3q2i

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Current revision (10:45, 21 February 2024) (edit) (undo)
 
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<StructureSection load='3q2i' size='340' side='right'caption='[[3q2i]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
<StructureSection load='3q2i' size='340' side='right'caption='[[3q2i]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3q2i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"chromobacterium_janthinum"_(zopf)_ford_1927 "chromobacterium janthinum" (zopf) ford 1927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q2I FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3q2i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q2I FirstGlance]. <br>
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</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=HP7:(2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[(2R,3S,4R,5R)-5-(2,4-DIOXOPYRIMIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXY-3,4-DIHYDROXY-OXANE-2-CARBOXYLIC+ACID'>HP7</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3q2k|3q2k]]</div></td></tr>
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<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=HP7:(2S,3S,4R,5R,6R)-5-ACETAMIDO-6-[[[(2R,3S,4R,5R)-5-(2,4-DIOXOPYRIMIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXY-3,4-DIHYDROXY-OXANE-2-CARBOXYLIC+ACID'>HP7</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CV_4127, wlbA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=536 "Chromobacterium janthinum" (Zopf) Ford 1927])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3q2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q2i OCA], [https://pdbe.org/3q2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q2i RCSB], [https://www.ebi.ac.uk/pdbsum/3q2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q2i ProSAT]</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=3q2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q2i OCA], [https://pdbe.org/3q2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q2i RCSB], [https://www.ebi.ac.uk/pdbsum/3q2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q2i ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q7NQL0_CHRVO Q7NQL0_CHRVO]
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The unusual sugar 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid, or ManNAc3NAcA1, has been observed in the lipopolysaccharides of both pathogenic and nonpathogenic Gram-negative bacteria. It is added to the lipopolysaccharides of these organisms by glycosyltransferases that use as substrates, UDP-ManNAc3NAcA. Five enzymes are ultimately required for the biosynthesis of UDP-ManNAc3NAcA starting from UDP-N-acetylglucosamine. The second enzyme in the pathway, encoded by the wlba gene and referred to as WlbA, catalyzes the NAD-dependent oxidation of the C-3' hydroxyl group of the UDP-linked sugar. Here we describe a combined structural and functional investigation of the WlbA enzymes from Bordetella pertussis and Chromobacterium violaceum. For this investigation, ternary structures were determined in the presence of NAD(H) and substrate to 2.13 A and 1.5 A resolution, respectively. Both of the enzymes display octameric quaternary structures with their active sites positioned far apart. The octamers can be envisioned as tetramers of dimers. Kinetic studies demonstrate that the reaction mechanisms for these enzymes are sequential and that they do not require alpha-ketoglutarate for activity. These results are in sharp contrast to those recently reported for the WlbA enzymes from Pseudomonas aeruginosa and Thermus thermophilus, which function via ping-pong mechanisms that involve alpha-ketoglutarate. Taken together the results reported here demonstrate that there are two distinct families of WlbA enzymes, which differ with respect to amino acid sequences, quaternary structures, active site architectures, and kinetic mechanisms.
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Biochemical and Structural Characterization of WlbA from Bordetella pertussis and Chromobacterium violaceum: Enzymes Required for the Biosynthesis of 2,3-Diacetamido-2,3-Dideoxy-D-Mannuronic Acid.,Thoden JB, Holden HM Biochemistry. 2011 Jan 17. PMID:21241053<ref>PMID:21241053</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3q2i" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Chromobacterium violaceum]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Holden, H M]]
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[[Category: Holden HM]]
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[[Category: Thoden, J B]]
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[[Category: Thoden JB]]
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[[Category: Dehydrogenase]]
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[[Category: Nad binding]]
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[[Category: Oxidoreductase]]
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[[Category: Rossmann fold]]
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[[Category: Udp-sugar binding]]
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Current revision

Crystal structure of the WlbA dehydrognase from Chromobactrium violaceum in complex with NADH and UDP-GlcNAcA at 1.50 A resolution

PDB ID 3q2i

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