1N2S | pdb_00001n2s

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.253 (Depositor), 0.338 (DCC) 
  • R-Value Work: 
    0.199 (Depositor) 
  • R-Value Observed: 
    0.202 (Depositor) 

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This is version 1.4 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

  • DOI: https://doi.org/10.1016/s0969-2126(02)00770-0
  • Primary Citation Related Structures: 
    1KBZ, 1KC1, 1KC3, 1N2S

  • 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 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.

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

Macromolecule Content 

  • Total Structure Weight: 33.4 kDa 
  • Atom Count: 2,503 
  • Modeled Residue Count: 298 
  • Deposited Residue Count: 299 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
dTDP-glucose oxidoreductase299Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: RFBA
EC: 1.1.1.133
UniProt
Find proteins for P26392 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P26392 
Go to UniProtKB:  P26392
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26392
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.253 (Depositor), 0.338 (DCC) 
  • R-Value Work:  0.199 (Depositor) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.435α = 90
b = 71.572β = 90
c = 82.281γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-01
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-11-06
    Changes: Non-polymer description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations