1WAM

Structure of UDP-galactopyranose mutase from Klebsiella Pneumoniae with FADH-


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1016/j.jmb.2005.02.057
  • Primary Citation of Related Structures:  
    1V0J, 1WAM, 2BI7, 2BI8

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-GALACTOPYRANOSE MUTASE384Klebsiella pneumoniaeMutation(s): 0 
EC: 5.4.99.9
UniProt
Find proteins for Q48485 (Klebsiella pneumoniae)
Explore Q48485 
Go to UniProtKB:  Q48485
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ48485
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.997α = 90
b = 85.997β = 90
c = 100.809γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 1.3: 2017-06-28
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description