This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1qpg

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:15, 14 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1qpg.gif|left|200px]]
 
-
{{Structure
+
==3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q==
-
|PDB= 1qpg |SIZE=350|CAPTION= <scene name='initialview01'>1qpg</scene>, resolution 2.4&Aring;
+
<StructureSection load='1qpg' size='340' side='right'caption='[[1qpg]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=MAP:MAGNESIUM-5&#39;-ADENYLY-IMIDO-TRIPHOSPHATE'>MAP</scene> and <scene name='pdbligand=3PG:3-PHOSPHOGLYCERIC ACID'>3PG</scene>
+
<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>
-
|ACTIVITY= [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]
+
</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>
-
|GENE=
+
<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>
-
'''3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q'''
+
==See Also==
-
 
+
*[[Phosphoglycerate kinase 3D structures|Phosphoglycerate kinase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
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.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1QPG is a [[Single protein]] structure of sequence from [http://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].
+
-
 
+
-
==Reference==
+
-
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://www.ncbi.nlm.nih.gov/pubmed/8672447 8672447]
+
-
[[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://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 13:22:32 2008''
+

Current revision

3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q

PDB ID 1qpg

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1qpg"
Personal tools