1wnd

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[[Image:1wnd.gif|left|200px]]<br /><applet load="1wnd" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1wnd, resolution 2.10&Aring;" />
 
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'''Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal stucture'''<br />
 
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==Overview==
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==Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal structure==
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In the context of a medium-scaled structural genomics program aiming at solving the structures of as many as possible bacterial unknown open reading frame products from Escherichia coli (Y prefix), we have solved the structure of YdcW at 2.1A resolution, using molecular replacement. According to its sequence identity, YdcW has been classified into the betaine aldehyde dehydrogenases family (EC 1.2.1.8), catalysing the oxidation of betaine aldehyde into glycine betaine. The structure of YdcW resembles that of other aldehyde dehydrogenases: it is tetrameric and binds a NADH molecule in each monomer. The NADH molecules, bound in the active site by soaking, are revealed to be in the "hydrolysis position". Activities experiments demonstrate that YdcW is more active on medium-chains aldehyde than on betaine aldehyde. However, soaking of betaine into YdcW crystals revealed its presence in one of the subunits, in two positions, a putative resting position and a hydride transfer ready position. Analysis of kinetics data and of the active site shape suggest an optimum binding of n-alkyl aldehydes up to seven to eight carbon atoms, possibly followed by a bulky cyclic or aromatic group.
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<StructureSection load='1wnd' size='340' side='right'caption='[[1wnd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1wnd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WND OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WND FirstGlance]. <br>
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1WND is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Betaine-aldehyde_dehydrogenase Betaine-aldehyde dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.8 1.2.1.8] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WND OCA].
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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]] 2.1&#8491;</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=CA:CALCIUM+ION'>CA</scene></td></tr>
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==Reference==
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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=1wnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wnd OCA], [https://pdbe.org/1wnd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wnd RCSB], [https://www.ebi.ac.uk/pdbsum/1wnd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wnd ProSAT]</span></td></tr>
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Crystal structure and kinetics identify Escherichia coli YdcW gene product as a medium-chain aldehyde dehydrogenase., Gruez A, Roig-Zamboni V, Grisel S, Salomoni A, Valencia C, Campanacci V, Tegoni M, Cambillau C, J Mol Biol. 2004 Oct 8;343(1):29-41. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15381418 15381418]
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</table>
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[[Category: Betaine-aldehyde dehydrogenase]]
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== Function ==
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[[Category: Escherichia coli]]
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[https://www.uniprot.org/uniprot/ABDH_ECOLI ABDH_ECOLI] Catalyzes the oxidation of 1-pyrroline, which is spontaneously formed from 4-aminobutanal, leading to 4-aminobutanoate (GABA). Can also oxidize n-alkyl medium-chain aldehydes, but with a lower catalytic efficiency.<ref>PMID:16023116</ref> <ref>PMID:15381418</ref>
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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: Cambillau, C.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Gruez, A.]]
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Check<jmol>
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[[Category: Roig-Zamboni, V.]]
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<jmolCheckbox>
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[[Category: Tegoni, M.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wn/1wnd_consurf.spt"</scriptWhenChecked>
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[[Category: CA]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: aldehyde dehydrogenase]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: crystal structure]]
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</jmolCheckbox>
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[[Category: fluorescence]]
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</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=1wnd ConSurf].
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[[Category: kinetics]]
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<div style="clear:both"></div>
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[[Category: nadh]]
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== References ==
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<references/>
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:46:15 2008''
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__TOC__
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</StructureSection>
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[[Category: Escherichia coli K-12]]
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[[Category: Large Structures]]
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[[Category: Cambillau C]]
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[[Category: Gruez A]]
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[[Category: Roig-Zamboni V]]
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[[Category: Tegoni M]]

Current revision

Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal structure

PDB ID 1wnd

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