1koj: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
New page: left|200px<br /><applet load="1koj" size="450" color="white" frame="true" align="right" spinBox="true" caption="1koj, resolution 1.90Å" /> '''Crystal structure of...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(17 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1koj.gif|left|200px]]<br /><applet load="1koj" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1koj, resolution 1.90&Aring;" />
'''Crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid'''<br />


==Overview==
==Crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid==
Phosphoglucose isomerase (EC ) catalyzes the second step in glycolysis, the reversible isomerization of D-glucose 6-phosphate to D-fructose, 6-phosphate. The reaction mechanism involves acid-base catalysis with, proton transfer and proceeds through a cis-enediol(ate) intermediate., 5-Phospho-D-arabinonohydroxamic acid (5PAH) is a synthetic small molecule, that resembles the reaction intermediate, differing only in that it has a, nitrogen atom in place of C1. Hence, 5PAH is the best inhibitor of the, isomerization reaction reported to date with a K(i) of 2 x 10(-7) M. Here, we report the crystal structure of rabbit phosphoglucose isomerase, complexed with 5PAH at 1.9 A resolution. The interaction of 5PAH with, amino acid residues in the enzyme active site supports a model of the, catalytic mechanism in which Glu-357 transfers a proton between C1 and C2, and Arg-272 helps stabilize the intermediate. It also suggests a mechanism, for proton transfer between O1 and O2.
<StructureSection load='1koj' size='340' side='right'caption='[[1koj]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1koj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KOJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KOJ 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]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PAN:5-PHOSPHO-D-ARABINOHYDROXAMIC+ACID'>PAN</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=1koj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1koj OCA], [https://pdbe.org/1koj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1koj RCSB], [https://www.ebi.ac.uk/pdbsum/1koj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1koj ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/G6PI_RABIT G6PI_RABIT] Besides it's role as a glycolytic enzyme, mammalian GPI can function as a tumor-secreted cytokine and an angiogenic factor (AMF) that stimulates endothelial cell motility. GPI is also a neurotrophic factor (Neuroleukin) for spinal and sensory neurons (By similarity).
== 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/ko/1koj_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1koj ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Phosphoglucose isomerase (EC ) catalyzes the second step in glycolysis, the reversible isomerization of D-glucose 6-phosphate to D-fructose 6-phosphate. The reaction mechanism involves acid-base catalysis with proton transfer and proceeds through a cis-enediol(ate) intermediate. 5-Phospho-D-arabinonohydroxamic acid (5PAH) is a synthetic small molecule that resembles the reaction intermediate, differing only in that it has a nitrogen atom in place of C1. Hence, 5PAH is the best inhibitor of the isomerization reaction reported to date with a K(i) of 2 x 10(-7) M. Here we report the crystal structure of rabbit phosphoglucose isomerase complexed with 5PAH at 1.9 A resolution. The interaction of 5PAH with amino acid residues in the enzyme active site supports a model of the catalytic mechanism in which Glu-357 transfers a proton between C1 and C2 and Arg-272 helps stabilize the intermediate. It also suggests a mechanism for proton transfer between O1 and O2.


==About this Structure==
The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid.,Arsenieva D, Hardre R, Salmon L, Jeffery CJ Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5872-7. PMID:11983887<ref>PMID:11983887</ref>
1KOJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with PAN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glucose-6-phosphate_isomerase Glucose-6-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.9 5.3.1.9] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KOJ OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid., Arsenieva D, Hardre R, Salmon L, Jeffery CJ, Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5872-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11983887 11983887]
</div>
[[Category: Glucose-6-phosphate isomerase]]
<div class="pdbe-citations 1koj" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Phosphoglucose isomerase 3D structures|Phosphoglucose isomerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Oryctolagus cuniculus]]
[[Category: Oryctolagus cuniculus]]
[[Category: Single protein]]
[[Category: Arsenieva D]]
[[Category: Arsenieva, D.]]
[[Category: Hardre R]]
[[Category: Hardre, R.]]
[[Category: Jeffery CJ]]
[[Category: Jeffery, C.J.]]
[[Category: Salmon L]]
[[Category: Salmon, L.]]
[[Category: PAN]]
[[Category: protein - inhibitor complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:30:18 2007''
Retrieved from "https://proteopedia.org/1koj"