2V8P

IspE in complex with ADP and CDP

PDB DOI: https://doi.org/10.2210/pdb2V8P/pdb
Entry: 2V8P supersedes: 2V2Y

Classification: TRANSFERASE
Organism(s): Aquifex aeolicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-08-13 Released: 2007-08-21
Deposition Author(s): Sgraja, T., Alphey, M.S., Hunter, W.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.252
R-Value Work: 0.208
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Characterization of Aquifex Aeolicus 4-Diphosphocytidyl-2C-Methyl-D-Erythritol Kinase -Ligand Recognition in a Template for Antimicrobial Drug Discovery.

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

(2008) FEBS J 275: 2779

PubMed: 18422643 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1111/j.1742-4658.2008.06418.x
Primary Citation of Related Structures:
2V2Z, 2V34, 2V8P

PubMed 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.

Organizational Affiliation

Division of Biological Chemistry and Drug Discovery, University of Dundee, UK.

Macromolecule Content

Total Structure Weight: 62.32 kDa
Atom Count: 5,144
Modelled Residue Count: 540
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL KINASE	A, B	271	Aquifex aeolicus	Mutation(s): 0 EC: 2.7.1.148
UniProt
Find proteins for O67060 (Aquifex aeolicus (strain VF5)) Explore O67060 Go to UniProtKB: O67060
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O67060
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B]	D [auth A], I [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
CDP Query on CDP Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A]	C [auth A], H [auth B]	CYTIDINE-5'-DIPHOSPHATE C₉ H₁₅ N₃ O₁₁ P₂ ZWIADYZPOWUWEW-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B]	E [auth A], F [auth A], J [auth B], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B]	G [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]