1G1A

THE CRYSTAL STRUCTURE OF DTDP-D-GLUCOSE 4,6-DEHYDRATASE (RMLB)FROM SALMONELLA ENTERICA SEROVAR TYPHIMURIUM

PDB DOI: 10.2210/pdb1G1A/pdb

Classification: LYASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-10-11 Released: 2001-03-21
Deposition Author(s): Allard, S.T.M., Giraud, M.-F., Whitfield, C., Graninger, M., Messner, P., Naismith, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.249
R-Value Work: 0.202
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of dTDP-D-Glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium, the second enzyme in the dTDP-l-rhamnose pathway.

Allard, S.T., Giraud, M.F., Whitfield, C., Graninger, M., Messner, P., Naismith, J.H.

(2001) J Mol Biol 307: 283-295

PubMed: 11243820 Search on PubMed
DOI: 10.1006/jmbi.2000.4470
Primary Citation of Related Structures:
1G1A

PubMed Abstract:

l-Rhamnose is a 6-deoxyhexose that is found in a variety of different glycoconjugates in the cell walls of pathogenic bacteria. The precursor of l-rhamnose is dTDP-l-rhamnose, which is synthesised from glucose- 1-phosphate and deoxythymidine triphosphate (dTTP) via a pathway requiring four enzymes. Significantly this pathway does not exist in humans and all four enzymes therefore represent potential therapeutic targets. dTDP-D-glucose 4,6-dehydratase (RmlB; EC 4.2.1.46) is the second enzyme in the dTDP-L-rhamnose biosynthetic pathway. The structure of Salmonella enterica serovar Typhimurium RmlB had been determined to 2.47 A resolution with its cofactor NAD(+) bound. The structure has been refined to a crystallographic R-factor of 20.4 % and an R-free value of 24.9 % with good stereochemistry.RmlB functions as a homodimer with monomer association occurring principally through hydrophobic interactions via a four-helix bundle. Each monomer exhibits an alpha/beta structure that can be divided into two domains. The larger N-terminal domain binds the nucleotide cofactor NAD(+) and consists of a seven-stranded beta-sheet surrounded by alpha-helices. The smaller C-terminal domain is responsible for binding the sugar substrate dTDP-d-glucose and contains four beta-strands and six alpha-helices. The two domains meet to form a cavity in the enzyme. The highly conserved active site Tyr(167)XXXLys(171) catalytic couple and the GlyXGlyXXGly motif at the N terminus characterise RmlB as a member of the short-chain dehydrogenase/reductase extended family. The quaternary structure of RmlB and its similarity to a number of other closely related short-chain dehydrogenase/reductase enzymes have enabled us to propose a mechanism of catalysis for this important enzyme.

Related Citations:

The purifiaction, crystallisation and structural elucidation of dTDP-D-glucose 4,6-dehydratase (RmlB), the second enzyme of the dTDP-L-rhamnose synthesis pathway from Salmonella enterica serovar Typhimurium.
Allard, S.T.M., Giraud, M.-F., Whitfield, C., Messner, P., Naismith, J.H.
(2000) Acta Crystallogr D Biol Crystallogr 56: 222

Organizational Affiliation:

Centre for Biomolecular Sciences, The University, North Haugh, St Andrews Fife, KY16 9ST, Scotland.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DTDP-D-GLUCOSE 4,6-DEHYDRATASE	A, B, C, D	361	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0 Gene Names: rmlB EC: 4.2.1.46
UniProt
Find proteins for Q9EU31 (Salmonella enterica) Explore Q9EU31 Go to UniProtKB: Q9EU31
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9EU31
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D]	G [auth A], K [auth B], N [auth C], Q [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain J [auth B]	E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction