Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 141.35 kDa 
• Atom Count: 10122 
• Modelled Residue Count: 1179 
• Deposited Residue Count: 1197 
• Unique protein chains: 1

4RPJ

Crystal structure of Micobacterium tuberculosis UDP-Galactopyranose mutase in complex with UDP

• PDB DOI: 10.2210/pdb4RPJ/pdb

• Classification: ISOMERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-10-30 Released: 2015-01-21 
• Deposition Author(s): Van Straaten, K.E., Sanders, D.A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.221 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Structural Basis of Ligand Binding to UDP-Galactopyranose Mutase from Mycobacterium tuberculosis Using Substrate and Tetrafluorinated Substrate Analogues.

van Straaten, K.E., Kuttiyatveetil, J.R., Sevrain, C.M., Villaume, S.A., Jimenez-Barbero, J., Linclau, B., Vincent, S.P., Sanders, D.A.

(2015) J Am Chem Soc 137: 1230-1244

• PubMed: 25562380 
• DOI: 10.1021/ja511204p
• Primary Citation of Related Structures:  
  4RPG, 4RPH, 4RPJ, 4RPK, 4RPL


• PubMed Abstract: 
  

UDP-Galactopyranose mutase (UGM) is a flavin-containing enzyme that catalyzes the reversible conversion of UDP-galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf) and plays a key role in the biosynthesis of the mycobacterial cell wall galactofuran. A soluble, active form of UGM from Mycobacterium tuberculosis (MtUGM) was obtained from a dual His6-MBP-tagged MtUGM construct. We present the first complex structures of MtUGM with bound substrate UDP-Galp (both oxidized flavin and reduced flavin). In addition, we have determined the complex structures of MtUGM with inhibitors (UDP and the dideoxy-tetrafluorinated analogues of both UDP-Galp (UDP-F4-Galp) and UDP-Galf (UDP-F4-Galf)), which represent the first complex structures of UGM with an analogue in the furanose form, as well as the first structures of dideoxy-tetrafluorinated sugar analogues bound to a protein. These structures provide detailed insight into ligand recognition by MtUGM and show an overall binding mode similar to those reported for other prokaryotic UGMs. The binding of the ligand induces conformational changes in the enzyme, allowing ligand binding and active-site closure. In addition, the complex structure of MtUGM with UDP-F4-Galf reveals the first detailed insight into how the furanose moiety binds to UGM. In particular, this study confirmed that the furanoside adopts a high-energy conformation ((4)E) within the catalytic pocket. Moreover, these investigations provide structural insights into the enhanced binding of the dideoxy-tetrafluorinated sugars compared to unmodified analogues. These results will help in the design of carbohydrate mimetics and drug development, and show the enormous possibilities for the use of polyfluorination in the design of carbohydrate mimetics.

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Organizational Affiliation: 

Department of Chemistry, University of Saskatchewan , 110 Science Place, Saskatoon S7N 5C9, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-galactopyranose mutase	A, B, C	399	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  Gene Names: glf, glfA, Rv3809c EC: 5.4.99.9
UniProt
Find proteins for P9WIQ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIQ1  Go to UniProtKB:  P9WIQ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], F [auth B], H [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
UDP	E [auth A], G [auth B], I [auth C]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.221 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.483	α = 90
b = 101.214	β = 109.23
c = 102.056	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxDC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-10-30 
• Released Date: 2015-01-21 
Deposition Author(s): Van Straaten, K.E., Sanders, D.A.R.

Revision History  

• Version 1.0: 2015-01-21
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Database references
• Version 1.2: 2015-02-11
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Database references