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.


1gky

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:22, 27 March 2024) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1gky.gif|left|200px]]<br /><applet load="1gky" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1gky, resolution 2.0&Aring;" />
 
-
'''REFINED STRUCTURE OF THE COMPLEX BETWEEN GUANYLATE KINASE AND ITS SUBSTRATE GMP AT 2.0 ANGSTROMS RESOLUTION'''<br />
 
-
==Overview==
+
==REFINED STRUCTURE OF THE COMPLEX BETWEEN GUANYLATE KINASE AND ITS SUBSTRATE GMP AT 2.0 ANGSTROMS RESOLUTION==
-
The crystal structure of guanylate kinase from Saccharomyces cerevisiae complexed with its substrate GMP has been refined at a resolution of 2.0 A. The final crystallographic R-factor is 17.3% in the resolution range 7.0 A to 2.0 A for all reflections of the 100% complete data set. The final model has standard geometry with root-mean-square deviations of 0.016 A in bond lengths and 3.0 in bond angles. It consists of all 186 amino acid residues, the N-terminal acetyl group, the substrate GMP, one sulfate ion and 174 water molecules. Guanylate kinase is structurally related to adenylate kinases and G-proteins with respect to its central beta-sheet with connecting helices and the giant anion hole that binds nucleoside triphosphates. These nucleotides are ATP and GTP for the kinases and GTP for the G-proteins. The chain segment binding the substrate GMP of guanylate kinase differs grossly from the respective part of the adenylate kinases; it has no counterpart in the G-proteins. The binding mode of GMP is described in detail. Probably, the observed structure represents one of several structurally quite different intermediate states of the catalytic cycle.
+
<StructureSection load='1gky' size='340' side='right'caption='[[1gky]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1gky]] 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=1GKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GKY 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&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</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=1gky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gky OCA], [https://pdbe.org/1gky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gky RCSB], [https://www.ebi.ac.uk/pdbsum/1gky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gky ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/KGUA_YEAST KGUA_YEAST] Essential for recycling GMP and indirectly, cGMP.
 +
== 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/gk/1gky_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=1gky ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1GKY 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 <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=ACE:'>ACE</scene> and <scene name='pdbligand=5GP:'>5GP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Guanylate_kinase Guanylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.8 2.7.4.8] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GKY OCA].
+
*[[Guanylate kinase 3D structures|Guanylate kinase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Refined structure of the complex between guanylate kinase and its substrate GMP at 2.0 A resolution., Stehle T, Schulz GE, J Mol Biol. 1992 Apr 20;224(4):1127-41. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1314905 1314905]
+
[[Category: Large Structures]]
-
[[Category: Guanylate kinase]]
+
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Single protein]]
+
[[Category: Schulz GE]]
-
[[Category: Schulz, G E.]]
+
[[Category: Stehle T]]
-
[[Category: Stehle, T.]]
+
-
[[Category: 5GP]]
+
-
[[Category: ACE]]
+
-
[[Category: SO4]]
+
-
[[Category: transferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:51:13 2008''
+

Current revision

REFINED STRUCTURE OF THE COMPLEX BETWEEN GUANYLATE KINASE AND ITS SUBSTRATE GMP AT 2.0 ANGSTROMS RESOLUTION

PDB ID 1gky

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/1gky"
Personal tools