3INT

Structure of UDP-galactopyranose mutase bound to UDP-galactose (reduced)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray crystallography reveals a reduced substrate complex of UDP-galactopyranose mutase poised for covalent catalysis by flavin .

Gruber, T.D.Westler, W.M.Kiessling, L.L.Forest, K.T.

(2009) Biochemistry 48: 9171-9173

  • DOI: 10.1021/bi901437v
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The flavoenzyme uridine 5'-diphosphate galactopyranose mutase (UGM or Glf) catalyzes the interconversion of UDP-galactopyranose and UDP-galactofuranose. The latter is a key building block for cell wall construction in numerous pathogens, including My ...

    The flavoenzyme uridine 5'-diphosphate galactopyranose mutase (UGM or Glf) catalyzes the interconversion of UDP-galactopyranose and UDP-galactofuranose. The latter is a key building block for cell wall construction in numerous pathogens, including Mycobacterium tuberculosis. Mechanistic studies of UGM suggested a novel role for the flavin, and we previously provided evidence that the catalytic mechanism proceeds through a covalent flavin-galactose iminium. Here, we describe 2.3 and 2.5 A resolution X-ray crystal structures of the substrate-bound enzyme in oxidized and reduced forms, respectively. In the latter, C1 of the substrate is 3.6 A from the nucleophilic flavin N5 position. This orientation is consistent with covalent catalysis by flavin.


    Organizational Affiliation

    Department of Biochemistry, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable UDP-galactopyranose mutase
A, B
390Klebsiella pneumoniaeMutation(s): 1 
Gene Names: rfbD
EC: 5.4.99.9
Find proteins for Q48485 (Klebsiella pneumoniae)
Go to UniProtKB:  Q48485
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDU
Query on GDU

Download SDF File 
Download CCD File 
B
GALACTOSE-URIDINE-5'-DIPHOSPHATE
UDP-D-GALACTOPYRANOSE
C15 H24 N2 O17 P2
HSCJRCZFDFQWRP-ABVWGUQPSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
FDA
Query on FDA

Download SDF File 
Download CCD File 
A, B
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 94.078α = 90.00
b = 94.078β = 90.00
c = 129.443γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance