PDBsum entry 6b5e

Transferase

PDB id: 6b5e

Contents

Protein chains

(+ 2 more) 283 a.a.

Ligands

DAU ×10

TYD ×6

EDO

Metals

_NA ×2

_MG ×9

_CL

Waters ×1477

PDB id:

6b5e

Name:

Transferase

Title:

Mycobacterium tuberculosis rmla in complex with dtdp-glucose

Structure:

Glucose-1-phosphate thymidylyltransferase. Chain: a, b, c, d, e, f, g, h. Synonym: dtdp-glucose pyrophosphorylase,dtdp-glucose synthase. Engineered: yes

Source:

Mycobacterium tuberculosis (strain atcc 25618 / h37rv). Organism_taxid: 83332. Strain: atcc 25618 / h37rv. Gene: rmla, rfba, rv0334. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

1.85Å R-factor: 0.174 R-free: 0.218

Authors:

H.A.Brown,H.M.Holden

Key ref:

H.A.Brown et al. (2018). The structure of glucose-1-phosphate thymidylyltransferase from Mycobacterium tuberculosis reveals the location of an essential magnesium ion in the RmlA-type enzymes. Protein Sci, 27, 441-450. PubMed id: 29076563

Date:

29-Sep-17 Release date: 21-Feb-18

Protein chains

P9WH13  (RMLA_MYCTU) -  Glucose-1-phosphate thymidylyltransferase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

Seq: 288 a.a.

Struc: 283 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 + alpha-D-glucose 1-phosphate + H(+) = dTDP-alpha-D-glucose + diphosphate (Bound ligand (Het Group name = DAU) corresponds exactly)

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

reference

Protein Sci 27:441-450 (2018)

PubMed id: 29076563

The structure of glucose-1-phosphate thymidylyltransferase from Mycobacterium tuberculosis reveals the location of an essential magnesium ion in the RmlA-type enzymes.

H.A.Brown, J.B.Thoden, P.A.Tipton, H.M.Holden.

ABSTRACT

Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, continues to be a major threat to populations worldwide. Whereas the disease is treatable, the drug regimen is arduous at best with the use of four antimicrobials over a six-month period. There is clearly a pressing need for the development of new therapeutics. One potential target for structure-based drug design is the enzyme RmlA, a glucose-1-phosphate thymidylyltransferase. This enzyme catalyzes the first step in the biosynthesis of l-rhamnose, which is a deoxysugar critical for the integrity of the bacterium's cell wall. Here, we report the X-ray structures of M. tuberculosis RmlA in complex with either dTTP or dTDP-glucose to 1.6 Å and 1.85 Å resolution, respectively. In the RmlA/dTTP complex, two magnesium ions were observed binding to the nucleotide, both ligated in octahedral coordination spheres. In the RmlA/dTDP-glucose complex, only a single magnesium ion was observed. Importantly, for RmlA-type enzymes with known three-dimensional structures, not one model shows the position of the magnesium ion bound to the nucleotide-linked sugar. As such, this investigation represents the first direct observation of the manner in which a magnesium ion is coordinated to the RmlA product and thus has important ramifications for structure-based drug design. In the past, molecular modeling procedures have been employed to derive a three-dimensional model of the M. tuberculosis RmlA for drug design. The X-ray structures presented herein provide a superior molecular scaffold for such endeavors in the treatment of one of the world's deadliest diseases.