5HHF | pdb_00005hhf

Crystal structure of Aspergillus fumigatus UDP-Galactopyranose mutase mutant H63A with covalent FAD-Galactopyranose and bound UDP

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

  • Deposited: 2016-01-10 Released: 2016-02-17 
  • Deposition Author(s): Tanner, J.J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.213 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

Literature

In Crystallo Capture of a Covalent Intermediate in the UDP-Galactopyranose Mutase Reaction.

Mehra-Chaudhary, R., Dai, Y., Sobrado, P., Tanner, J.J.

(2016) Biochemistry 55: 833-836

  • DOI: https://doi.org/10.1021/acs.biochem.6b00035
  • Primary Citation Related Structures: 
    5HHF

  • PubMed Abstract: 

    UDP-galactopyranose mutase (UGM) plays an essential role in galactofuranose biosynthesis in pathogens by catalyzing the conversion of UDP-galactopyranose to UDP-galactofuranose. Here we report the first crystal structure of a covalent intermediate in the UGM reaction. The 2.3 Å resolution structure reveals UDP bound in the active site and galactopyranose linked to the FAD through a covalent bond between the anomeric C of galactopyranose and N5 of the FAD. The structure confirms the role of the flavin as nucleophile and supports the hypothesis that the proton destined for O5 of galactofuranose is shuttled from N5 of the FAD via O4 of the FAD.

    • Organizational Affiliation: 
    • Structural Biology Core, University of Missouri-Columbia , Columbia, Missouri 65211, United States.

Macromolecule Content 

  • Total Structure Weight: 233.98 kDa 
  • Atom Count: 16,554 
  • Modeled Residue Count: 2,015 
  • Deposited Residue Count: 2,052 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-galactopyranose mutase
A, B, C, D
513Aspergillus fumigatusMutation(s): 3 
Gene Names: glf, glfA
EC: 5.4.99.9
UniProt
Find proteins for Q4W1X2 (Aspergillus fumigatus)
Explore Q4W1X2 
Go to UniProtKB:  Q4W1X2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4W1X2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
62F

Query on 62F


Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]		[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-7,8-dimethyl-2,4-bis(oxidanyl)benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate
C33 H45 N9 O20 P2
KSCHBBHODWJJRH-MORZIXKLSA-N
FDA

Query on FDA


Download:Ideal Coordinates CCD File
S [auth C],
X [auth D]		DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
UDP

Query on UDP


Download:Ideal Coordinates CCD File
H [auth A],
M [auth B]		URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
MRY

Query on MRY


Download:Ideal Coordinates CCD File
F [auth A],
K [auth B],
R [auth C],
W [auth D]		MESO-ERYTHRITOL
C4 H10 O4
UNXHWFMMPAWVPI-ZXZARUISSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
E [auth A]
I [auth B]
J [auth B]
N [auth C]
O [auth C]
E [auth A],
I [auth B],
J [auth B],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
T [auth D],
U [auth D],
V [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.213 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.515α = 90
b = 217.515β = 90
c = 319.8γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2016-02-17 
    • Deposition Author(s): Tanner, J.J.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM094469
National Science Foundation (NSF, United States)United StatesCHE-1506206

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description