1k3d
From Proteopedia
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|PDB= 1k3d |SIZE=350|CAPTION= <scene name='initialview01'>1k3d</scene>, resolution 2.0Å | |PDB= 1k3d |SIZE=350|CAPTION= <scene name='initialview01'>1k3d</scene>, resolution 2.0Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=AF3:ALUMINUM+FLUORIDE'>AF3</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(ATP) Phosphoenolpyruvate carboxykinase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.49 4.1.1.49] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(ATP) Phosphoenolpyruvate carboxykinase (ATP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.49 4.1.1.49] </span> |
|GENE= PCKA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= PCKA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1k3c|1K3C]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k3d OCA], [http://www.ebi.ac.uk/pdbsum/1k3d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1k3d RCSB]</span> | ||
}} | }} | ||
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[[Category: Prasad, L.]] | [[Category: Prasad, L.]] | ||
[[Category: Sudom, A M.]] | [[Category: Sudom, A M.]] | ||
| - | [[Category: ADP]] | ||
| - | [[Category: AF3]] | ||
| - | [[Category: MG]] | ||
[[Category: gluconeogenesis]] | [[Category: gluconeogenesis]] | ||
[[Category: kinase]] | [[Category: kinase]] | ||
[[Category: nucleotide-triphosphate hydrolase.]] | [[Category: nucleotide-triphosphate hydrolase.]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:42:48 2008'' |
Revision as of 18:42, 30 March 2008
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| , resolution 2.0Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | PCKA (Escherichia coli) | ||||||
| Activity: | Phosphoenolpyruvate carboxykinase (ATP), with EC number 4.1.1.49 | ||||||
| Related: | 1K3C
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Phosphoenolpyruvate carboxykinase in complex with ADP and AlF3
Overview
The mechanism of reversible transfer of the gamma-phosphate group of ATP by Escherichia coli phosphoenolpyruvate carboxykinase (PCK) on to its substrate is of great interest. It is known that metallofluorides are accurate analogs of the transition state in the context of kinase mechanisms. Therefore, two complexes of PCK, one with AlF(3), Mg(2+) and ADP (complex I), the other with AlF(3), Mg(2+), ADP and pyruvate (complex II) were crystallized. The X-ray crystal structures of these two complexes were determined at 2.0 A resolution. The Al atom has trigonal bipyramidal geometry that mimics the transition state of phosphoryl transfer. The Al atom is at a distance of 2.8 A and 2.9 A from an oxygen atom of the beta-phosphoryl group of ADP in complex I and II, respectively. A water molecule in complex I and an oxygen atom of the pyruvate in complex II are located along the axis of the trigonal bipyramid on the side opposite to the beta-phosphoryl oxygen with respect to the equatorial plane, suggesting that the complexes are close mimics of the transition state. Along with the presence of positively charged species around the AlF(3) moiety, these results indicate that phosphoryl transfer occurs via a direct displacement mechanism with associative qualities.
About this Structure
1K3D is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
The phosphoryl-transfer mechanism of Escherichia coli phosphoenolpyruvate carboxykinase from the use of AlF(3)., Sudom AM, Prasad L, Goldie H, Delbaere LT, J Mol Biol. 2001 Nov 16;314(1):83-92. PMID:11724534
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