Biological Assembly 1  

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

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 463.62 kDa 
• Atom Count: 32560 
• Modelled Residue Count: 4072 
• Deposited Residue Count: 4072 
• Unique protein chains: 1

3UKP

Crystal structure of R327A UDP-galactopyranose mutase from Aspergillus fumigatus in complex with UDPgalp

• PDB DOI: 10.2210/pdb3UKP/pdb

• Classification: ISOMERASE
• Organism(s): Aspergillus fumigatus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-11-09 Released: 2012-02-22 
• Deposition Author(s): Van Straaten, K.E., Sanders, D.A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.260 
• R-Value Work: 0.202 
• R-Value Observed: 0.206 

Literature

Structural Insight into the Unique Substrate Binding Mechanism and Flavin Redox State of UDP-galactopyranose Mutase from Aspergillus fumigatus.

van Straaten, K.E., Routier, F.H., Sanders, D.A.

(2012) J Biol Chem 287: 10780-10790

• PubMed: 22334662 
• DOI: 10.1074/jbc.M111.322974
• Primary Citation of Related Structures:  
  3UKA, 3UKF, 3UKH, 3UKK, 3UKL, 3UKP, 3UKQ


• 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). As in prokaryotic UGMs, the flavin needs to be reduced for the enzyme to be active. Here we present the first eukaryotic UGM structures from Aspergillus fumigatus (AfUGM). The structures are of UGM alone, with the substrate UDP-Galp and with the inhibitor UDP. Additionally, we report the structures of AfUGM bound to substrate with oxidized and reduced flavin. These structures provide insight into substrate recognition and structural changes observed upon substrate binding involving the mobile loops and the critical arginine residues Arg-182 and Arg-327. Comparison with prokaryotic UGM reveals that despite low sequence identity with known prokaryotic UGMs the overall fold is largely conserved. Structural differences between prokaryotic UGM and AfUGM result from inserts in AfUGM. A notable difference from prokaryotic UGMs is that AfUGM contains a third flexible loop (loop III) above the si-face of the isoalloxazine ring that changes position depending on the redox state of the flavin cofactor. This loop flipping has not been observed in prokaryotic UGMs. In addition we have determined the crystals structures and steady-state kinetic constants of the reaction catalyzed by mutants R182K, R327K, R182A, and R327A. These results support our hypothesis that Arg-182 and Arg-327 play important roles in stabilizing the position of the diphosphates of the nucleotide sugar and help to facilitate the positioning of the galactose moiety for catalysis.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-galactopyranose mutase	A, B, C, D, E, F, G, H	509	Aspergillus fumigatus	Mutation(s): 1  Gene Names: glf, glfA EC: 5.4.99.9
UniProt
Find proteins for Q4W1X2 (Neosartorya fumigata) Explore Q4W1X2  Go to UniProtKB:  Q4W1X2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], V [auth H]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GDU	J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F]	GALACTOSE-URIDINE-5'-DIPHOSPHATE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-ABVWGUQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.260 
• R-Value Work: 0.202 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.6	α = 90
b = 175.71	β = 90.01
c = 135.347	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-09 
• Released Date: 2012-02-22 
Deposition Author(s): Van Straaten, K.E., Sanders, D.A.R.

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2012-03-07
  Changes: Database references
• Version 1.2: 2012-07-18
  Changes: Database references
• Version 1.3: 2017-11-08
  Changes: Refinement description