PDBsum entry 1mrs

Transferase

PDB id: 1mrs

Contents

Protein chain

208 a.a. *

Ligands

SO4 ×2

5HU

Metals

_MG

Waters ×77

* Residue conservation analysis

PDB id:

1mrs

Name:

Transferase

Title:

Crystal structure of mycobacterium tuberculosis thymidylate kinase complexed with 5-ch2oh deoxyuridine monophosphate

Structure:

Thymidylate kinase. Chain: a. Synonym: dtmp kinase, thymidylic acid kinase, tmpk. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.228 R-free: 0.265

Authors:

A.Haouz,V.Vanheusden,H.Munier-Lehmann,M.Froeyen,P.Herdewijn,S.Van Calenbergh,M.Delarue

Key ref:

A.Haouz et al. (2003). Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism. J Biol Chem, 278, 4963-4971. PubMed id: 12454011 DOI: 10.1074/jbc.M209630200

Date:

18-Sep-02 Release date: 07-Jan-03

Protein chain

P9WKE1  (KTHY_MYCTU) -  Thymidylate kinase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 214 a.a.

Struc: 208 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.4.9 - dTMP kinase.
• Reaction: dTMP + ATP = dTDP + ADP

dTMP + ATP (Bound ligand (Het Group name = 5HU) matches with 95.45% similarity) = dTDP + ADP

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

reference

DOI no: 10.1074/jbc.M209630200

J Biol Chem 278:4963-4971 (2003)

PubMed id: 12454011

Enzymatic and structural analysis of inhibitors designed against Mycobacterium tuberculosis thymidylate kinase. New insights into the phosphoryl transfer mechanism.

A.Haouz, V.Vanheusden, H.Munier-Lehmann, M.Froeyen, P.Herdewijn, S.Van Calenbergh, M.Delarue.

ABSTRACT

The chemical synthesis of new compounds designed as inhibitors of Mycobacterium tuberculosis TMP kinase (TMPK) is reported. The synthesis concerns TMP analogues modified at the 5-position of the thymine ring as well as a novel compound with a six-membered sugar ring. The binding properties of the analogues are compared with the known inhibitor azido-TMP, which is postulated here to work by excluding the TMP-bound Mg(2+) ion. The crystallographic structure of the complex of one of the compounds, 5-CH(2)OH-dUMP, with TMPK has been determined at 2.0 A. It reveals a major conformation for the hydroxyl group in contact with a water molecule and a minor conformation pointing toward Ser(99). Looking for a role for Ser(99), we have identified an unusual catalytic triad, or a proton wire, made of strictly conserved residues (including Glu(6), Ser(99), Arg(95), and Asp(9)) that probably serves to protonate the transferred PO(3) group. The crystallographic structure of the commercially available bisubstrate analogue P(1)-(adenosine-5')-P(5)-(thymidine-5')-pentaphosphate bound to TMPK is also reported at 2.45 A and reveals an alternative binding pocket for the adenine moiety of the molecule compared with what is observed either in the Escherichia coli or in the yeast enzyme structures. This alternative binding pocket opens a way for the design of a new family of specific inhibitors.

Selected figure(s)

Figure 1.
Fig. 1. Chemical structure of synthesized TMP analogues.

Figure 3.
Fig. 3. Network of interactions of the analogue 1 in the active site of TMP kinase (drawn with Chemdraw).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 4963-4971) copyright 2003.

Figures were selected by an automated process.