Difference between revisions of "Polysaccharide Lyase Family 8"

Revision as of 07:50, 7 November 2013

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Author: ^^^Michael Suits^^^
Responsible Curator: ^^^Michael Suits^^^

Polysaccharide Lyase Family PL8
3D Structure	(α/α)₆ barrel + anti-parallel β-sheet
Mechanism	β-elimination
Active site residues	Pneumonococcal hyaluronidase: Asn249, His399, Tyr408.
CAZy DB link
http://www.cazy.org/PL8.html

Known Activities

Depending on the subfamily, PL8s display a broad range of enzymatic activities including: hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); and chondroitin ABC lyase (EC 4.2.2.20) actions.

Substrate specificities

PL8s are active on a variety of uronic acid-containing polysaccharides including hyaluronan [4)-β-D-Glucuronate-1,3-β -D-N-Acetyl-Glucosamine(1]_n, chondroitin AC [4)-β-D-Glucuronate-1,3-β-D-N-Acetyl-GalactosamineΔ4,6S(1]_n, xanthan [4)-β-D-Glucuronate-1,4-β-D-Glucuronate (1]_n, and chondroitin ABC [chondroitin AC and chondroitin B (aka. dermatan sulfate: 4)-β-L-Iduronate2S-1,3-β-D-N-Acetyl-Galactosamine4S(1]_n.

Kinetics and Mechanism

One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas et al. proposed that in the Streptococcus pneumoniae hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor [1, 2]. However, for two other PL8 family members: the Bacillus sp. GL1 xanthanase and Streptomyces coelicolor A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction [3, 4]. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with H399 participating in the neutralization of the C5-carboxylate group [5]. Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that opening/closing and twisting domain motions of the (α/α)₆ barrel with respect to the anti-parallel β-sheet domains underly processive substrate translocation [6].

Catalytic Residues

In S. pneumoniae, mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation [1]. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng et al. for discussions [4, 5]. An Asp for Asn mutation in Proteus vulgaris was suggested to provide the mechanism for enzymatic distinguishing between the two epimers [7].

Three-dimensional structures

Structure by Activity: Hyaluronidase – 'S. pneumoniae' R6 [2](PDB 1OJM). Chondroitin AC lyase – 'Bacteroides stercoris' HJ-15 [8](PDB 1CB8). Xanthanase – 'Bacillus' sp GL1 [9](PDB 1J0M). Chondroitin ABC lyase – 'Proteus vulgaris' [7](PDB 1HN0).

Family Firsts

First stereochemistry determination: Content is to be added here.
First catalytic nucleophile identification: Content is to be added here.
First general acid/base residue identification: Content is to be added here.
First 3-D structure: Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 [8](PDB 1CB8).

First Structures by Activity

Hyaluronan lyase: Streptococcus pneumoniae R6 [2](PDB 1OJM).
Chondroitin AC lyase: Bacteroides stercoris HJ-15 [8](PDB 1CB8).
Xanthan lyase: Bacillus sp GL1 [9](PDB 1J0M).
Chondroitin ABC lyase: Proteus vulgaris [7](PDB 1HN0).

References

Rapport1951 pmid=14917676
Li2000 pmid=10716923
Fethiere1999 pmid=10329169
Sato1994 pmid=7512814
Huang2003 pmid=12706721
Hashimoto1998 pmid=9758797
Hashimoto2003 pmid=16348550
Maruyama2005 pmid=15979090
Kelly2001 pmid=11358878
Elmabrouk2011 pmid=21287626
Zheng2013 pmid=23944739
Joshi2009 pmid=19089975

@@ Line 30: / Line 30: @@
 == Known Activities ==
-Depending on the subfamily, PL8s display a broad range of enzymatic activities including: hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); and chondroitin ABC lyase (EC 4.2.2.20).
+Depending on the subfamily, PL8s display a broad range of enzymatic activities including: hyaluronate lyase (EC 4.2.2.1); chondroitin AC lyase (EC 4.2.2.5); xanthan lyase (EC 4.2.2.12); and chondroitin ABC lyase (EC 4.2.2.20) actions.
 == Substrate specificities ==
@@ Line 36: / Line 36: @@
 == Kinetics and Mechanism ==
-One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''S. pneumoniae'' hyaluronidase His399 acts as the general base, Asn349 act to neutralize the C5-carboxylate group, and Tyr408 is the protein donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that equivalent tyrosine residues served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggest the latter hypothesis is favored, with H399 participating in the neutralization of the C5 <cite>Zheng2013</cite>.   Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel and anti-parallel β-sheet domains underly processive substrate translocation <cite>Joshi2009</cite>.
+One of the major unresolved controversies around the PL8 catalytic mechanism is the candidate of the general base. Jedrzejas ''et al''. proposed that in the ''Streptococcus pneumoniae'' hyaluronidase, His399 acts as the general base, Asn349 acts to neutralize the C5-carboxylate group, and Tyr408 is the proton donor <cite>Kelly2001, Li2000</cite>. However, for two other PL8 family members: the ''Bacillus'' sp. GL1 xanthanase and ''Streptomyces coelicolor'' A3 hyaluronidase, it was suggested that an equivalent tyrosine residue served as the general acid and general base throughout the reaction <cite>Maruyama2005, Elmabrouk2011</cite>. Combined quantum mechanical and molecular mechanical (QM/MM) simulations suggests the latter hypothesis is favored, with H399 participating in the neutralization of the C5-carboxylate group <cite>Zheng2013</cite>.   Molecular dynamic simulations of the pneumococcal hyaluronidase with hyaluronan fragments suggest that opening/closing and twisting domain motions of the (α/α)<sub>6</sub> barrel with respect to the anti-parallel β-sheet domains underly processive substrate translocation <cite>Joshi2009</cite>.
 == Catalytic Residues ==
-In Streptococcus pneumoniae, mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng et al. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. An Asp for Asn mutation in Proteus vulgaris was suggested to provide the mechanism for distinguishing between the two epimers <cite>Huang2003</cite>.
+In ''S. pneumoniae'', mutagenesis and kinetic analysis of the HysA mutant suggested three residues were involved in catalysis Asn249, His399, Tyr408 and that two residues, Arg243 and Asn580 were responsible for substrate binding and translocation <cite>Kelly2001</cite>. However, there is some question over what the identity is over the general base (please see Elmabrouk or Zheng ''et al''. for discussions <cite>Elmabrouk2011, Zheng2013</cite>. An Asp for Asn mutation in ''Proteus vulgaris'' was suggested to provide the mechanism for enzymatic distinguishing between the two epimers <cite>Huang2003</cite>.
 == Three-dimensional structures ==
 Structure by Activity:
-Hyaluronidase – 'Streptococcus pneumoniae' R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).
+Hyaluronidase – 'S. pneumoniae' R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).
 Chondroitin AC lyase – 'Bacteroides stercoris' HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).
 Xanthanase – 'Bacillus' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1J0M PDB 1J0M]).
@@ Line 54: / Line 54: @@
 ;First 3-D structure: Chondroitin AC lyase – “Bacteroides stercoris” HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).
-== First Structure by Activity ==
+== First Structures by Activity ==
-;Hyaluroniate lyase: Streptococcus pneumoniae R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).
+;Hyaluronan lyase: ''Streptococcus pneumoniae'' R6 <cite>Li2000</cite>([{{PDBlink}}1OJM PDB 1OJM]).
-;Chondroitin AC lyase: Bacteroides stercoris HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).
+;Chondroitin AC lyase: ''Bacteroides stercoris'' HJ-15 <cite>Fethiere1999</cite>([{{PDBlink}}1CB8 PDB 1CB8]).
-;Xanthan lyase: Bacillus sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1J0M PDB 1J0M]).
+;Xanthan lyase: ''Bacillus'' sp GL1 <cite>Hashimoto2003</cite>([{{PDBlink}}1J0M PDB 1J0M]).
-;Chondroitin ABC lyase: Proteus vulgaris <cite>Huang2003</cite>([{{PDBlink}}1HN0 PDB 1HN0]).
+;Chondroitin ABC lyase: ''Proteus vulgaris'' <cite>Huang2003</cite>([{{PDBlink}}1HN0 PDB 1HN0]).
 == References ==