PDBsum entry 1g0r

Transferase

PDB id: 1g0r

Contents

Protein chains

(+ 2 more) 292 a.a. *

Ligands

G1P ×7

SO4 ×23

THM ×16

Waters ×2236

* Residue conservation analysis

PDB id:

1g0r

Name:

Transferase

Title:

The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (rmla). Thymidine/glucose- 1-phosphate complex.

Structure:

Glucose-1-phosphate thymidylyltransferase. Chain: a, b, c, d, e, f, g, h. Synonym: glucose-1-phosphate thymidylyltransferase (rmla). Engineered: yes

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.87Å R-factor: 0.151 R-free: 0.221

Authors:

W.Blankenfeldt,M.Asuncion,J.S.Lam,J.H.Naismith

Key ref:

W.Blankenfeldt et al. (2000). The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA). EMBO J, 19, 6652-6663. PubMed id: 11118200 DOI: 10.1093/emboj/19.24.6652

Date:

07-Oct-00 Release date: 27-Dec-00

Protein chains

Q9HU22  (Q9HU22_PSEAE) -  Glucose-1-phosphate thymidylyltransferase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 293 a.a.

Struc: 292 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.7.24 - glucose-1-phosphate thymidylyltransferase.
• Pathway: 6-Deoxyhexose Biosynthesis
• Reaction: dTTP + alpha-D-glucose 1-phosphate + H⁺ = dTDP-alpha-D-glucose + diphosphate

dTTP (Bound ligand (Het Group name = G1P) corresponds exactly) + alpha-D-glucose 1-phosphate (Bound ligand (Het Group name = THM) matches with 58.62% similarity) + H(+) = dTDP-alpha-D-glucose + diphosphate

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

reference

DOI no: 10.1093/emboj/19.24.6652

EMBO J 19:6652-6663 (2000)

PubMed id: 11118200

The structural basis of the catalytic mechanism and regulation of glucose-1-phosphate thymidylyltransferase (RmlA).

W.Blankenfeldt, M.Asuncion, J.S.Lam, J.H.Naismith.

ABSTRACT

The synthesis of deoxy-thymidine di-phosphate (dTDP)-L-rhamnose, an important component of the cell wall of many microorganisms, is a target for therapeutic intervention. The first enzyme in the dTDP-L-rhamnose biosynthetic pathway is glucose-1-phosphate thymidylyltransferase (RmlA). RmlA is inhibited by dTDP-L-rhamnose thereby regulating L-rhamnose production in bacteria. The structure of Pseudomonas aeruginosa RmlA has been solved to 1.66 A resolution. RmlA is a homotetramer, with the monomer consisting of three functional subdomains. The sugar binding and dimerization subdomains are unique to RmlA-like enzymes. The sequence of the core subdomain is found not only in sugar nucleotidyltransferases but also in other nucleotidyltransferases. The structures of five distinct enzyme substrate- product complexes reveal the enzyme mechanism that involves precise positioning of the nucleophile and activation of the electrophile. All the key residues are within the core subdomain, suggesting that the basic mechanism is found in many nucleotidyltransferases. The dTDP-L-rhamnose complex identifies how the protein is controlled by its natural inhibitor. This work provides a platform for the design of novel drugs against pathogenic bacteria.

Selected figure(s)

Figure 1.
Figure 1 (A) The mechanism of the reaction catalysed by RmlA. (B) The distinct chemical groups that form the ternary complex with the protein.

Figure 2.
Figure 2 (A) Stereo ribbon diagram of the RmlA monomer with location of secondary structure elements. The different colours denote the three subdomains. Yellow is the core binding subdomain, light blue is the sugar-binding subdomain and magenta the dimerization subdomain. The character represents a 3[10] helix, and and have their normal meaning. Secondary structure was assigned with DSSP (Kabsch and Sander, 1983). (B) A ribbon representation of the RmlA tetramer. The monomers are coloured red, monomer A; blue, monomer B; yellow, monomer A'; and light blue, monomer B'. G-1-P (black) and dTTP (green) are shown at the active sites in ball-and-stick format. dTDP–L-rhamnose (magenta) is shown in the secondary binding sites, again as a ball-and-stick diagram. (C) Same as (B), rotated by 90° around the y-axis. All molecular representations are prepared with BOBSCRIPT (Esnouf, 1997) through the GL_RENDER interface (L.Esser and J.Deisenhofer, unpublished data) and were rendered with POV-Ray™.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 6652-6663) copyright 2000.

Figures were selected by an automated process.