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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 [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: 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]]
| + | |
| Structural highlights
5k8c is a 1 chain structure with sequence from Shewanella oneidensis MR-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.85Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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).[1]
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Gattis SG, Chung HS, Trent MS, Raetz CR. The origin of 8-amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N) in the lipopolysaccharide of Shewanella oneidensis. J Biol Chem. 2013 Mar 29;288(13):9216-25. doi: 10.1074/jbc.M113.453324. Epub 2013, Feb 14. PMID:23413030 doi:http://dx.doi.org/10.1074/jbc.M113.453324
- ↑ Zachman-Brockmeyer TR, Thoden JB, Holden HM. Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-D-Manno-Octulosonic Acid. Biochemistry. 2016 Jun 8. PMID:27275764 doi:http://dx.doi.org/10.1021/acs.biochem.6b00439
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