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1obf

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(New page: 200px<br /> <applet load="1obf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1obf, resolution 1.7&Aring;" /> '''THE CRYSTAL STRUCTUR...)
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[[Image:1obf.gif|left|200px]]<br />
 
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<applet load="1obf" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1obf, resolution 1.7&Aring;" />
 
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'''THE CRYSTAL STRUCTURE OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ALCALIGENES XYLOSOXIDANS AT 1.7 RESOLUTION.'''<br />
 
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==Overview==
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==The crystal structure of Glyceraldehyde 3-phosphate Dehydrogenase from Alcaligenes xylosoxidans at 1.7A resolution.==
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The enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the, Gram-negative denitrifying bacterial species Alcaligenes xylosoxidans was, purified and crystallized as a contaminant protein during purification of, nitrous oxide reductase. This is the first structure of a GAPDH from a, denitrifying species. The crystal structure was solved at 1.7 A resolution, by molecular replacement using the structure of GAPDH from Bacillus, stearothermophilus as a starting model. The quality of the structure, enabled the amino-acid sequence of the A. xylosoxidans GAPDH to be, assigned. The structure is that of the apo-enzyme, lacking the NAD+, cofactor and with the active-site residue Cys154 oxidized. The global, structure of the enzyme has a homotetrameric quaternary structure similar, to that ... [[http://ispc.weizmann.ac.il/pmbin/getpm?12777799 (full description)]]
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<StructureSection load='1obf' size='340' side='right'caption='[[1obf]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1obf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_xylosoxidans Achromobacter xylosoxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OBF FirstGlance]. <br>
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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]] 1.7&#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=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1obf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1obf OCA], [https://pdbe.org/1obf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1obf RCSB], [https://www.ebi.ac.uk/pdbsum/1obf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1obf ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/P83696_ALCXX P83696_ALCXX]
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== Evolutionary Conservation ==
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ob/1obf_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=1obf ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the Gram-negative denitrifying bacterial species Alcaligenes xylosoxidans was purified and crystallized as a contaminant protein during purification of nitrous oxide reductase. This is the first structure of a GAPDH from a denitrifying species. The crystal structure was solved at 1.7 A resolution by molecular replacement using the structure of GAPDH from Bacillus stearothermophilus as a starting model. The quality of the structure enabled the amino-acid sequence of the A. xylosoxidans GAPDH to be assigned. The structure is that of the apo-enzyme, lacking the NAD+ cofactor and with the active-site residue Cys154 oxidized. The global structure of the enzyme has a homotetrameric quaternary structure similar to that observed for its bacterial and eukaryotic counterparts. The essential role of Cys154 in the enzyme activity has been confirmed. In monomer O two half-occupancy sulfate ions were found at the active site, which are analogous to the substrate and the "attacking" phosphate seen in B. stearothermophilus. One half-occupancy sulfate ion is also located in the substrate-binding site of monomer P.
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==About this Structure==
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The structure of glyceraldehyde 3-phosphate dehydrogenase from Alcaligenes xylosoxidans at 1.7 A resolution.,Antonyuk SV, Eady RR, Strange RW, Hasnain SS Acta Crystallogr D Biol Crystallogr. 2003 May;59(Pt 5):835-42. Epub 2003, Apr 25. PMID:12777799<ref>PMID:12777799</ref>
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1OBF is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/ ]] with SO4, K and PG4 as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/ ]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12]]. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OBF OCA]].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The structure of glyceraldehyde 3-phosphate dehydrogenase from Alcaligenes xylosoxidans at 1.7 A resolution., Antonyuk SV, Eady RR, Strange RW, Hasnain SS, Acta Crystallogr D Biol Crystallogr. 2003 May;59(Pt 5):835-42. Epub 2003, Apr 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12777799 12777799]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 1obf" style="background-color:#fffaf0;"></div>
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[[Category: Antonyuk, S.V.]]
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[[Category: Eady, R.R.]]
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[[Category: Hasnain, S.S.]]
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[[Category: Strange, R.W.]]
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[[Category: K]]
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[[Category: PG4]]
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[[Category: SO4]]
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[[Category: free-nad gapdh]]
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[[Category: glycolytic pathway]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Oct 29 17:30:03 2007''
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==See Also==
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*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
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*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Achromobacter xylosoxidans]]
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[[Category: Large Structures]]
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[[Category: Antonyuk SV]]
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[[Category: Eady RR]]
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[[Category: Hasnain SS]]
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[[Category: Strange RW]]

Current revision

The crystal structure of Glyceraldehyde 3-phosphate Dehydrogenase from Alcaligenes xylosoxidans at 1.7A resolution.

PDB ID 1obf

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