Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 235.63 kDa 
• Atom Count: 16,989 
• Modelled Residue Count: 2,020 
• Deposited Residue Count: 2,052 
• Unique protein chains: 1

 4U8I

Structure of Aspergillus fumigatus UDP-Galactopyranose mutase mutant F66A

• PDB DOI: 10.2210/pdb4U8I/pdb

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


• Deposited: 2014-08-03 Released: 2014-12-03 
• Deposition Author(s): Qureshi, I.A., Chaudhary, R., Tanner, J.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.214 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4U8M

Literature

Contributions of Unique Active Site Residues of Eukaryotic UDP-Galactopyranose Mutases to Substrate Recognition and Active Site Dynamics.

Da Fonseca, I., Qureshi, I.A., Mehra-Chaudhary, R., Kizjakina, K., Tanner, J.J., Sobrado, P.

(2014) Biochemistry 53: 7794-7804

• PubMed: 25412209 
• DOI: 10.1021/bi501008z
• Primary Citation of Related Structures:  
  4U8I, 4U8J, 4U8K, 4U8L, 4U8M, 4U8N, 4U8O, 4U8P, 4WX1


• PubMed Abstract: 
  

UDP-galactopyranose mutase (UGM) catalyzes the interconversion between UDP-galactopyranose and UDP-galactofuranose. Absent in humans, galactofuranose is found in bacterial and fungal cell walls and is a cell surface virulence factor in protozoan parasites. For these reasons, UGMs are targets for drug discovery. Here, we report a mutagenesis and structural study of the UGMs from Aspergillus fumigatus and Trypanosoma cruzi focused on active site residues that are conserved in eukaryotic UGMs but are absent or different in bacterial UGMs. Kinetic analysis of the variants F66A, Y104A, Q107A, N207A, and Y317A (A. fumigatus numbering) show decreases in k(cat)/K(M) values of 200-1000-fold for the mutase reaction. In contrast, none of the mutations significantly affect the kinetics of enzyme activation by NADPH. These results indicate that the targeted residues are important for promoting the transition state conformation for UDP-galactofuranose formation. Crystal structures of the A. fumigatus mutant enzymes were determined in the presence and absence of UDP to understand the structural consequences of the mutations. The structures suggest important roles for Asn207 in stabilizing the closed active site, and Tyr317 in positioning of the uridine ring. Phe66 and the corresponding residue in Mycobacterium tuberculosis UGM (His68) play a role as the backstop, stabilizing the galactopyranose group for nucleophilic attack. Together, these results provide insight into the essentiality of the targeted residues for realizing maximal catalytic activity and a proposal for how conformational changes that close the active site are temporally related and coupled together.

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Organizational Affiliation: 

Department of Biochemistry, Virginia Tech , Blacksburg, Virginia 24061, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-galactopyranose mutase	A, B, C, D	513	Aspergillus fumigatus	Mutation(s): 4  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDA	AB [auth D], E [auth A], MA [auth C], S [auth B]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C27 H35 N9 O15 P2 YPZRHBJKEMOYQH-UYBVJOGSSA-N
SO4	FA [auth B], FB [auth D], GA [auth B], GB [auth D], HA [auth B], HB [auth D], IA [auth B], IB [auth D], JA [auth B], JB [auth D], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	AA [auth B], BA [auth B], BB [auth D], CA [auth B], CB [auth D], DA [auth B], DB [auth D], EA [auth B], EB [auth D], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth C], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.214 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.126	α = 90
b = 217.126	β = 90
c = 320.348	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Qureshi, I.A., Chaudhary, R., Tanner, J.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM094469

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence