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| - | [[Image:2pzk.jpg|left|200px]] | |
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| - | <!--
| + | ==Crystal structure of the Bordetella bronchiseptica enzyme WbmG in complex with NAD== |
| - | The line below this paragraph, containing "STRUCTURE_2pzk", creates the "Structure Box" on the page.
| + | <StructureSection load='2pzk' size='340' side='right'caption='[[2pzk]], [[Resolution|resolution]] 2.10Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[2pzk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bordetella_bronchiseptica Bordetella bronchiseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PZK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PZK FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | -->
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> |
| - | {{STRUCTURE_2pzk| PDB=2pzk | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pzk OCA], [https://pdbe.org/2pzk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pzk RCSB], [https://www.ebi.ac.uk/pdbsum/2pzk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pzk ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''Crystal structure of the Bordetella bronchiseptica enzyme WbmG in complex with NAD'''
| + | == Function == |
| - | | + | [https://www.uniprot.org/uniprot/O87988_BORBO O87988_BORBO] |
| - | | + | == Evolutionary Conservation == |
| - | ==Overview== | + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | The pathogenic bacteria Bordetella parapertussis and Bordetella bronchiseptica express a lipopolysaccharide O antigen containing a polymer of 2,3-diacetamido-2,3-dideoxy-l-galacturonic acid. The O-antigen cluster contains three neighbouring genes that encode proteins belonging to the short-chain dehydrogenase/reductase (SDR) family, wbmF, wbmG and wbmH, and we aimed to elucidate their individual functions. Mutation and complementation implicate each gene in O-antigen expression but, as their putative sugar nucleotide substrates are not currently available, biochemical characterisation of WbmF, WbmG and WbmH is impractical at the present time. SDR family members catalyse a wide range of chemical reactions including oxidation, reduction and epimerisation. Because they typically share low sequence conservation, however, catalytic function cannot be predicted from sequence analysis alone. In this context, structural characterisation of the native proteins, co-crystals and small-molecule soaks enables differentiation of the functions of WbmF, WbmG and WbmH. These proteins exhibit typical SDR architecture and coordinate NAD. In the substrate-binding domain, all three enzymes bind uridyl nucleotides. WbmG contains a typical SDR catalytic TYK triad, which is required for oxidoreductase function, but the active site is devoid of additional acid-base functionality. Similarly, WbmH possesses a TYK triad, but an otherwise feature-poor active site. Consequently, 3,5-epimerase function can probably be ruled out for these enzymes. The WbmF active site contains conserved 3,5-epimerase features, namely, a positionally conserved cysteine (Cys133) and basic side chain (His90 or Asn213), but lacks the serine/threonine component of the SDR triad and therefore may not act as an oxidoreductase. The data suggest a pathway for synthesis of the O-antigen precursor UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid and illustrate the usefulness of structural data in predicting protein function.
| + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==About this Structure== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pz/2pzk_consurf.spt"</scriptWhenChecked> |
| - | 2PZK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bordetella_bronchiseptica Bordetella bronchiseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PZK OCA].
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==Reference== | + | </jmolCheckbox> |
| - | Predicting protein function from structure--the roles of short-chain dehydrogenase/reductase enzymes in Bordetella O-antigen biosynthesis., King JD, Harmer NJ, Preston A, Palmer CM, Rejzek M, Field RA, Blundell TL, Maskell DJ, J Mol Biol. 2007 Nov 30;374(3):749-63. Epub 2007 Sep 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17950751 17950751]
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pzk ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Bordetella bronchiseptica]] | | [[Category: Bordetella bronchiseptica]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Blundell, T L.]] | + | [[Category: Blundell TL]] |
| - | [[Category: Harmer, N J.]] | + | [[Category: Harmer NJ]] |
| - | [[Category: King, J D.]] | + | [[Category: King JD]] |
| - | [[Category: Maskell, D J.]] | + | [[Category: Maskell DJ]] |
| - | [[Category: Protein-nad complex]]
| + | |
| - | [[Category: Rossman fold]]
| + | |
| - | [[Category: Sugar binding protein]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 14:04:22 2008''
| + | |
