Auxiliary Activity Family 5 - Revision history

Harry Brumer: deleted double Forget2020 citation in biblio section

2022-04-19T17:17:14Z

deleted double Forget2020 citation in biblio section

Harry Brumer: Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

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Text replacement - "\^\^\^(.*)\^\^\^" to "$1"

Harry Brumer at 00:51, 26 November 2021

2021-11-26T00:51:29Z

Harry Brumer: /* Three-dimensional Structures */

2021-11-26T00:51:01Z

Three-dimensional Structures

Harry Brumer: /* Family Firsts */

2021-11-26T00:48:49Z

Family Firsts

Harry Brumer: /* Three-dimensional Structures */

2021-11-26T00:47:04Z

Three-dimensional Structures

Harry Brumer: /* Three-dimensional Structures */

2021-11-26T00:45:48Z

Three-dimensional Structures

Harry Brumer: /* Three-dimensional Structures */

2021-11-26T00:45:24Z

Three-dimensional Structures

Harry Brumer: /* Kinetics and Mechanism */

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Kinetics and Mechanism

Harry Brumer: /* Catalytic Residues */

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Catalytic Residues

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 #Sousa2015 Sousa, A. F.;  Vilela, C.;  Fonseca, A. C.;  Matos, M.;  Freire, C. S. R.;  Gruter, G.-J. M.;  Coelho, J. F. J.; Silvestre, A. J. D. (2015) Biobased polyesters and other polymers from 2,5-furandicarboxylic acid: a tribute to furan excellency. ''Polym. Chem.'' '''6''', 5961-5983. [https://doi.org/10.1039/C5PY00686D DOI:10.1039/C5PY00686D]
 #Rosatella2011 Rosatella, A. A.;  Simeonov, S. P.;  Frade, R. F. M.; Afonso, C. A. M. (2011) 5-Hydroxymethylfurfural (HMF) as a building block platform: Biological properties, synthesis and synthetic applications. ''Green Chem.'' '''13''', 754-793. [https://doi.org/10.1039/C0GC00401D DOI:10.1039/C0GC00401D]
 #Monosik2012 Monosik, R.;  Stredansky, M.;  Tkac, J.; Sturdik, E. (2012) Application of Enzyme Biosensors in Analysis of Food and Beverages. ''Food Anal. Methods.'' '''5''', 40-53. [https://doi.org/10.1007/s12161-011-9222-4 DOI:10.1007/s12161-011-9222-4]
 #Huffman2019 pmid=31806816

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 {{CuratorApproved}}
-* [[Author]]: ^^^Maria Cleveland^^^ and ^^^Yann Mathieu^^^
+* [[Author]]: [[User:Maria Cleveland|Maria Cleveland]] and [[User:Yann Mathieu|Yann Mathieu]]
-* [[Responsible Curator]]:  ^^^Harry Brumer^^^
+* [[Responsible Curator]]:  [[User:Harry Brumer|Harry Brumer]]
 ----

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 In AA5_2 the Tyr-Cys cofactor exhibits an unusually low reduction potential (+275 mV)  <cite>Cowley2016,Thomas2002,Wright2001</cite> compared to unmodified tyrosine in solution (> +800 mV) or in other enzymatic systems <cite>Itoh2000</cite>. Several factors such as the increased stability of the protein free radical through π-stacking with aromatic residues and the electron donating effect of the thioether linkage could contribute to this phenomenon <cite>Jazdzewski2000,Whittaker2003,Rogers2007</cite>. In contrast, AA5_1 have a reduction potential around +640 mV <cite>Whittaker1996</cite> possibly caysed by the substitution of the secondary shell amino acid Trpin AA5_2 with a His in AA5_1 leading to the different oxidizing power of these two subfamilies <cite>Wright2001,Kersten2014</cite>. Furthermore, in the archetypal AA5_2 member, ''Fgr''GalOx, the Trp290His substitution increased the reduction potential of the resulting enzyme from +400 mV to +730 mV <cite>Saysell1997</cite>; however, it also decreased the catalytic efficiency by 1000-fold <cite>Baron1994</cite> and affected the stability of the [Cu2+ Tyr·] metallo-radical complex at neutral pH <cite>Rogers1998</cite>. ''Cgr''AlcOx and ''Cgr''AAO have been speculated to have a lower reduction potential than ''Fgr''GalOx due to their secondary shell amino acid substitutions (Phe in ''Cgr''AlcOx and Tyr in ''Cgr''AAO) <cite>Yin2015,Mathieu2020</cite>.
- == Three-dimensional Structures ==
+== Three-dimensional Structures ==
 [[File:CRO_tertiary_structure.png|thumb|400px|right|'''Figure 3.''' Crystal structure of copper radical oxidases. A. ''Fgr''GalOx (PDB ID [{{PDBlink}}1gof 1GOF]), Copper ion in orange and B. ''Cgr''AlcOx (PDB ID [{{PDBlink}}5c86 5C86]), Copper ion in grey. This figure is reproduced from <cite>Yin2015</cite> (CC BY 4.0).]]
 AA5 members share a core seven-bladed β-propeller fold containing the active site (Figure 3) <cite>Ito1991 Ito1994 Yin2015 Mathieu2020</cite>. The structure of the archetype, ''Fgr''GalOx, was first reported in 1991 and comprises three domains: Domain 1 has a beta-sandwich structure now known as [[Carbohydrate Binding Module Family 32]], Domain 2 is the catalytic domain, and Domain 3 is a small, β-strand domain that packs against the catalytic domain on the side opposite from the active-site <cite>Ito1991 Ito1994</cite>. Notably, the original structural analysis of ''Fgr''GalOx revealed the distinct crosslinked Tyr-Cys active site residue of CROs, provided the first [[CBM32]] tertiary structure, and indicated the ability of Domain 1/[[CBM32]] to bind galactose <cite>Ito1991</cite>.

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 In AA5_2 the Tyr-Cys cofactor exhibits an unusually low reduction potential (+275 mV)  <cite>Cowley2016,Thomas2002,Wright2001</cite> compared to unmodified tyrosine in solution (> +800 mV) or in other enzymatic systems <cite>Itoh2000</cite>. Several factors such as the increased stability of the protein free radical through π-stacking with aromatic residues and the electron donating effect of the thioether linkage could contribute to this phenomenon <cite>Jazdzewski2000,Whittaker2003,Rogers2007</cite>. In contrast, AA5_1 have a reduction potential around +640 mV <cite>Whittaker1996</cite> possibly caysed by the substitution of the secondary shell amino acid Trpin AA5_2 with a His in AA5_1 leading to the different oxidizing power of these two subfamilies <cite>Wright2001,Kersten2014</cite>. Furthermore, in the archetypal AA5_2 member, ''Fgr''GalOx, the Trp290His substitution increased the reduction potential of the resulting enzyme from +400 mV to +730 mV <cite>Saysell1997</cite>; however, it also decreased the catalytic efficiency by 1000-fold <cite>Baron1994</cite> and affected the stability of the [Cu2+ Tyr·] metallo-radical complex at neutral pH <cite>Rogers1998</cite>. ''Cgr''AlcOx and ''Cgr''AAO have been speculated to have a lower reduction potential than ''Fgr''GalOx due to their secondary shell amino acid substitutions (Phe in ''Cgr''AlcOx and Tyr in ''Cgr''AAO) <cite>Yin2015,Mathieu2020</cite>.
-== Three-dimensional Structures ==
+ == Three-dimensional Structures ==
 [[File:CRO_tertiary_structure.png|thumb|400px|right|'''Figure 3.''' Crystal structure of copper radical oxidases. A. ''Fgr''GalOx (PDB ID [{{PDBlink}}1gof 1GOF]), Copper ion in orange and B. ''Cgr''AlcOx (PDB ID [{{PDBlink}}5c86 5C86]), Copper ion in grey. This figure is reproduced from <cite>Yin2015</cite> (CC BY 4.0).]]
-AA5 members share a core seven-bladed β-propeller fold containing the active site (Figure 3) <cite>Ito1994 Yin2015 Mathieu2020</cite>. The structure of the archetype, ''Fgr''GalOx, was first reported in 1991 and comprises three domains: Domain 1 has a beta-sandwich structure now known as [[Carbohydrate Binding Module Family 32]], Domain 2 is the catalytic domain, and Domain 3 is a small, β-strand domain that packs against the catalytic domain on the side opposite from the active-site <cite>Ito1991 Ito1994</cite>. Notably, the original structural analysis of ''Fgr''GalOx revealed the distinct crosslinked Tyr-Cys active site residue of CROs, provided the first [[CBM32]] tertiary structure, and indicated the ability of Domain 1/[[CBM32]] to bind galactose <cite>Ito1991</cite>.
+AA5 members share a core seven-bladed β-propeller fold containing the active site (Figure 3) <cite>Ito1991 Ito1994 Yin2015 Mathieu2020</cite>. The structure of the archetype, ''Fgr''GalOx, was first reported in 1991 and comprises three domains: Domain 1 has a beta-sandwich structure now known as [[Carbohydrate Binding Module Family 32]], Domain 2 is the catalytic domain, and Domain 3 is a small, β-strand domain that packs against the catalytic domain on the side opposite from the active-site <cite>Ito1991 Ito1994</cite>. Notably, the original structural analysis of ''Fgr''GalOx revealed the distinct crosslinked Tyr-Cys active site residue of CROs, provided the first [[CBM32]] tertiary structure, and indicated the ability of Domain 1/[[CBM32]] to bind galactose <cite>Ito1991</cite>.
 The [[CBM32]] domain is widely, but not exclusively, conserved among many AA5_2 members, especially from ''Fusarium'' species <cite>Paukner2014 Paukner2015 Faria2019 Cleveland2021b</cite> (including some that do not posses predominant galactose 6-oxidase activity, e.g. ''Fgr''AAO and ''Fox''AAO <cite>Cleveland2021a Cleveland2021b</cite>.) In other cases, PAN  and WSC domains are found in place of the [[CBM32]].  The function of PAN domains in ''Colletotrichum graminicola'' aryl alchohol oxidase and raffinose oxidase is unclear <cite>Mathieu2020 Andberg2017</cite>, while the WSC domain in ''Pyricularia oryzae'' alchohol oxidase was able to bind xylans and fungal chitin/β-1,3-glucan, implicating the involvement of this domain in enzyme anchoring <cite>Oide2019</cite>.  Finally, several general alcohol oxidases (i.e. those with little activity toward galactosides) do not possess a corresponding N-terminal domain, but rather comprise only the core seven-bladed β-propeller and the C-terminal domain (Figure 3) <cite>Yin2015 Oide2019</cite>. Glyoxal oxidases of AA5_1 also appear to lack the N-terminal [[CBM32]] domain found in ''Fgr''GalOx <cite>Whittaker1999</cite>.

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 ;First AA5_1 enzyme discovered: The glyoxal oxidase from ''Phanerochaete chrysosporium'' discovered in 1987 <cite>Kersten1987</cite>.
 ;First AA5_2 enzyme discovered:  The archetypal galactose-6 oxidase from ''Fusarium graminearum'' (''Fgr''GalOx) discovered in 1959 <cite>Cooper1959</cite>.
-;Copper requirement confirmed: While this first report already established FgrGalOx as a metalloenzyme; its copper requirement was later confirmed <cite>Amaral1963</cite>.
+;Copper requirement confirmed: While the original report established FgrGalOx as a metalloenzyme <cite>Cooper1959</cite>, its copper requirement was later confirmed <cite>Amaral1963</cite>.
-;First 3-D structure: The first crystallography structure of AA5 was of the archetypal ''Fgr''GalOx in 1991 <cite>Ito1991</cite>.
+;First 3-D structure: The first crystallographic structure of AA5 was of ''Fgr''GalOx in 1991 <cite>Ito1991</cite>.
 == References ==

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 AA5 members share a core seven-bladed β-propeller fold containing the active site (Figure 3) <cite>Ito1994 Yin2015 Mathieu2020</cite>. The structure of the archetype, ''Fgr''GalOx, was first reported in 1991 and comprises three domains: Domain 1 has a beta-sandwich structure now known as [[Carbohydrate Binding Module Family 32]], Domain 2 is the catalytic domain, and Domain 3 is a small, β-strand domain that packs against the catalytic domain on the side opposite from the active-site <cite>Ito1991 Ito1994</cite>. Notably, the original structural analysis of ''Fgr''GalOx revealed the distinct crosslinked Tyr-Cys active site residue of CROs, provided the first [[CBM32]] tertiary structure, and indicated the ability of Domain 1/[[CBM32]] to bind galactose <cite>Ito1991</cite>.
-The [[CBM32]] domain is widely, but not exclusively, conserved among many AA5_2 members, especially from ''Fusarium'' species <cite>Paukner2014 Paukner2015 Faria2019 Cleveland2021b</cite> (including some that do not posses predominant galactose 6-oxidase activity, e.g. ''Fgr''AAO and ''Fox''AAO <cite>Cleveland2021a Cleveland2021b</cite>.) In other cases, PAN  and WSC domains are found in place of the [[CBM32]].  The function of PAN domains in ''Colletotrichum graminicola'' aryl alchohol oxidase and raffinose oxidase is unclear <cite>Mathieu2020 Andberg2017</cite>, while the WSC domain in ''Pyricularia oryzae'' alchohol oxidase was able to bind xylans and fungal chitin/β-1,3-glucan, implicating the involvement of this domain in enzyme anchoring <cite>Oide2019</cite>.  Finally, several general alcohol oxidases (i.e. those with little activity toward galactosides) do not possess a corresponding N-terminal domain, but rather comprise only the seven-bladed β-propeller and C-terminal domain (Figure 3) <cite>Yin2015 Oide2019</cite>. Glyoxal oxidases of AA5_1 also appear to lack the N-terminal [[CBM32]] domain found in ''Fgr''GalOx <cite>Whittaker1999</cite>.
+The [[CBM32]] domain is widely, but not exclusively, conserved among many AA5_2 members, especially from ''Fusarium'' species <cite>Paukner2014 Paukner2015 Faria2019 Cleveland2021b</cite> (including some that do not posses predominant galactose 6-oxidase activity, e.g. ''Fgr''AAO and ''Fox''AAO <cite>Cleveland2021a Cleveland2021b</cite>.) In other cases, PAN  and WSC domains are found in place of the [[CBM32]].  The function of PAN domains in ''Colletotrichum graminicola'' aryl alchohol oxidase and raffinose oxidase is unclear <cite>Mathieu2020 Andberg2017</cite>, while the WSC domain in ''Pyricularia oryzae'' alchohol oxidase was able to bind xylans and fungal chitin/β-1,3-glucan, implicating the involvement of this domain in enzyme anchoring <cite>Oide2019</cite>.  Finally, several general alcohol oxidases (i.e. those with little activity toward galactosides) do not possess a corresponding N-terminal domain, but rather comprise only the core seven-bladed β-propeller and the C-terminal domain (Figure 3) <cite>Yin2015 Oide2019</cite>. Glyoxal oxidases of AA5_1 also appear to lack the N-terminal [[CBM32]] domain found in ''Fgr''GalOx <cite>Whittaker1999</cite>.
 == Family Firsts ==

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 == Kinetics and Mechanism ==
 [[File:CRO_mechanism.png|thumb|400px|right|'''Figure 1.''' Reaction mechanism of copper radical oxidases. A. First half-reaction – oxidation of substrate. B. Second-half reaction – regeneration of active site radical. PT – proton transfer, HAT – hydrogen atom transfer, ET – electron transfer. This figure is reproduced from <cite>Yin2015</cite> (CC BY 4.0).]]
-The majority of what is known about the mechanism of AA5 enzymes comes from studies on the archetype, ''Fgr''GalOx.  AA5 enzymes oxidize their substrates through a ping-pong mechanism involving a corresponding reduction of oxygen to hydrogen peroxide mediated by a mononuclear copper center, which is complexed via a distinct, crosslinked tyrosyl-cysteine residue (see below) <cite>Whittaker2003,Whittaker2005,Baron1994,Humphreys2009,Whittaker1993,Whittaker1996,Whittaker1999,Kersten2014</cite>. The first half-reaction results in a two-electron oxidation of the substrate and corresponding reduction of the Cu[II]-tyrosyl radical to a Cu[I]-tyrosine (phenol). The second half-reaction regenerates the oxidation state of the active-site through reduction of molecular oxygen to hydrogen peroxide. Detailed kinetic studies, including kinetic isotope effects, suggest that each half reaction consists of three steps: proton transfer (PT), hydrogen atom transfer (HAT), and electron transfer (ET) <cite>Whittaker2004 Humphreys2009</cite>. Due to its fundamental uniqueness, the mechanism of AA5 CROs has received significant theoretical treatment and the synthesis of many chemical mimetics has been attempted <cite>Wang1998,Himo2000</cite>.
+The majority of what is known about the mechanism of AA5 enzymes comes from studies on the archetype, ''Fgr''GalOx.  AA5 enzymes oxidize their substrates through a ping-pong mechanism involving a corresponding reduction of oxygen to hydrogen peroxide mediated by a mononuclear copper center, which is complexed via a distinct, crosslinked tyrosyl-cysteine residue (see below) <cite>Whittaker2003,Whittaker2005,Baron1994,Humphreys2009,Whittaker1993,Whittaker1996,Whittaker1999,Kersten2014</cite>. The first half-reaction results in a two-electron oxidation of the substrate and corresponding reduction of the Cu[II]-tyrosyl radical to a Cu[I]-tyrosine (phenol). The second half-reaction regenerates the oxidation state of the active-site through reduction of molecular oxygen to hydrogen peroxide. Detailed kinetic studies, including kinetic isotope effects, suggest that each half reaction consists of three steps: proton transfer (PT), hydrogen atom transfer (HAT), and electron transfer (ET) <cite>Whittaker2004 Humphreys2009</cite>. Due to its fundamental uniqueness, the mechanism of AA5 CROs has received significant theoretical treatment and the synthesis of many chemical mimetics has been attempted <cite>Wang1998 Itoh2000 Himo2000</cite>.
 Practically, AA5 enzymes are conveniently assayed by measuring hydrogen peroxide (co-product) generatation, e.g. in coupled reactions with horseradish peroxidase and a chromogenic substrate.  In preparative reactions, catalase is typically added to prevent accumulation of hydrogen peroxide. AA5 enzymes are prone to inactivation by one-electron reduction to a Cu[I]-tyrosyl radical.  The resulting off-cycle species can be rescued by oxidation by  peroxidases or transition metal ions (ferricyanide, Mg(III), etc.), the inclusion of which in reactions is required to obtain maximal activity and substrate conversion <cite>Kersten1990 Cleveland1975 Hamilton1978 Pedersen2015 Forget2020 Johnson2021 Roncal2012</cite>.

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 == Catalytic Residues ==
 [[File: FgrGalOx_Active_site_CAZY.png|thumb|250px|right|'''Figure 2.''' Active site residues of copper radical oxidases FgrGalOx, Cu ion in orange (PDB ID [{{PDBlink}}1gof 1GOF]). ]]
-The redox-active center of AA5 oxidases comprises a copper ion that coordinated by two tyrosine sidechains and two histidine sidechains (in the archetype, ''Fgr''GalOx, these are Tyr495, Tyr272, His496, and His581, respectively), resulting in a distorted square pyramidal geometry <cite>Ito1991 Ito1994 Yin2015 Mathieu2020</cite>. Based on the copper coordination environment, AA5 proteins are type 2 "non-blue" copper enzymes due to the nitrogen and oxygen ligands <cite>Ito1994</cite>.
+The redox-active center of AA5 oxidases comprises a copper ion that coordinated by two tyrosine sidechains and two histidine sidechains (in the archetype ''Fgr''GalOx these are Tyr495, Tyr272, His496, and His581, respectively), resulting in a distorted square pyramidal geometry <cite>Ito1991 Ito1994 Yin2015 Mathieu2020</cite>. Based on the copper coordination environment, AA5 proteins are type 2 "non-blue" copper enzymes due to the nitrogen and oxygen ligands <cite>Ito1994</cite>.
 The unique feature of AA5 enzymes is the covalently linked equatorial tyrosine with an adjacent cysteine by a thioether bond (Tyr272 and Cys228 in ''Fgr''GalOx) <cite>Ito1991</cite>. The thioether linkage forms spontaneously in the presence of copper and has been shown to stabilize the radical though delocalization onto the equatorial tyrosine during catalysis <cite>Rogers2008</cite>.