PDBsum entry 3d40

Transferase

PDB id: 3d40

Contents

Protein chain

252 a.a. *

Ligands

DPO

Waters ×231

* Residue conservation analysis

PDB id:

3d40

Name:

Transferase

Title:

Crystal structure of fosfomycin resistance kinase foma from streptomyces wedmorensis complexed with diphosphate

Structure:

Foma protein. Chain: a. Engineered: yes

Source:

Streptomyces wedmorensis. Gene: foma. Expressed in: escherichia coli.

Resolution:

1.53Å R-factor: 0.169 R-free: 0.198

Authors:

S.Pakhomova,S.G.Bartlett,A.Augustus,T.Kuzuyama,M.E.Newcomer

Key ref:

S.Pakhomova et al. (2008). Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis. J Biol Chem, 283, 28518-28526. PubMed id: 18701452 DOI: 10.1074/jbc.M803709200

Date:

13-May-08 Release date: 12-Aug-08

Protein chain

Q56187  (Q56187_STRWE) -  Isopentenyl phosphate kinase from Streptomyces wedmorensis

Seq: 266 a.a.

Struc: 252 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.7.4.26 - isopentenyl phosphate kinase.
• Reaction: isopentenyl phosphate + ATP = isopentenyl diphosphate + ADP

isopentenyl phosphate + ATP = isopentenyl diphosphate + ADP (Bound ligand (Het Group name = DPO) matches with 64.29% similarity)

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

reference

DOI no: 10.1074/jbc.M803709200

J Biol Chem 283:28518-28526 (2008)

PubMed id: 18701452

Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis.

S.Pakhomova, S.G.Bartlett, A.Augustus, T.Kuzuyama, M.E.Newcomer.

ABSTRACT

The fosfomycin resistance protein FomA inactivates fosfomycin by phosphorylation of the phosphonate group of the antibiotic in the presence of ATP and Mg(II). We report the crystal structure of FomA from the fosfomycin biosynthetic gene cluster of Streptomyces wedmorensis in complex with diphosphate and in ternary complex with the nonhydrolyzable ATP analog adenosine 5'-(beta,gamma-imido)-triphosphate (AMPPNP), Mg(II), and fosfomycin, at 1.53 and 2.2A resolution, respectively. The polypeptide exhibits an open alphabetaalpha sandwich fold characteristic for the amino acid kinase family of enzymes. The diphosphate complex shows significant disorder in loops surrounding the active site. As a result, the nucleotide-binding site is wide open. Binding of the substrates is followed by the partial closure of the active site and ordering of the alpha2-helix. Structural comparison with N-acetyl-l-glutamate kinase shows several similarities in the site of phosphoryl transfer: 1) preservation of architecture of the catalytical amino acids of N-acetyl-l-glutamate kinase (Lys(9), Lys(216), and Asp(150) in FomA); 2) good superposition of the phosphate acceptor groups of the substrates, and 3) good superposition of the diphosphate molecule with the beta- and gamma-phosphates of AMPPNP, suggesting that the reaction could proceed by an associative in-line mechanism. However, differences in conformations of the triphosphate moiety of AMPPNP molecules, the long distance (5.1A) between the phosphate acceptor and donor groups in FomA, and involvement of Lys(18) instead of Lys(9) in binding with the gamma-phosphate may indicate a different reaction mechanism. The present work identifies the active site residues of FomA responsible for substrate binding and specificity and proposes their roles in catalysis.

Selected figure(s)

Figure 2.
F[o] - F[c] electron density omit map contoured at 3 σ for DPO in the FomA·DPO complex (A) and MgAMPPNP and fosfomycin in the FomA·MgAMPPNP·fosfomycin complex (B). Mg^2+ cation is shown as a sphere.

Figure 5.
Stereo views of the active site. A, FomA·DPO complex. B, FomA·MgAMPPNP·fosfomycin complex. The ligand molecules are shown in ball-and-stick format. The Mg^2+ (green) and coordinated water molecules are represented as spheres. The interacting protein residues are shown in stick format. C, a stereo view of the superposition of the AMPPNP binding sites in FomA·MgAMPPNP·fosfomycin (blue) and NAGK·MgAMPPNP·NAD (red) structures. Mg^2+ cations are shown as spheres, and water molecules are shown as crosses.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 28518-28526) copyright 2008.

Figures were selected by an automated process.