1N2S

CRYSTAL STRUCTURE OF DTDP-6-DEOXY-L-LYXO-4-HEXULOSE REDUCTASE (RMLD) IN COMPLEX WITH NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Variation on a Theme of SDR. dTDP-6-Deoxy-L- lyxo-4-Hexulose Reductase (RmlD) Shows a New Mg(2+)-Dependent Dimerization Mode

Blankenfeldt, W.Kerr, I.D.Giraud, M.F.McMiken, H.J.Leonard, G.A.Whitfield, C.Messner, P.Graninger, M.Naismith, J.H.

(2002) Structure 10: 773-786

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) catalyzes the final step in the conversion of dTDP-D-glucose to dTDP-L-rhamnose in an NAD(P)H- and Mg2+-dependent reaction. L-rhamnose biosynthesis is an antibacterial target. The structure of RmlD from ...

    dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) catalyzes the final step in the conversion of dTDP-D-glucose to dTDP-L-rhamnose in an NAD(P)H- and Mg2+-dependent reaction. L-rhamnose biosynthesis is an antibacterial target. The structure of RmlD from Salmonella enterica serovar Typhimurium has been determined, and complexes with NADH, NADPH, and dTDP-L-rhamnose are reported. RmlD differs from other short chain dehydrogenases in that it has a novel dimer interface that contains Mg2+. Enzyme catalysis involves hydride transfer from the nicotinamide ring of the cofactor to the C4'-carbonyl group of the substrate. The substrate is activated through protonation by a conserved tyrosine. NAD(P)H is bound in a solvent-exposed cleft, allowing facile replacement. We suggest a novel role for the conserved serine/threonine residue of the catalytic triad of SDR enzymes.


    Related Citations: 
    • The rhamnose pathway
      Giraud, M.F.,Naismith, J.H.
      (2000) Curr.Opin.Struct.Biol. 10: 687
    • Overexpression, purification, crystallisation and preliminary structural study of dTDP-6-deoxy-lyxo-4-reductase (RmlD) the fourth enzyme of the dTDP-rhanose synthesis pathway,from Salmonella entrica serovar Typhimurim
      Giraud, M.F.,McMiken, H.J.,Leonard, G.A.,Messner, P.,Whitfield, C.,Naismith, J.H.
      (1999) Acta Crystallogr.,Sect.D 55: 2043


    Organizational Affiliation

    The Centre for Biomolecular Sciences, The University, St. Andrews, KY16 9ST, Scotland, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
dTDP-glucose oxidoreductase
A
299Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: rfbD (rmlD)
EC: 1.1.1.133
Find proteins for P26392 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P26392
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.435α = 90.00
b = 71.572β = 90.00
c = 82.281γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CCP4data scaling
SOLVEphasing
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-01
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-11-06
    Type: Non-polymer description