1wnd

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[[Image:1wnd.gif|left|200px]]
 
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{{Structure
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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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|PDB= 1wnd |SIZE=350|CAPTION= <scene name='initialview01'>1wnd</scene>, resolution 2.10&Aring;
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<StructureSection load='1wnd' size='340' side='right'caption='[[1wnd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>
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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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|ACTIVITY= <span class='plainlinks'>[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] </span>
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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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|GENE=
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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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|DOMAIN=
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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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|RELATEDENTRY=[[1wnb|1WNB]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wnd OCA], [http://www.ebi.ac.uk/pdbsum/1wnd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1wnd RCSB]</span>
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== Function ==
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}}
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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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== Evolutionary Conservation ==
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'''Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal stucture'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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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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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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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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1WND is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WND OCA].
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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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<div style="clear:both"></div>
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==Reference==
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== References ==
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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://www.ncbi.nlm.nih.gov/pubmed/15381418 15381418]
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<references/>
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[[Category: Betaine-aldehyde dehydrogenase]]
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__TOC__
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[[Category: Escherichia coli]]
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</StructureSection>
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[[Category: Single protein]]
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[[Category: Escherichia coli K-12]]
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[[Category: Cambillau, C.]]
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[[Category: Large Structures]]
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[[Category: Gruez, A.]]
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[[Category: Cambillau C]]
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[[Category: Roig-Zamboni, V.]]
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[[Category: Gruez A]]
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[[Category: Tegoni, M.]]
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[[Category: Roig-Zamboni V]]
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[[Category: aldehyde dehydrogenase]]
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[[Category: Tegoni M]]
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[[Category: crystal structure]]
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[[Category: fluorescence]]
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[[Category: kinetic]]
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[[Category: nadh]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:38:36 2008''
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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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