1wnd
From Proteopedia
(New page: 200px<br /><applet load="1wnd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wnd, resolution 2.10Å" /> '''Escherichia coli Ydc...) |
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| - | [[Image:1wnd.gif|left|200px]]<br /><applet load="1wnd" size=" | + | [[Image:1wnd.gif|left|200px]]<br /><applet load="1wnd" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1wnd, resolution 2.10Å" /> | caption="1wnd, resolution 2.10Å" /> | ||
'''Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal stucture'''<br /> | '''Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal stucture'''<br /> | ||
==Overview== | ==Overview== | ||
| - | In the context of a medium-scaled structural genomics program aiming at | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 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 CA 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:// | + | 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]. |
==Reference== | ==Reference== | ||
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[[Category: nadh]] | [[Category: nadh]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:46:15 2008'' |
Revision as of 13:46, 21 February 2008
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Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal stucture
Overview
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.
About this Structure
1WND is a Single protein structure of sequence from Escherichia coli with as ligand. Active as Betaine-aldehyde dehydrogenase, with EC number 1.2.1.8 Full crystallographic information is available from OCA.
Reference
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:15381418
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