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[[Image: | ==STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 ANGSTROMS RESOLUTION: A MODEL FOR A CATALYTIC TRANSITION STATE== | ||
<StructureSection load='1ake' size='340' side='right' caption='[[1ake]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1ake]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AKE FirstGlance]. <br> | |||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene><br> | |||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr> | |||
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ake FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ake OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ake RCSB], [http://www.ebi.ac.uk/pdbsum/1ake PDBsum]</span></td></tr> | |||
<table> | |||
== 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/ak/1ake_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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The structure of adenylate kinase from Escherichia coli ligated with the two-substrate-mimicking inhibitor P1,P5-bis(adenosine-5'-)pentaphosphate has been determined by X-ray diffraction and refined to a resolution of 1.9 A. The asymmetric unit of the crystals contains two copies of the complex, the structures of which agree well with each other. One of these copies is less well ordered in the crystals than the other, it shows generally higher temperature factors. The molecular packing in the crystals is discussed and correlated to crystal habit and anisotropic X-ray diffraction. The bound inhibitor simulates well the binding of substrates ATP and AMP, which are clearly assigned. The alpha-phosphate of AMP is well positioned for a nucleophilic attack on the gamma-phosphate of ATP. The observed structure readily allows the construction of a stabilized pentaco-ordinated transition state, as proposed for the known in-line mechanism of the enzyme, with nucleophile and leaving group in the apical positions of a trigonal bipyramid. The kinetic data of numerous mutations reported in the literature are correlated with the detailed structure of the enzyme. The mutants were classified. The concomitant increase of the Michaelis constants for ATP and AMP in the group of mutants that modify only the ATP-binding site cannot be explained. | |||
Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state.,Muller CW, Schulz GE J Mol Biol. 1992 Mar 5;224(1):159-77. PMID:1548697<ref>PMID:1548697</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[Adenylate kinase|Adenylate kinase]] | *[[Adenylate kinase|Adenylate kinase]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Adenylate kinase]] | [[Category: Adenylate kinase]] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Mueller, C W.]] | [[Category: Mueller, C W.]] | ||
[[Category: Schulz, G E.]] | [[Category: Schulz, G E.]] | ||
Revision as of 11:12, 30 July 2014
STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 ANGSTROMS RESOLUTION: A MODEL FOR A CATALYTIC TRANSITION STATESTRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 ANGSTROMS RESOLUTION: A MODEL FOR A CATALYTIC TRANSITION STATE
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe structure of adenylate kinase from Escherichia coli ligated with the two-substrate-mimicking inhibitor P1,P5-bis(adenosine-5'-)pentaphosphate has been determined by X-ray diffraction and refined to a resolution of 1.9 A. The asymmetric unit of the crystals contains two copies of the complex, the structures of which agree well with each other. One of these copies is less well ordered in the crystals than the other, it shows generally higher temperature factors. The molecular packing in the crystals is discussed and correlated to crystal habit and anisotropic X-ray diffraction. The bound inhibitor simulates well the binding of substrates ATP and AMP, which are clearly assigned. The alpha-phosphate of AMP is well positioned for a nucleophilic attack on the gamma-phosphate of ATP. The observed structure readily allows the construction of a stabilized pentaco-ordinated transition state, as proposed for the known in-line mechanism of the enzyme, with nucleophile and leaving group in the apical positions of a trigonal bipyramid. The kinetic data of numerous mutations reported in the literature are correlated with the detailed structure of the enzyme. The mutants were classified. The concomitant increase of the Michaelis constants for ATP and AMP in the group of mutants that modify only the ATP-binding site cannot be explained. Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state.,Muller CW, Schulz GE J Mol Biol. 1992 Mar 5;224(1):159-77. PMID:1548697[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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