1obf: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1obf.gif|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_1obf", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_1obf|  PDB=1obf  |  SCENE=  }}
'''THE CRYSTAL STRUCTURE OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ALCALIGENES XYLOSOXIDANS AT 1.7 RESOLUTION.'''


==The crystal structure of Glyceraldehyde 3-phosphate Dehydrogenase from Alcaligenes xylosoxidans at 1.7A resolution.==
<StructureSection load='1obf' size='340' side='right'caption='[[1obf]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/P83696_ALCXX P83696_ALCXX]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ob/1obf_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==Overview==
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>
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.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1OBF is a [[Single protein]] structure of sequence from [http://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].
</div>
<div class="pdbe-citations 1obf" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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://www.ncbi.nlm.nih.gov/pubmed/12777799 12777799]
*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Achromobacter xylosoxidans]]
[[Category: Achromobacter xylosoxidans]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Antonyuk, S V.]]
[[Category: Antonyuk SV]]
[[Category: Eady, R R.]]
[[Category: Eady RR]]
[[Category: Hasnain, S S.]]
[[Category: Hasnain SS]]
[[Category: Strange, R W.]]
[[Category: Strange RW]]
[[Category: Free-nad gapdh]]
[[Category: Glycolytic pathway]]
[[Category: Oxidoreductase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 03:37:48 2008''
Retrieved from "https://proteopedia.org/1obf"