5k8c - Revision history

OCA at 09:54, 27 September 2023

OCA — Wed, 27 Sep 2023 09:54:40 GMT

←Older revision		Revision as of 09:54, 27 September 2023
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	<StructureSection load='5k8c' size='340' side='right'caption='[[5k8c]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5k8c' size='340' side='right'caption='[[5k8c]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k8c]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sheon Sheon~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K8C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k8c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K8C FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.85Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdnB, SO_2477 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-alpha-D-manno-octulosonate_8-oxidase 3-deoxy-alpha-D-manno-octulosonate 8-oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.48 1.1.3.48] </span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5k8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8c OCA], [https://pdbe.org/5k8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k8c RCSB], [https://www.ebi.ac.uk/pdbsum/5k8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8c ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5k8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8c OCA], [~~http~~://pdbe.org/5k8c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k8c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k8c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8c ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KDNB_SHEON KDNB_SHEON]] Catalyzes the first step of the biosynthesis of Kdo8N (8-amino-3,8-dideoxy-D-manno-octulosonate) from Kdo (3-deoxy-D-manno-octulosonate).<ref>PMID:23413030</ref>	+	[https://www.uniprot.org/uniprot/KDNB_SHEON KDNB_SHEON] Catalyzes the first step of the biosynthesis of Kdo8N (8-amino-3,8-dideoxy-D-manno-octulosonate) from Kdo (3-deoxy-D-manno-octulosonate).<ref>PMID:23413030</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sheon~~]]	+	[[Category: Shewanella oneidensis MR-1]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Holden HM]]
-	[[Category: Thoden~~, J B~~]]	+	[[Category: Thoden JB]]
-	[[Category: Zachman-Brockmeyer~~, T R]]~~	+	[[Category: Zachman-Brockmeyer TR]]
-	~~[[Category: 8-amino-3]]~~	+
-	~~[[Category: 8-dideoxy-d-manno-octulosonic acid]]~~	+
-	~~[[Category: Deoxy sugar]]~~	+
-	~~[[Category: Group iii alcohol dehydrogenase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 12:08, 25 December 2019

OCA — Wed, 25 Dec 2019 12:08:46 GMT

←Older revision		Revision as of 12:08, 25 December 2019
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	==X-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, from Shewanella oneidensis==		==X-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, from Shewanella oneidensis==
-	<StructureSection load='5k8c' size='340' side='right' caption='[[5k8c]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5k8c' size='340' side='right'caption='[[5k8c]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5k8c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8C FirstGlance]. <br>		<table><tr><td colspan='2'>[[5k8c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8C FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase]]		[[Category: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Sheon]]		[[Category: Sheon]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]

OCA at 18:10, 15 November 2017

OCA — Wed, 15 Nov 2017 18:10:06 GMT

←Older revision		Revision as of 18:10, 15 November 2017
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	<StructureSection load='5k8c' size='340' side='right' caption='[[5k8c]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5k8c' size='340' side='right' caption='[[5k8c]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k8c]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k8c]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8C FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdnB, SO_2477 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-alpha-D-manno-octulosonate_8-oxidase 3-deoxy-alpha-D-manno-octulosonate 8-oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.48 1.1.3.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-alpha-D-manno-octulosonate_8-oxidase 3-deoxy-alpha-D-manno-octulosonate 8-oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.48 1.1.3.48] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8c OCA], [http://pdbe.org/5k8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8c RCSB], [http://www.ebi.ac.uk/pdbsum/5k8c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8c ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8c OCA], [http://pdbe.org/5k8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8c RCSB], [http://www.ebi.ac.uk/pdbsum/5k8c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8c ProSAT]</span></td></tr>
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase]]		[[Category: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase]]
		+	[[Category: Sheon]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]
	[[Category: Thoden, J B]]		[[Category: Thoden, J B]]

OCA at 02:41, 13 July 2016

OCA — Wed, 13 Jul 2016 02:41:13 GMT

←Older revision		Revision as of 02:41, 13 July 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-alpha-D-manno-octulosonate_8-oxidase 3-deoxy-alpha-D-manno-octulosonate 8-oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.48 1.1.3.48] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-alpha-D-manno-octulosonate_8-oxidase 3-deoxy-alpha-D-manno-octulosonate 8-oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.48 1.1.3.48] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8c OCA], [http://pdbe.org/5k8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8c RCSB], [http://www.ebi.ac.uk/pdbsum/5k8c PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8c OCA], [http://pdbe.org/5k8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8c RCSB], [http://www.ebi.ac.uk/pdbsum/5k8c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8c ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 15:45, 23 June 2016

OCA — Thu, 23 Jun 2016 15:45:01 GMT

←Older revision		Revision as of 15:45, 23 June 2016
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/KDNB_SHEON KDNB_SHEON]] Catalyzes the first step of the biosynthesis of Kdo8N (8-amino-3,8-dideoxy-D-manno-octulosonate) from Kdo (3-deoxy-D-manno-octulosonate).<ref>PMID:23413030</ref>		[[http://www.uniprot.org/uniprot/KDNB_SHEON KDNB_SHEON]] Catalyzes the first step of the biosynthesis of Kdo8N (8-amino-3,8-dideoxy-D-manno-octulosonate) from Kdo (3-deoxy-D-manno-octulosonate).<ref>PMID:23413030</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	8-amino-3,8-dideoxy-d-manno-octulosonic acid (Kdo8N) is a unique amino sugar that has thus far only been observed on the lipopolysaccharides of marine bacteria belonging to the genus Shewanella. Although its biological function is still unclear, it is thought that the sugar is important for the integrity of the bacterial cell outer membrane. A three-gene cluster required for the biosynthesis of Kdo8N was first identified in Shewanella oneidensis. Here we describe the three-dimensional structures of two of the enzymes required for Kdo8N biosynthesis in S. oneidensis, namely KdnB and KdnA. The structure of KdnB was solved to 1.85-A resolution, and its overall three-dimensional architecture places it into the Group III alcohol dehydrogenase family. A previous study suggested that KdnB did not require NAD(P) for activity. Strikingly, although the protein was crystallized in the absence of any cofactors, the electron density map clearly revealed the presence of a tightly bound NAD(H). In addition, a bound metal ion was observed, which was shown via X-ray fluorescence to be a zinc ion. Unlike other members of the Group III alcohol dehydrogenases, the dinucleotide cofactor in KdnB is tightly bound and cannot be removed without leading to protein precipitation. With respect to KdnA, it is a pyridoxal 5'-phosphate or (PLP)-dependent aminotransferase. For this analysis, the structure of KdnA, trapped in the presence of the external aldimine with PLP and glutamate, was determined to 2.15-A resolution. The model of KdnA represents the first structure of a sugar aminotransferase that functions on an 8-oxo sugar. Taken together the results reported herein shed new molecular insight into the biosynthesis of Kdo8N.
		+
		+	Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-D-Manno-Octulosonic Acid.,Zachman-Brockmeyer TR, Thoden JB, Holden HM Biochemistry. 2016 Jun 8. PMID:27275764<ref>PMID:27275764</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5k8c" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA: Protected "5k8c" [edit=sysop:move=sysop]

OCA — Mon, 20 Jun 2016 22:29:00 GMT

Protected "5k8c" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:29, 20 June 2016

OCA: New page: ==X-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, from Shewanella oneidensis== == Structural highlights ==
<table><tr><td colspan='2'>[[5k8c]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8C OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8C FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/3-deoxy-alpha-D-manno-octulosonate_8-oxidase 3-deoxy-alpha-D-manno-octulosonate 8-oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.3.48 1.1.3.48] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8c OCA], [http://pdbe.org/5k8c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8c RCSB], [http://www.ebi.ac.uk/pdbsum/5k8c PDBsum]</td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/KDNB_SHEON KDNB_SHEON]] Catalyzes the first step of the biosynthesis of Kdo8N (8-amino-3,8-dideoxy-D-manno-octulosonate) from Kdo (3-deoxy-D-manno-octulosonate).<ref>PMID:23413030</ref>
== References ==
<references/>
TOC
</StructureSection>
[[Category: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase]]
[[Category: Holden, H M]]
[[Category: Thoden, J B]]
[[Category: Zachman-Brockmeyer, T R]]
[[Category: 8-amino-3]]
[[Category: 8-dideoxy-d-manno-octulosonic acid]]
[[Category: Deoxy sugar]]
[[Category: Group iii alcohol dehydrogenase]]
[[Category: Transferase]]