2IXH

RmlC P aeruginosa with dTDP-rhamnose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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This is version 1.2 of the entry. See complete history. 


Literature

RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation.

Dong, C., Major, L.L., Srikannathasan, V., Errey, J.C., Giraud, M.F., Lam, J.S., Graninger, M., Messner, P., McNeil, M.R., Field, R.A., Whitfield, C., Naismith, J.H.

(2007) J Mol Biol 365: 146-159

  • DOI: 10.1016/j.jmb.2006.09.063
  • Primary Citation of Related Structures:  
    2IXC, 2IXH, 2IXI, 2IXJ, 2IXK, 2IXL

  • PubMed Abstract: 

    • The striking feature of carbohydrates is their constitutional, conformational and configurational diversity. Biology has harnessed this diversity and manipulates carbohydrate residues in a variety of ways, one of which is epimerization. RmlC catalyzes the epimerization of the C3' and C5' positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose ...

    The striking feature of carbohydrates is their constitutional, conformational and configurational diversity. Biology has harnessed this diversity and manipulates carbohydrate residues in a variety of ways, one of which is epimerization. RmlC catalyzes the epimerization of the C3' and C5' positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose. RmlC is the third enzyme of the rhamnose pathway, and represents a validated anti-bacterial drug target. Although several structures of the enzyme have been reported, the mechanism and the nature of the intermediates have remained obscure. Despite its relatively small size (22 kDa), RmlC catalyzes four stereospecific proton transfers and the substrate undergoes a major conformational change during the course of the transformation. Here we report the structure of RmlC from several organisms in complex with product and product mimics. We have probed site-directed mutants by assay and by deuterium exchange. The combination of structural and biochemical data has allowed us to assign key residues and identify the conformation of the carbohydrate during turnover. Clear knowledge of the chemical structure of RmlC reaction intermediates may offer new opportunities for rational drug design.

    Organizational Affiliation: 

    Centre for Biomolecular Sciences, The University, St. Andrews KY16 9ST, UK.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASEA, B184Pseudomonas aeruginosaMutation(s): 0 
EC: 5.1.3.13
UniProt
Find proteins for Q9HU21 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HU21 
Go to UniProtKB:  Q9HU21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HU21
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRH
Query on TRH
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
C16 H26 N2 O15 P2
ZOSQFDVXNQFKBY-CGAXJHMRSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TRH Binding MOAD:  2IXH Ka: 1.16e+4 (M^-1) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.915α = 90
b = 125.537β = 90
c = 109.366γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-06-06
    Changes: Data collection, Database references, Derived calculations