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PDBsum entry 1pym

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Phosphotransferase PDB id
1pym
Jmol
Contents
Protein chains
291 a.a. *
Ligands
OXL ×2
Metals
_MG ×2
Waters ×590
* Residue conservation analysis

References listed in PDB file
Key reference
Title Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound mg(2+)-Oxalate.
Authors K.Huang, Z.Li, Y.Jia, D.Dunaway-Mariano, O.Herzberg.
Ref. Structure, 1999, 7, 539-548. [DOI no: 10.1016/S0969-2126(99)80070-7]
PubMed id 10378273
Abstract
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.
Figure 4.
Figure 4. Cartoon representation of ligand binding to four α/β-barrel PEP/pyruvate-utilizing enzymes. The β/α motifs are numbered sequentially. For PEP mutase, helix 8 is colored yellow because it is contributed by a neighboring molecule. The loop connecting the β/α motif 3 in pyruvate kinase corresponds to a whole domain and is shown as a broken yellow line. Motifs 1 and 2 in enolase do not obey the classical topology of β/α motifs. Residues that interact with PEP/pyruvate/oxalate are colored red. Residues that interact with Mg^2+ are colored blue.
The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 539-548) copyright 1999.
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