolymers of the two monomers created by these epimerases. In alginates the epimerization is from d-mannuronic acid to l-guluronic acid, while in the glycosaminoglycans it is from d-glucuronic acid to l-iduronic acid [3, 4, 5, 6].

Alginate and glucosaminoglycan epimerases share a deprotonation/reprotonation mechanism where neutralization of the sugar carboxyl group is followed by proton abstraction from one side of the sugar ring, creating an intermediate that is resonance stabilized by the carboxyl group. The pKa of the hydrogen is lowered due to this resonance stabilization [1, 6]. For the mannuronan C5-epimerase the intermediate is thought to be an enolate anion, while for the heparin epimerase it could be a neutral enol [7]. For the dermatan epimerases it is proposed to be a 4,5-unsaturated residue where the glycosidic bond is cleaved and subsequently reformed [8], and this is also proposed as an alternative hypothesis for the alginate epimerases [9]. Addition of another proton to the opposite face of the sugar ring creates the epimer. The mechanism is probably similar to that of the corresponding polysaccharide lyases, see Polysaccharide Lyases [10]. For the lyases, the intermediate created by the proton abstraction results in a β-elimination where the leaving group is protonated by the enzyme instead of the C5-carbon, and 4,5-unsaturated residue is the reaction product.

Despite performing similar reactions, the three hexuronyl C5-epimerase families share almost no sequence or structural identity [2, 11].

Mannuronan C5-epimerases

Substrate specificity

Figure 1. A. Haworth structures of d-mannuronic acid (M) and l-guluronic acid (G). B. The three different block structures found in alginate: non-epimerized M-blocks, MG-blocks and G-blocks.

Mannuronan C5-epimerases are a group of enzymes that catalyze epimerization at the polymer-level of β-d-mannuronic acid residues (hereafter denoted M) into α-l-guluronic acid residues (hereafter denoted G) in alginate [3, 12, 13]. Alginate is an anionic polysaccharide made by brown seaweeds, some species of red algae, and the gram-negative bacterial genera Pseudomonas and Azotobacter [14, 15, 16, 17, 18]. The function of alginate in the different organisms are various, and related to structure, protection and surface adhesion [19, 20, 21, 22]. Alginate is a copolymer of the two 1-4 linked epimers [23, 24, 25], and by changing the composition of the two monomers the epimerases fine-tune the properties of the polymer [26]. At first, alginate is made as a homopolymer of M in the cell. Epimerases then convert some of the M-residues in the polymer into G-residues [13, 27, 28]. This epimerization is not random and creates block structures of M, G or alternating MG [29, 30], see Figure 1. Alginate residues that are oxidized or acetylated are not substrates for the epimerases, and acetylation of alginate could be a way to control epimerization in nature [31, 32].

Mannuronan C5-epimerases exist both in algae and in bacteria [3, 33]. Gene analyses propose as many as 31 different genes encoding putative mannuronan C-5 epimerases in the brown algae Ectocarpus [34]. However, the algal epimerases are difficult to express and it is the bacterial enzymes that have been studied most extensively [34, 35]. Two categories of bacterial mannuronan C-5-epimerases have been described: the periplasmic AlgG and the extracellular and calcium dependent AlgE. AlgG creates single G residues in stretches of mannuronan, while the AlgE enzymes are processive and create MG-blocks and G-blocks. Pseudomonas is only known to produce AlgG [28, 36, 37], while A. vinelandii contains seven active AlgE enzymes in addition to AlgG [38, 39, 40, 41]. A mutant strain of P. fluorescens without the algG gene creates pure mannuronan [42]. This strain can be used to produce unepimerized substrate, which is useful for the study of the epimerization reaction. Methods for studying this are discussed in a later section.

Product profiles

The abundance of epimerases giving slightly different product profiles in A. vinelandii makes it possible for the bacteria to tailor alginate so it can fulfill different functions [39, 43]. This is done in three different ways. Firstly, some AlgE enzymes are only capable of creating MG-blocks, while others also create G-blocks. Secondly, different epimerases create block stretches of different lengths. Lastly, one of the known AlgE epimerases has a dual epimerase/lyase activity and thus modifies the polymer length [41]. Weak lyase activity has also been observed in other AlgEs [44, 45]. It is not certain whether this serves a function or if it is the result of failed epimerization.

Catalytic reaction

The extracellular A. vinelandii AlgE enzymes are studied extensively. They consist of different combinations of an independently catalytic module, the A-module, and a smaller R-module thought to modify binding [43, 46]. The enzymes' direction of movement along the substrate is not determined, but there are indications that they move along their polymeric substrate from the non-reducing to the reducing end [45, 47]. The epimerases show various degrees of processivity [45, 48, 49, 50], where AlgE4 catalyzes around 10-12 epimerizations before disassociating from the substrate [47, 51]. Epimerases are thought to only epimerize every other residue in one binding event, which means that the G-block formers will need to bind the MG-product of the first reaction again to form G-blocks [45, 47]. The reason why some epimerases can not form G-blocks may be related to their interactions with poly-MG [51].

Mechanism

Figure 2. The three-step mechanism as put forward by Gacesa, 1987 [10]. AA1, AA2 and AA3 denotes the amino acids, or potentially also water molecules, responsible for each step. After neutralization of the negative charge on the mannuronate carboxyl group by AA1, AA2 can abstract the proton bound to C5. This results in resonance stabilization of the enolate anion intermediate. A proton is subsequently donated to different groups depending on whether it is an epimerase or lyase reaction. In lyases, cleavage of the glycosidic bond forms an unsaturated residue denoted Δ and a proton is donated to the leaving group. In epimerases AA3 donates a proton to the C5 carbanion on the opposite side of the ring from the one that was abstracted, forming guluronate.

The mechanism is suggested to be similar to the lyase mechanism, as illustrated in Figure 2 [10]. This is supported by several of the A. vinelandii enzymes having both lyase and epimerase activity [41, 44, 45, 52]. Different versions of NNHSY is a common motif in both epimerases and lyases, and it is implicated to be important for catalysis or binding [42, 53, 54].

The proposed epimerase mechanism is initiated with neutralization of the negative charge of the carboxylate group. This is followed by abstraction of H-5 by a catalytic base and ends with an addition of another proton to the opposite side of the sugar ring by a catalytic acid. The conformation of the monomer flips from 4C1 to 1C4, and changes it from β-d-mannuronate to α-l-guluronate. In the lyase mechanism, the second step is a β-elimination of the 4-O-glycosidic bond to form a 4-deoxy-l-erythro-hex-4-enepyranosyluronate, called Δ, at the non-reducing end.

Methods to study the reaction

Several methods have been used either to measure catalytic rates, or to characterize the epimerized product in terms of relative amounts of M, G and block compositions at different conditions and treatment times.

The Dische carbazole reaction [55] was used in the 1970s to measure both initial activity and end point conversion [13, 56, 57]. In this method an increase in color intensity from mannuronic to guluronic acid is used to quantify the degree of epimerization.

In the 1980s, epimerization activity on 5-3H-alginate was measured by observing tritium released into the solvent [58, 59]. This method had an increased accuracy compared to the carbazole method and was more suited to determine kinetic constants. Although the substrate changes during epimerization so classical Michaelis-Menten kinetics cannot be applied, apparent values for Vmax and kcat for AlgE4 were determined to be 14.8 μmol min-1 mg-1 protein and 14 s-1, respectively [48].

Around the same time, another fast and sensitive method that did not require tritiated alginate was established [60]. The non-saturated product of alginate lyase reactions, Δ, has absorbance at 230 nm. This can be used to measure lyase activity directly [61], but it can also be used to measure epimerization indirectly. This is done by treating epimerized alginate with an alginate lyase, e.g., AlyA from Klebsiella pneumoniae that specifically cleaves at G-M and G-G linkages [62]. Formation of Δ, monitored by measuring absorbance at 230 nm, is then assumed to be directly proportional to the amount of G produced by the epimerase. Block composition was initially measured by acid hydrolysis of alginate [3, 29, 30]. Alternating blocks are readily hydrolysed and appear in the soluble fraction, while homopolymeric blocks are more protected and remain insoluble. By subsequently dissolving the insoluble part followed by acid precipitation of G-blocks, relative amounts of the three block structures was roughly determined. A much more precise method was later established, using either 13C-NMR [63, 64] or the more sensitive 1H-NMR [65, 66] to calculate block composition of alginate. This is done by measuring relative amounts of monomer dyads and triads. These are important methods for characterization of alginate today.

Both 13C- and 1H-NMR have been used to follow the epimerization reaction over time, making it possible to observe both kinetics and mode of action [52, 67, 68, 69].

Another method that can distinguish between M and G is circular dichroism [70, 71], and this has also been used to measure epimerase activity [72].

To get knowledge about block length and distribution, lyases with four different specificities (cutting the alginate chain at either M-M, G-G, M or G) can be used [73]. Size Exclusion Chromatography (SEC) can then separate the products, before the resulting block fractions can be analyzed with High Performance Anion Exchange Chromatography with Pulsed Amperometric Detection (HPAEC-PAD) [74, 75], NMR or SEC with multiangle laser light scattering (SEC-MALLS) [76].

Catalytic residues

Figure 3. Electrostatic surface potential and catalytic sites of A. AlgE4 (PDB ID 2PYH, [77]) and B. AlgG (PDB ID 4NK6, [78]). The maps are created using the APBS electrostatics plug-in [79] in PyMOL [80]. The scale is from -5 to +5 kT/e, where negative potential is colored red and positive potential is colored blue. The mannuronate trimer in the crystal strucutre of AlgE4 is shown as ball-and-stick with carbon atoms in green and oxygen atoms in red.

All known epimerases share a YG(F/I)DPH(D/E) motif located in the +1 subsite. In the AlgE epimerases the catalytic residues are identified as the four essential amino acids Y149, D152 and H154 of this motif, in addition to D178 that is lacking in AlgG [35, 52, 77, 81] (See Figure 3A). A lot is still unclear about the catalytic mechanism and of the exact role of each catalytic residue. It has been suggested that tyrosine acts as the catalytic base in the reaction, marked AA2 in Figure 2, while the histidine is the catalytic acid, AA3 [77]. The two acidic residues might be important in maintaining the pKa of this site, as well as orienting the catalytic base. In AlgG (Figure 3B), H319 is hypothesized to be the catalytic base, water to be the catalytic acid and R345 to neutralize the carboxyl group [78].

Role of calcium

The seven secreted epimerases of A. vinelandii, AlgE1-AlgE7, are all calcium-dependent [3, 43, 82]. Activity increases with increasing calcium concentration up to around 5 mM calcium, with the optimum depending on the enzyme [13, 44, 48, 52, 83]. At the same time increased calcium concentration gives a decrease in end point conversion due to gelation of product [13]. It is unknown whether calcium is important for the mechanism itself or if its only role is to stabilize the structure (see the section about three-dimensional structures). Early studies indicated it had a role in enzyme stability, as the temperature stability increased at higher calcium concentrations [13]. In the resolved crystal structure of AlgE4's A-module, a calcium ion is bound in a hairpin loop away from the active site [77] (PDB ID 2PYH). Without the calcium ion the loop would likely change conformation, which could destabilize the active fold of the enzyme. If calcium has an additional role in the catalytic activity, it could be in neutralizing the negative charge of the carboxylic anion. This is observed in the structurally similar alginate lyases from the polysaccharide lyase family 6 [84, 85, 86, 87]. The periplasmic AlgG epimerases do not require calcium for their activity [28, 40].

Substrate binding

Alginate is a polyelectrolyte, and substrate binding probably occurs mainly through electrostatic interactions. The A. vinelandii epimerases are modular, and together the modules form an extended binding groove lined by charged residues [46, 88] (see Figure 3 for electrostatic surface potential maps). Assuming a monomer length of about 0.5 nm [51] and a binding groove length of about 5 nm [77], the catalytically active A-module can accommodate around 10 sugar residues. The R-module seems to be able to bind around 5 alginate monomers [46]. The epimerases probably require different substrate lengths to be able to start epimerization. For instance, AlgE4 seems to need at least a hexamer [47], while AlgE6 and AlgE1 need eight to ten monomers [45].

They also create different block lengths: the larger epimerase AlgE1 appears to create longer blocks than AlgE6, which in turn seems to be create longer blocks than AlgE4 [45, 47]. This could be due to differences in processivity. Since the alginate epimerases are processive, a too strong substrate binding could actually decrease their activity. The R-modules could have a role here: even though the R-module from AlgE4 increases its binding compared to the A-module alone, R-modules from AlgE6 are not individually able to bind alginate [46]. The R-modules probably modulate binding and processivity in complex ways, not simply by increasing the binding strength [43, 46, 51, 68, 88, 89].

Another discovery related to substrate specificity is the importance of residue 307, located in a large loop in the A-module of the AlgE enzymes. In the G-block formers this residue is a tyrosine, whereas in the MG-block formers it is a phenylalanine [68]. Mutations of this residue have been shown to change the epimerization pattern accordingly [69]. As this residue is relatively far away from the active site it could be the substrate binding, not the catalytic mechanism, that gives rise to different product profiles.

Three-dimensional structures

Figure 4. A. Cartoon representations of the A-module of AlgG (left) and AlgE4 (right). The three β-sheets are called PB1 (teal), PB2 (olive) and PB3 (maroon) according to nomenclature of β-helix folds [90]. A bound mannuronan trimer is shown in sticks in the binding groove of AlgE4. A calcium ion is coordinated close to the N-terminal, shown as an orange sphere. The N-terminal alpha helix capping the hydrophobic interior is shown in yellow. In AlgG, this is more complex and consists of two β-sheets in addition to the helix. B. The same structure as in A but seen from the C-terminal end. T1, T2 and T3 denotes the turns between the three sheets. The shape of the protein from this angle illustrates why the beta-helix is also called an L-solenoid. C. The C-terminal R-module of AlgE4. Five calcium ions are coordinated by the structure, shown as orange spheres.

In 2008 the structure of the AlgE4 A-module from A. vinelandii was solved at 2.1 Å resolution [77]. This represents the first crystal structure of a mannuronan C5-epimerase. It shows a right-handed parallel β-helix fold with an N-terminal α-helix cap and an extended binding groove, see Figure 4B. Protruding from the binding groove are three flexible loops, slightly enclosing the binding surface. One of the two molecules of the asymmetric unit has a mannuronan trimer bound in its binding groove. A calcium ion is coordinated in proximity to the active site, at the N-terminal end. The next crystal structure to be solved was of the P. aeruginosa non-modular AlgG epimerase, also at 2.1 Å resolution [78] (Figure 4A). It is structurally similar to AlgE4's A-module. In 2016 the A-module of AlgE6 was deposited in the PDB (PDB ID 5LW3) at 1.19 Å resolution, and it is almost identical to AlgE4's A-module. These two A-modules also share the highest sequence homology of the AlgE A-modules [41]. The three structures are all around 70 Å long. R-modules of AlgE4 [88] (PDB ID 2AGM) and AlgE6 [46] (PDB IDs 2ML1, 2ML2, and 2ML3) from A. vinelandii were solved by NMR. The R-modules have an overall ellipsoid or spherical shape, continuing the parallel β-sheets of the A-module with a parallel β-roll fold (See Figure 4C). A common feature of this fold is a repeated nonapeptide motif LXGGAGXDXn, a circular permutation of the motif GGXGXDX(L/I/F)X first found in RTX (repeats in toxins) toxins from Gram-negative bacteria [91, 92]. The motifs stabilize the fold by binding calcium ions tightly [93], and the R-modules of AlgE contains four to seven of them [26, 88]. The core part of the R-modules is around 40 Å long. At the C-terminal of the last R-module of each enzyme is an unstructured region of about 20 amino acids. This is thought to function as a secretion signal for a transporter that secretes the enzymes out of the cell [38, 88, 94].

A structure of a complete modular epimerase is lacking. From SAXS-measurements of AlgE4 and AlgE6 the enzymes appear elongated, with the R-modules extending the binding grooves of the A-modules [46]. Some flexibility between the modules is observed, and NMR-studies indicate a flexible linker between the A- and the R-modules. Radii of gyration are calculated to be 31 Å for AlgE4 and from 52-55 Å for AlgE6. Maximum distances are around 100 Å for AlgE4 and around 180 Å for AlgE6 [46].

The parallel β-helix fold found in the active modules of the epimerases was first encountered in another enzyme active on polyanionic substrate, namely the pectate lyase C of Erwinia chrysanthemi [95]. It is also called a β-solenoid-type fold as it consists of repeated β strands, and it is a type L β-solenoid [96]. In the epimerases it is found together with an N-terminal α-helix cap that shields the hydrophobic interior of the β-helix from the solvent. This combination is found in several other enzyme families of glycoside hydrolases (GH28, GH49, GH55, GH82, and GH87 in the CAZy database [97]) and of polysaccharide lyases (PL1, PL3, PL6, and PL9 [98]): alginate lyases [86], dextranases [99], rhamnogalacturonases [100], polygalacturonase [101], β-1,3-glucanases [102], ι-carrageenases [103], endorhamnosidases [104], pectate and pectin lyases [95, 105, 106, 107] and chondroitin B (dermatan sulfate) lyases [84]. Since these enzymes have a high degree of structural similarity, it is thought that at least some of them diverged from a common ancestor [108], although convergent evolution is not unlikely [96].

Heparosan-N-sulfate-glucuronate 5-epimerase

Substrate specificities

File:XXX.png
Figure 5. Heparan sulfate

The heparin/heparan epimerase catalyze the polymer level epimerization of β-d-glucuronic acid (GlcA) to α-l-iduronic acid (IdoA) in the glycosaminoglycan heparan sulfate [109]. Heparan sulfate consists of long chains of a repeating disaccharide motif, 1-4 linked alternating monomers of GlcA or IdoA and α-d-glucosamine (GlcN). GlcN monomers can be acetylated, and all three sugar units can be either O-sulfated or N-sulfated. While GlcA adopts a 4C1 chair conformation, IdoA exists in an equilibrium between 1C4 and the skew-boat conformation 2S0 [6]. Domains in heparan sulfate have various compositions of monomers and modifications, and long domains with high amounts of N-sulfated disaccharide units are called heparin [110].

Heparan sulfate is found in all animal cells as proteoglycans. Due to its negative charge and diverse sequence motifs, the polysaccharide is known to interact with many different proteins and affect most cellular processes mainly through electrostatic interactions. Heparin is stored in secretory granules in mast cells and released when tissue is injured. When it binds to antithrombin it aids in inhibiting blood coagulation. Heparin is produced industrially as an anticoagulant, but its roles in tissue injury and repair in cells are diverse and complex [6, 111].

Activity of the heparin/heparan epimerase requires that the residue to be epimerased has a deacetylated and N-sulfated glucosamine linked to its C-4 (subsite -1). O-sulfation of the residue in the active site or of neighbouring residues inhibits epimerization. The residue linked to C-1 of the sugar unit in the active site can be either N-sulfated or N-acetylated for epimerization to occur, but N-sulfated is the better substrate. An octasaccharide is found to be the minimal substrate size [112, 113].

The enzymatic reaction is reversible when the substrate has a glucosamine or sulfated glucosamine three residues away from the epimerization site towards the nonreducing end, or if this site is unoccupied. On the other hand, if the substrate has an acetylated glucosamine in the same site the enzyme irreversibly introduce l-iduronic acid residues to the heparin chains. The reaction is also irreversible in vivo, probably due to the structure of the biosynthetic pathway [114, 115, 116].

An enzyme with a slightly different substrate specificity has been identified from the giant African snail Achatina fulica [117]. The glycosaminoglycan acharan sulfate contains repeating units of acetylated glucosamine and O-sulfated IdoA. The epimerase creating IdoA in this polymer is named heparosan-glucuronate 5-epimerase since it is active on heparosan, as opposed to the heparosan-N-sulfate-glucuronate 5-epimerase that requires a deacetylated and sulfated substrate.

Catalytic reaction and mechanism

The catalytic reaction is thought to follow a similar mechanism to the mannuronan C5-epimerases described in an earlier section, and also to that of heparin and dermatan sulfate lyases [118, 119]. A tyrosine is recognized as the proton acceptor, and a glutamate as the proton donor. Based on structural analysis of substrate and product complexes it is thought that the reaction proceeds through a neutral enol intermediate, with ring distortion to facilitate epimerization [7]. Originally this intermediate was proposed to be an α-carbanion [120], or an enolate as for the other polysaccharide epimerases [11]. Two other tyrosines are shown to be essential for activity, and they are hypothesized to be part of proton relay pathways between the active site and the solvent [7, 11]. The readdition of the proton is the rate-limiting step [7, 121]. heparin/heparan epimerases do not require divalent cations for activity, unlike the alginate and dermatan sulfate epimerases [122]. However, one calcium ion is bound to each subunit in the crystal structure of human heparin/heparan epimerase [7]. In the crystal structure of zebrafish heparin/heparan epimerase, a water molecule is bound in the same position [11].

Three-dimensional structures

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Figure 6. Cartoon representation of the dimeric assembly of human glucuronyl C5-epimerase (PDB ID 6HZZ) [7]. The N-terminal β-hairpin domain is colored in purple, the β-sandwich domain is colored in red and the (α/α)4-barrel domain is colored in green. One calcium ion is coordinated in the sandwich domain of each subunit and shown as an orange sphere. Three N-glycans bound to each subunit are shown in sticks and spheres.

In 2015 the first crystal structure was solved, d-Glucuronyl C5-epimerase from zebrafish (PDB ID 4PW2) [11]. The protein crystallizes as a homodimer and has three domains: an α-helical transmembrane region, a β-barrel domain and a flexible N-terminal loop. Enzyme complexed with an inhibiting heparin hexamer was also crystallized (PDB ID 4PXQ).

The next structure to be solved was human d-Glucuronyl C5-epimerase (PDB ID 6HZZ) [7]. Like the zebrafish enzyme it is a dimer where each subunit has three domains. The N-terminal domain consists of two antiparallel β-hairpins connected by a helix. This is followed by a β-sandwich domain, and a C-terminal (α/α)4-barrel domain containing the active site. The dimer is probably the active form of the enzyme. Figure 6 shows the dimeric structure of human glucuronyl C5-epimerase. Structures of an inactive mutant bound to a substrate and a product were also deposited (PDB IDs 6I01 and 6I02) [7].


Dermatan sulfate C5-epimerase

Substrate specificities

Just like the heparin epimerase, the two dermatan sulfate epimerases catalyze the epimerization of β-d-glucuronic acid (GlcA) to α-l-iduronic acid (IdoA) in polymers of glycosaminoglycans [123, 124, 125]. The repeating disaccharide unit of dermatan sulfate is 1-3 linked GlcA or IdoA and 1-4 linked β-d-N-acetyl galactosamine (GalNAc). Sulfation can occur at C-2 of iduronic acid and at C-4 and/or C-6 of galactosamine. The polymer can have various length, epimerization and sulfation, and bind to a variety of proteins [126]. The unepimerized polymer is called chondroitin sulfate. Although dermatan sulfate was earlier known as chondroitin B it is no longer classified as a chondroitin sulfate [127]. Chondroitin/dermatan sulfate exists as proteoglycans in extracellular matrixes in mammalian tissues, especially skin. The polysaccharide is involved in many different cell processes due to its sequence variability and diverse protein partners [126].

Dermatan sulfate consists of block structures of (IdoA-GalNAc)n, (GlcA-GalNAc)n and hybrid domains containing both uronic acids. Two epimerases are characterized, dermatan sulfate epimerase 1 and 2, and they have slightly different product pattern which could be important in regulating domain formation. They are found in a variety of animals, including humans [125].

Dermatan is a better substrate for the epimerases than chondroitin, and the epimerases are not active on sulfated substrates [128]. However, the co-incubation of epimerases and sulfotransferases synergistically promotes formation of iduronic acid. To be able to processively form long iduronic acid containing domains, the epimerases physically interact with the sulfotransferase [5, 129]. The minimal substrate length for optimal binding has been shown to be an octamer [130].

Catalytic reaction and mechanism

A mechanism is suggested where a proton is abstracted from one side of glucuronic acid by a histidine, the glycosidic bond is cleaved by involvement of a tyrosine and another histidine attaching a proton to the other side of the ring. This will involve a 4,5-unsaturated intermediate, similar to the end product of polysaccharide lyases. The glycosidic bond would be formed again by the tyrosinate ion or a second general acid [8]. The two histidines could switch roles as acid and base, giving rise to the reversibility seen in vitro [131]. The enzyme requires divalent cations, preferably Mn2+, and N-glycosylation for activity [8, 123]. It processively epimerizes four to five monomers from the reducing towards the non-reducing end, with decreased binding affinity for each processive step [130]. In vivo the concomitant action of epimerase and sulfotransferase could account for a higher processivity, as well as irreversible formation of iduronic acid [128, 129, 132].

Three-dimensional structures

The crystal structure of human dermatan sulfate epimerase 1 was deposited in PDB in 2020 (PDB ID 6HZN). It contains an (α/α)6 toroid N-terminal domain, a β-sheet domain and a C-terminal domain with a long α-helix. A manganese ion is bound close to the putative active site, which is located in a groove between the two main domains.

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