PDBsum entry 1pym

Phosphotransferase

PDB id: 1pym

Contents

Protein chains

291 a.a. *

Ligands

OXL ×2

Metals

_MG ×2

Waters ×590

* Residue conservation analysis

PDB id:

1pym

Name:

Phosphotransferase

Title:

Phosphoenolpyruvate mutase from mollusk in with bound mg2-oxalate

Structure:

Protein (phosphoenolpyruvate mutase). Chain: a, b. Synonym: phosphoenolpyruvate phosphomutase. Engineered: yes. Other_details: with bound mg2+-oxalate inhibitor

Source:

Mytilus edulis. Organism_taxid: 6550. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.80Å R-factor: 0.188 R-free: 0.256

Authors:

K.Huang,Z.Li,O.Herzberg

Key ref:

K.Huang et al. (1999). Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate. Structure, 7, 539-548. PubMed id: 10378273 DOI: 10.1016/S0969-2126(99)80070-7

Date:

25-Feb-99 Release date: 21-Jul-99

Protein chains

P56839  (PEPM_MYTED) -  Phosphoenolpyruvate phosphomutase from Mytilus edulis

Seq: 295 a.a.

Struc: 291 a.a.

Enzyme reactions

• Enzyme class: E.C.5.4.2.9 - phosphoenolpyruvate mutase.
• Pathway: Phosphoenolpyruvate Mutase
• Reaction: phosphoenolpyruvate + H⁺ = 3-phosphonopyruvate

phosphoenolpyruvate + H(+) (Bound ligand (Het Group name = OXL) matches with 45.45% similarity) = 3-phosphonopyruvate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/S0969-2126(99)80070-7

Structure 7:539-548 (1999)

PubMed id: 10378273

Helix swapping between two alpha/beta barrels: crystal structure of phosphoenolpyruvate mutase with bound Mg(2+)-oxalate.

K.Huang, Z.Li, Y.Jia, D.Dunaway-Mariano, O.Herzberg.

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.

Selected figure(s)

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.

Figure was selected by an automated process.