PDBsum entry 2v8p

Transferase

PDB id: 2v8p

Contents

Protein chains

270 a.a. *

Ligands

CDP ×2

ADP ×2

SO4 ×4

Metals

_CL ×2

Waters ×494

* Residue conservation analysis

PDB id:

2v8p

Name:

Transferase

Title:

Ispe in complex with adp and cdp

Structure:

4-diphosphocytidyl-2-c-methyl-d-erythritol kinase. Chain: a, b. Synonym: cmk, 4-(cytidine-5'-diphospho)-2-c-methyl-d-erythritol kinase. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

2.10Å R-factor: 0.211 R-free: 0.252

Authors:

T.Sgraja,M.S.Alphey,W.N.Hunter

Key ref:

T.Sgraja et al. (2008). Characterization of Aquifex aeolicus 4-diphosphocytidyl-2C-methyl-d-erythritol kinase - ligand recognition in a template for antimicrobial drug discovery. Febs J, 275, 2779-2794. PubMed id: 18422643

Date:

13-Aug-07 Release date: 21-Aug-07

Supersedes:

2v2y

Protein chains

O67060  (ISPE_AQUAE) -  4-diphosphocytidyl-2-C-methyl-D-erythritol kinase from Aquifex aeolicus (strain VF5)

Seq: 268 a.a.

Struc: 270 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.1.148 - 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase.
• Reaction: 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H⁺

4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + H(+)

• Cofactor: Mn(2+) or Mg(2+)

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

Added reference

Febs J 275:2779-2794 (2008)

PubMed id: 18422643

Characterization of Aquifex aeolicus 4-diphosphocytidyl-2C-methyl-d-erythritol kinase - ligand recognition in a template for antimicrobial drug discovery.

T.Sgraja, M.S.Alphey, S.Ghilagaber, R.Marquez, M.N.Robertson, J.L.Hemmings, S.Lauw, F.Rohdich, A.Bacher, W.Eisenreich, V.Illarionova, W.N.Hunter.

ABSTRACT

4-Diphosphocytidyl-2C-methyl-D-erythritol kinase (IspE) catalyses the ATP-dependent conversion of 4-diphosphocytidyl-2C-methyl-D-erythritol (CDPME) to 4-diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate with the release of ADP. This reaction occurs in the non-mevalonate pathway of isoprenoid precursor biosynthesis and because it is essential in important microbial pathogens and absent from mammals it represents a potential target for anti-infective drugs. We set out to characterize the biochemical properties, determinants of molecular recognition and reactivity of IspE and report the cloning and purification of recombinant Aquifex aeolicus IspE (AaIspE), kinetic data, metal ion, temperature and pH dependence, crystallization and structure determination of the enzyme in complex with CDP, CDPME and ADP. In addition, 4-fluoro-3,5-dihydroxy-4-methylpent-1-enylphosphonic acid (compound 1) was designed to mimic a fragment of the substrate, a synthetic route to 1 was elucidated and the complex structure determined. Surprisingly, this ligand occupies the binding site for the ATP alpha-phosphate not the binding site for the methyl-D-erythritol moiety of CDPME. Gel filtration and analytical ultracentrifugation indicate that AaIspE is a monomer in solution. The enzyme displays the characteristic alpha/beta galacto-homoserine-mevalonate-phosphomevalonate kinase fold, with the catalytic centre positioned in a deep cleft between the ATP- and CDPME-binding domains. Comparisons indicate a high degree of sequence conservation on the IspE active site across bacterial species, similarities in structure, specificity of substrate recognition and mechanism. The biochemical characterization, attainment of well-ordered and reproducible crystals and the models resulting from the analyses provide reagents and templates to support the structure-based design of broad-spectrum antimicrobial agents.