1qpg: Difference between revisions

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New page: left|200px<br /><applet load="1qpg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1qpg, resolution 2.4Å" /> '''3-PHOSPHOGLYCERATE KI...
 
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[[Image:1qpg.gif|left|200px]]<br /><applet load="1qpg" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1qpg, resolution 2.4&Aring;" />
'''3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q'''<br />


==Overview==
==3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q==
The structure of a ternary complex of the R65Q mutant of yeast, 3-phosphoglycerate kinase (PGK) with magnesium 5'-adenylylimidodiphosphate, (Mg-AMP-PNP) and 3-phospho-D-glycerate (3-PG) has been determined by X-ray, crystallography to 2.4 angstrom resolution. The structure was solved by, single isomorphous replacement, anamalous scattering, and solvent, flattening and has been refined to an R-factor of 0.185, with rms, deviations from ideal bond distance and angles of 0.009 angstrom and 1.78, degrees, respectively. PGK consists of two domains, with the 3-PG bound to, a "basic patch" of residues from the N-terminal domain and the Mg-AMP-PNP, interacting with residues from the C-terminal domain. The two ligands are, separated by approximately 11 angstrom across the interdomain cleft. The, model of the R65Q mutant of yeast PGK is very similar to the structures of, PGK isolated from horse, pig, and Bacillus stearothermophilus (rms, deviations between equivalent alpha-carbons in the individual domains &lt;, 1.0 angstrom) but exhibits substantial variations with a previously, reported yeast structure (rms deviations between equivalent alpha-carbons, in the individual domains of 2.9-3.2 angstrom). The most significant, tertiary structural differences among the yeast R65Q, equine, porcine, and, B. stearothermophilus PGK structures occur in the relative orientations of, the two domains. However, the relationships between the observed, conformations of PGK are inconsistent with a "hinge-bending" behavior that, would close the interdomain cleft. It is proposed that the available, structural and biochemical data on PGK may indicate that the basic patch, primarily represents the site of anion activation and not the, catalytically active binding site for 3-PG.
<StructureSection load='1qpg' size='340' side='right'caption='[[1qpg]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1qpg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QPG 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]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PG:3-PHOSPHOGLYCERIC+ACID'>3PG</scene>, <scene name='pdbligand=MAP:MAGNESIUM-5-ADENYLY-IMIDO-TRIPHOSPHATE'>MAP</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=1qpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qpg OCA], [https://pdbe.org/1qpg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qpg RCSB], [https://www.ebi.ac.uk/pdbsum/1qpg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qpg ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PGK_YEAST PGK_YEAST]
== 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/qp/1qpg_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=1qpg ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1QPG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with MAP and 3PG as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phosphoglycerate_kinase Phosphoglycerate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.3 2.7.2.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1QPG OCA].
*[[Phosphoglycerate kinase 3D structures|Phosphoglycerate kinase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Structure of the R65Q mutant of yeast 3-phosphoglycerate kinase complexed with Mg-AMP-PNP and 3-phospho-D-glycerate., McPhillips TM, Hsu BT, Sherman MA, Mas MT, Rees DC, Biochemistry. 1996 Apr 2;35(13):4118-27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8672447 8672447]
[[Category: Large Structures]]
[[Category: Phosphoglycerate kinase]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Single protein]]
[[Category: Hsu BT]]
[[Category: Hsu, B.T.]]
[[Category: Mas MT]]
[[Category: Mas, M.T.]]
[[Category: Mcphillips TM]]
[[Category: Mcphillips, T.M.]]
[[Category: Rees DC]]
[[Category: Rees, D.C.]]
[[Category: Sherman MA]]
[[Category: Sherman, M.A.]]
[[Category: 3PG]]
[[Category: MAP]]
[[Category: acetylation]]
[[Category: glycolysis]]
[[Category: kinase]]
[[Category: phosphotransferase (carboxyl acceptor)]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:51:55 2007''

Latest revision as of 11:15, 14 February 2024

3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q

Structural highlights

1qpg is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PGK_YEAST

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1qpg, resolution 2.40Å

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