5HHF

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

PDB DOI: https://doi.org/10.2210/pdb5HHF/pdb

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 ?
R-Value Free: 0.213
R-Value Work: 0.184
R-Value Observed: 0.185

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

PubMed: 26836146 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.6b00035
Primary Citation of 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 ? 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
Modelled Residue Count: 2,015
Deposited Residue Count: 2,052
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-galactopyranose mutase	A, B, C, D	513	Aspergillus fumigatus	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4W1X2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
62F Query on 62F Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	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		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
FDA Query on FDA Download Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain S [auth C] MOL2 format, chain X [auth D] MOL2 format, chain S [auth C] mmCIF format, chain X [auth D] mmCIF format, chain S [auth C]	S [auth C], X [auth D]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C₂₇ H₃₅ N₉ O₁₅ P₂ YPZRHBJKEMOYQH-UYBVJOGSSA-N		Interactions Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain S [auth C] Focus chain X [auth D]
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], M [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
MRY Query on MRY Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] SDF format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D]	F [auth A], K [auth B], R [auth C], W [auth D]	MESO-ERYTHRITOL C₄ H₁₀ O₄ UNXHWFMMPAWVPI-ZXZARUISSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain W [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain V [auth D] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain V [auth D] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain V [auth D]	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		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
R-Value Free: 0.213
R-Value Work: 0.184
R-Value Observed: 0.185
Space Group: P 6₅ 2 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 217.515	α = 90
b = 217.515	β = 90
c = 319.8	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-02-17

Deposition Author(s):

Tanner, J.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM094469
National Science Foundation (NSF, United States)	United States	CHE-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

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Help and Resources

5HHF

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)