PDBsum entry: 1mc3

Transferase

PDB id: 1mc3

Contents

Protein chains

291 a.a. *

Ligands

TTP ×2

Metals

_MG ×2

Waters ×165

* Residue conservation analysis

PDB id:

1mc3

Name:

Transferase

Title:

Crystal structure of rffh

Structure:

Glucose-1-phosphate thymidylyltransferase. Chain: a, b. Synonym: rffh, dtdp-glucose synthase, dtdp-glucose pyrophosphorylase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.60Å R-factor: 0.223 R-free: 0.280

Authors:

J.Sivaraman,V.Sauve,A.Matte,M.Cygler,Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)

Key ref:

J.Sivaraman et al. (2002). Crystal structure of Escherichia coli glucose-1-phosphate thymidylyltransferase (RffH) complexed with dTTP and Mg2+. J Biol Chem, 277, 44214-44219. PubMed id: 12171937 DOI: 10.1074/jbc.M206932200

Date:

05-Aug-02 Release date: 20-Nov-02

Protein chains

P61887  (RMLA2_ECOLI) -  Glucose-1-phosphate thymidylyltransferase 2

Seq: 293 a.a.

Struc: 291 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 = diphosphate + dTDP-glucose

dTTP (Bound ligand (Het Group name = TTP) corresponds exactly) + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose

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

 Gene Ontology (GO) functional annotation 

• Biological process: biosynthetic process (3 terms)
• Biochemical function: protein binding (6 terms)

reference

DOI no: 10.1074/jbc.M206932200

J Biol Chem 277:44214-44219 (2002)

PubMed id: 12171937

Crystal structure of Escherichia coli glucose-1-phosphate thymidylyltransferase (RffH) complexed with dTTP and Mg2+.

J.Sivaraman, V.Sauvé, A.Matte, M.Cygler.

ABSTRACT

The enzyme glucose-1-phosphate thymidylyltransferase (RffH), the product of the rffh gene, catalyzes one of the steps in the synthesis of enterobacterial common antigen (ECA), a cell surface glycolipid found in Gram-negative enteric bacteria. In Escherichia coli two gene products, RffH and RmlA, catalyze the same enzymatic reaction and are homologous in sequence; however, they are part of different operons and function in different pathways. We report the crystal structure of RffH bound to deoxythymidine triphosphate (dTTP), the phosphate donor, and Mg(2+), refined at 2.6 A to an R-factor of 22.3% (R(free) = 28.4%). The crystal structure of RffH shows a tetrameric enzyme best described as a dimer of dimers. Each monomer has an overall alpha/beta fold and consists of two domains, a larger nucleotide binding domain (residues 1-115, 222-291) and a smaller sugar-binding domain (116-221), with the active site located at the domain interface. The Mg(2+) ion is coordinated by two conserved aspartates and the alpha-phosphate of deoxythymidine triphosphate. Its location corresponds well to that in a structurally similar domain of N-acetylglucosamine-1-phosphate uridylyltransferase (GlmU). Analysis of the RffH, RmlA, and GlmU complexes with substrates and products provides an explanation for their different affinities for Mg(2+) and leads to a proposal for the dynamics along the reaction pathway.

Selected figure(s)

Figure 2.
Fig. 2. Stereo view of the tetramer organization of RffH (monomer A, cyan, monomer B, blue; monomers A' and B', green) and its comparison with the tetramer of RmlA from P. aeroginosa (red). The superposition is based on AB dimers and shows a difference in disposition of A' and B' dimers.

Figure 3.
Fig. 3. Stereo view of the dTTP bound to RffH. The hydrogen bonds are shown as red lines. Coordination bonds to the Mg2+ ion are shown in black lines. The electron density at the 3.0 level of the simulated annealing F[o] F[c] omit map, with residues within 3 Å of the dTTP and Mg2+ removed from calculations, is shown in blue lines. Figure was created with Bobscript (26).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 44214-44219) copyright 2002.

Figures were selected by an automated process.