2PK3

Crystal Structure of a GDP-4-keto-6-deoxy-D-mannose reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The structural basis for catalytic function of GMD and RMD, two closely related enzymes from the GDP-D-rhamnose biosynthesis pathway.

King, J.D.Poon, K.K.Webb, N.A.Anderson, E.M.McNally, D.J.Brisson, J.R.Messner, P.Garavito, R.M.Lam, J.S.

(2009) FEBS J 276: 2686-2700

  • DOI: https://doi.org/10.1111/j.1742-4658.2009.06993.x
  • Primary Citation of Related Structures:  
    2PK3

  • PubMed Abstract: 

    The rare 6-deoxysugar D-rhamnose is a component of bacterial cell surface glycans, including the D-rhamnose homopolymer produced by Pseudomonas aeruginosa, called A-band O polysaccharide. GDP-D-rhamnose synthesis from GDP-D-mannose is catalyzed by two enzymes. The first is a GDP-D-mannose-4,6-dehydratase (GMD). The second enzyme, RMD, reduces the GMD product (GDP-6-deoxy-D-lyxo-hexos-4-ulose) to GDP-d-rhamnose. Genes encoding GMD and RMD are present in P. aeruginosa, and genetic evidence indicates they act in A-band O-polysaccharide biosynthesis. Details of their enzyme functions have not, however, been previously elucidated. We aimed to characterize these enzymes biochemically, and to determine the structure of RMD to better understand what determines substrate specificity and catalytic activity in these enzymes. We used capillary electrophoresis and NMR analysis of reaction products to precisely define P. aeruginosa GMD and RMD functions. P. aeruginosa GMD is bifunctional, and can catalyze both GDP-d-mannose 4,6-dehydration and the subsequent reduction reaction to produce GDP-D-rhamnose. RMD catalyzes the stereospecific reduction of GDP-6-deoxy-D-lyxo-hexos-4-ulose, as predicted. Reconstitution of GDP-D-rhamnose biosynthesis in vitro revealed that the P. aeruginosa pathway may be regulated by feedback inhibition in the cell. We determined the structure of RMD from Aneurinibacillus thermoaerophilus at 1.8 A resolution. The structure of A. thermoaerophilus RMD is remarkably similar to that of P. aeruginosa GMD, which explains why P. aeruginosa GMD is also able to catalyze the RMD reaction. Comparison of the active sites and amino acid sequences suggests that a conserved amino acid side chain (Arg185 in P. aeruginosa GMD) may be crucial for orienting substrate and cofactor in GMD enzymes.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Guelph, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GDP-6-deoxy-D-lyxo-4-hexulose reductase
A, B
321Aneurinibacillus thermoaerophilusMutation(s): 0 
Gene Names: rmd
UniProt
Find proteins for Q6T1X6 (Aneurinibacillus thermoaerophilus)
Explore Q6T1X6 
Go to UniProtKB:  Q6T1X6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6T1X6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A2R
Query on A2R

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE
C15 H24 N5 O17 P3
ICNHOLCERMYLRZ-KEOHHSTQSA-N
GDD
Query on GDD

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
C16 H25 N5 O16 P2
MVMSCBBUIHUTGJ-GDJBGNAASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.882α = 72.54
b = 55.744β = 82.95
c = 79.244γ = 75.61
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MrBUMPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description