The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.148 

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Toward a structural understanding of the dehydratase mechanism.

Allard, S.T.Beis, K.Giraud, M.F.Hegeman, A.D.Gross, J.W.Wilmouth, R.C.Whitfield, C.Graninger, M.Messner, P.Allen, A.G.Maskell, D.J.Naismith, J.H.

(2002) Structure 10: 81-92

  • DOI: https://doi.org/10.1016/s0969-2126(01)00694-3
  • Primary Citation of Related Structures:  
    1KEP, 1KER, 1KET, 1KEU, 1KEW

  • PubMed Abstract: 

    dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5'-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5'-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5'-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 A and 2.4 A. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
dTDP-D-glucose 4,6-dehydratase
A, B
348Streptococcus suisMutation(s): 0 
Gene Names: rmlB
Find proteins for Q8GIP9 (Streptococcus suis)
Explore Q8GIP9 
Go to UniProtKB:  Q8GIP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GIP9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.449α = 90
b = 97.182β = 90
c = 185.471γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-01-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-02-01
    Changes: Structure summary
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description