2bef: Difference between revisions
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|PDB= 2bef |SIZE=350|CAPTION= <scene name='initialview01'>2bef</scene>, resolution 2.3Å | |PDB= 2bef |SIZE=350|CAPTION= <scene name='initialview01'>2bef</scene>, resolution 2.3Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> | ||
|ACTIVITY= [http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bef OCA], [http://www.ebi.ac.uk/pdbsum/2bef PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2bef RCSB]</span> | |||
}} | }} | ||
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[[Category: Cherfils, J.]] | [[Category: Cherfils, J.]] | ||
[[Category: Xu, Y W.]] | [[Category: Xu, Y W.]] | ||
[[Category: beryllium fluoride]] | [[Category: beryllium fluoride]] | ||
[[Category: nucleoside diphosphate kinase]] | [[Category: nucleoside diphosphate kinase]] | ||
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[[Category: phosphotransferase]] | [[Category: phosphotransferase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:05:12 2008'' | ||
Revision as of 02:05, 31 March 2008
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| , resolution 2.3Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Nucleoside-diphosphate kinase, with EC number 2.7.4.6 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF NDP KINASE COMPLEXED WITH MG, ADP, AND BEF3
OverviewOverview
Nucleoside diphosphate kinase reversibly transfers the gamma-phosphate of ATP onto its active site histidine. We have investigated the transition state of histidine phosphorylation with the high-resolution crystal structures of the enzyme from Dictyostelium discoideum with MgADP and either aluminium or beryllium fluoride. The bound aluminium fluoride species is the neutral species AlF3 and not the more common AlF4-. AlF3 forms a trigonal bipyramid that makes it an accurate analog of the transition state of the gamma-phosphate of ATP undergoing transfer to the catalytic histidine. Its axial ligands are a histidine nitrogen and a beta-phosphate oxygen. Beryllium fluoride also binds at the same position and with the same ligands but in a tetrahedral geometry resembling the Michaelis complex rather than the transition state. The two x-ray structures show explicit enzyme-substrate interactions that discriminate between the ground and the transition states of the reaction. They also illustrate the partially dissociative geometry of the transition state of phosphoryl transfer and demonstrate the potential applications of metallofluorides for the study of kinase mechanisms.
About this StructureAbout this Structure
2BEF is a Single protein structure of sequence from Dictyostelium discoideum. Full crystallographic information is available from OCA.
ReferenceReference
AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP., Xu YW, Morera S, Janin J, Cherfils J, Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3579-83. PMID:9108019
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