2BI7

udp-galactopyranose mutase from Klebsiella pneumoniae oxidised FAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of Mycobacteria Tuberculosis and Klebsiella Pneumoniae Udp-Galactopyranose Mutase in the Oxidised State and Klebsiella Pneumoniae Udp-Galactopyranose Mutase in the (Active) Reduced State.

Beis, K.Srikannathasan, V.Liu, H.Fullerton, S.W.B.Bamford, V.A.Sanders, D.A.R.Whitfield, C.Mcneil, M.R.Naismith, J.H.

(2005) J.Mol.Biol. 348: 971

  • DOI: 10.1016/j.jmb.2005.02.057
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Uridine diphosphogalactofuranose (UDP-Galf) is the precursor of the d-galactofuranose sugar found in bacterial and parasitic cell walls, including those of many pathogens. UDP-Galf is made from UDP-galactopyranose by the enzyme UDP-galactopyranose mu ...

    Uridine diphosphogalactofuranose (UDP-Galf) is the precursor of the d-galactofuranose sugar found in bacterial and parasitic cell walls, including those of many pathogens. UDP-Galf is made from UDP-galactopyranose by the enzyme UDP-galactopyranose mutase. The enzyme requires the reduced FADH- co-factor for activity. The structure of the Mycobacterium tuberculosis mutase with FAD has been determined to 2.25 A. The structures of Klebsiella pneumoniae mutase with FAD and with FADH- bound have been determined to 2.2 A and 2.35 A resolution, respectively. This is the first report of the FADH(-)-containing structure. Two flavin-dependent mechanisms for the enzyme have been proposed, one, which involves a covalent adduct being formed at the flavin and the other based on electron transfer. Using our structural data, we have examined the two mechanisms. The electron transfer mechanism is consistent with the structural data, not surprisingly, since it makes fewer demands on the precise positioning of atoms. A model based on a covalent adduct FAD requires repositioning of the enzyme active site and would appear to require the isoalloxazine ring of FADH- to buckle in a particular way. However, the FADH- structure reveals that the isoalloxazine ring buckles in the opposite sense, this apparently requires the covalent adduct to trigger profound conformational changes in the protein or to buckle the FADH- opposite to that seen in the apo structure.


    Related Citations: 
    • Udp-Galactopyranose Mutase Has a Novel Structure and Mechanism
      Sanders, D.A.,Staines, A.G.,Mcmahon, S.A.,Mcneil, M.R.,Whitfield, C.,Naismith, J.H.
      (2001) Nat.Struct.Mol.Biol. 8: 858


    Organizational Affiliation

    Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife, Scotland KY16 9ST, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-GALACTOPYRANOSE MUTASE
A
384Klebsiella pneumoniaeMutation(s): 0 
Gene Names: rfbD
EC: 5.4.99.9
Find proteins for Q48485 (Klebsiella pneumoniae)
Go to UniProtKB:  Q48485
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.675α = 90.00
b = 85.675β = 90.00
c = 99.793γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2015-03-25
    Type: Database references, Derived calculations, Structure summary
  • Version 1.3: 2017-06-28
    Type: Data collection