1pym
From Proteopedia
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|PDB= 1pym |SIZE=350|CAPTION= <scene name='initialview01'>1pym</scene>, resolution 1.8Å | |PDB= 1pym |SIZE=350|CAPTION= <scene name='initialview01'>1pym</scene>, resolution 1.8Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Phosphoenolpyruvate_mutase Phosphoenolpyruvate mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.9 5.4.2.9] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoenolpyruvate_mutase Phosphoenolpyruvate mutase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.4.2.9 5.4.2.9] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pym OCA], [http://www.ebi.ac.uk/pdbsum/1pym PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pym RCSB]</span> | ||
}} | }} | ||
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[[Category: Huang, K.]] | [[Category: Huang, K.]] | ||
[[Category: Li, Z.]] | [[Category: Li, Z.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: OXL]] | ||
[[Category: p-c bond formation]] | [[Category: p-c bond formation]] | ||
[[Category: phosphomutase]] | [[Category: phosphomutase]] | ||
[[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 Sun Mar 30 23:06:22 2008'' |
Revision as of 20:06, 30 March 2008
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| , resolution 1.8Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Phosphoenolpyruvate mutase, with EC number 5.4.2.9 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
PHOSPHOENOLPYRUVATE MUTASE FROM MOLLUSK IN WITH BOUND MG2-OXALATE
Overview
BACKGROUND: Phosphonate compounds are important secondary metabolites in nature and, when linked to macromolecules in eukaryotes, they might play a role in cell signaling. The first obligatory step in the biosynthesis of phosphonates is the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-pyr), a reaction that is catalyzed by PEP mutase. The PEP mutase functions as a tetramer and requires magnesium ions (Mg2+). RESULTS: The crystal structure of PEP mutase from the mollusk Mytilus edulis, bound to the inhibitor Mg(2+)-oxalate, has been determined using multiwavelength anomalous diffraction, exploiting the selenium absorption edge of a selenomethionine-containing protein. The structure has been refined at 1.8 A resolution. PEP mutase adopts a modified alpha/beta barrel fold, in which the eighth alpha helix projects away from the alpha/beta barrel instead of packing against the beta sheet. A tightly associated dimer is formed, such that the two eighth helices are swapped, each packing against the beta sheet of the neighboring molecule. A dimer of dimers further associates into a tetramer. Mg(2+)-oxalate is buried close to the center of the barrel, at the C-terminal ends of the beta strands. CONCLUSIONS: The tetramer observed in the crystal is likely to be physiologically relevant. Because the Mg(2+)-oxalate is inaccessible to solvent, substrate binding and dissociation might be accompanied by conformational changes. A mechanism involving a phosphoenzyme intermediate is proposed, with Asp58 acting as the nucleophilic entity that accepts and delivers the phosphoryl group. The active-site architecture and the chemistry performed by PEP mutase are different from other alpha/beta-barrel proteins that bind pyruvate or PEP, thus the enzyme might represent a new family of alpha/beta-barrel proteins.
About this Structure
1PYM is a Single protein structure of sequence from Mytilus edulis. Full crystallographic information is available from OCA.
Reference
Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate., Huang K, Li Z, Jia Y, Dunaway-Mariano D, Herzberg O, Structure. 1999 May;7(5):539-48. PMID:10378273
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