5k8b - Revision history

OCA at 09:54, 27 September 2023

OCA — Wed, 27 Sep 2023 09:54:37 GMT

←Older revision		Revision as of 09:54, 27 September 2023
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	<StructureSection load='5k8b' size='340' side='right'caption='[[5k8b]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5k8b' size='340' side='right'caption='[[5k8b]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k8b]] is a 4 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=5K8B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K8B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k8b]] is a 4 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=5K8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K8B 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PDG:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC+ACID'>PDG</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]] 2.15Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k8c\|5k8c]]</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PDG:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC+ACID'>PDG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdnA, SO_2476 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</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=5k8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8b OCA], [https://pdbe.org/5k8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k8b RCSB], [https://www.ebi.ac.uk/pdbsum/5k8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8b ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/8-amino-3,8-dideoxy-alpha-D-manno-octulosonate_transaminase 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.109 2.6.1.109] </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=5k8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8b OCA], [~~http~~://pdbe.org/5k8b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k8b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k8b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8b ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KDNA_SHEON KDNA_SHEON]] Catalyzes the second (last) 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/KDNA_SHEON KDNA_SHEON] Catalyzes the second (last) 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: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase]]
	[[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: Transaminase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 12:08, 25 December 2019

OCA — Wed, 25 Dec 2019 12:08:28 GMT

←Older revision		Revision as of 12:08, 25 December 2019
Line 1:		Line 1:

	==X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase, from Shewanella oneidensis in the presence of the external aldimine with PLP and glutamate==		==X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase, from Shewanella oneidensis in the presence of the external aldimine with PLP and glutamate==
-	<StructureSection load='5k8b' size='340' side='right' caption='[[5k8b]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5k8b' size='340' side='right'caption='[[5k8b]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5k8b]] is a 4 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=5K8B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8B FirstGlance]. <br>		<table><tr><td colspan='2'>[[5k8b]] is a 4 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=5K8B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8B FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase]]		[[Category: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase]]
		+	[[Category: Large Structures]]
	[[Category: Sheon]]		[[Category: Sheon]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]

OCA at 18:09, 15 November 2017

OCA — Wed, 15 Nov 2017 18:09:53 GMT

←Older revision		Revision as of 18:09, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5k8b' size='340' side='right' caption='[[5k8b]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5k8b' size='340' side='right' caption='[[5k8b]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k8b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k8b]] is a 4 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=5K8B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8B 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PDG:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC+ACID'>PDG</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PDG:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC+ACID'>PDG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k8c\|5k8c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k8c\|5k8c]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdnA, SO_2476 ([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/8-amino-3,8-dideoxy-alpha-D-manno-octulosonate_transaminase 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.109 2.6.1.109] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/8-amino-3,8-dideoxy-alpha-D-manno-octulosonate_transaminase 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.109 2.6.1.109] </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=5k8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8b OCA], [http://pdbe.org/5k8b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8b RCSB], [http://www.ebi.ac.uk/pdbsum/5k8b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8b 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=5k8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8b OCA], [http://pdbe.org/5k8b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8b RCSB], [http://www.ebi.ac.uk/pdbsum/5k8b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8b ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase]]		[[Category: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase]]
		+	[[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 02:41:11 GMT

←Older revision		Revision as of 02:41, 13 July 2016
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k8c\|5k8c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k8c\|5k8c]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/8-amino-3,8-dideoxy-alpha-D-manno-octulosonate_transaminase 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.109 2.6.1.109] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/8-amino-3,8-dideoxy-alpha-D-manno-octulosonate_transaminase 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.109 2.6.1.109] </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=5k8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8b OCA], [http://pdbe.org/5k8b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8b RCSB], [http://www.ebi.ac.uk/pdbsum/5k8b 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=5k8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8b OCA], [http://pdbe.org/5k8b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8b RCSB], [http://www.ebi.ac.uk/pdbsum/5k8b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k8b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 15:54, 23 June 2016

OCA — Thu, 23 Jun 2016 15:54:57 GMT

←Older revision		Revision as of 15:54, 23 June 2016
Line 11:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/KDNA_SHEON KDNA_SHEON]] Catalyzes the second (last) 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/KDNA_SHEON KDNA_SHEON]] Catalyzes the second (last) 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 5k8b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA: Protected "5k8b" [edit=sysop:move=sysop]

OCA — Mon, 20 Jun 2016 22:28:59 GMT

Protected "5k8b" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:28, 20 June 2016

OCA: New page: ==X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase, from Shewanella oneidensis in the presence of the external aldimine with PLP and glutamate==
OCA — Mon, 20 Jun 2016 22:28:53 GMT

New page: ==X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase, from Shewanella oneidensis in the presence of the external aldimine with PLP and glutamate== <Struc...

New page

==X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase, from Shewanella oneidensis in the presence of the external aldimine with PLP and glutamate==
<StructureSection load='5k8b' size='340' side='right' caption='[[5k8b]], [[Resolution|resolution]] 2.15Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5k8b]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K8B OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K8B 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PDG:N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC+ACID'>PDG</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[5k8c|5k8c]]</td></tr>
<tr id='activity'><td class="sblockLbl">Activity:</td><td class="sblockDat">[http://en.wikipedia.org/wiki/8-amino-3,8-dideoxy-alpha-D-manno-octulosonate_transaminase 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.109 2.6.1.109] </td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k8b OCA], [http://pdbe.org/5k8b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k8b RCSB], [http://www.ebi.ac.uk/pdbsum/5k8b PDBsum]</td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/KDNA_SHEON KDNA_SHEON]] Catalyzes the second (last) 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: 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase]]
[[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: Transaminase]]
[[Category: Transferase]]