3INT

Experimental Data Snapshot

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

(2009) Biochemistry 48: 9171-9173

PubMed Abstract:
The flavoenzyme uridine 5'-diphosphate galactopyranose mutase (UGM or Glf) catalyzes the interconversion of UDP-galactopyranose and UDP-galactofuranose. The latter is a key building block for cell wall construction in numerous pathogens, including Mycobacterium tuberculosis. Mechanistic studies of UGM suggested a novel role for the flavin, and we previously provided evidence that the catalytic mechanism proceeds through a covalent flavin-galactose iminium. Here, we describe 2.3 and 2.5 A resolution X-ray crystal structures of the substrate-bound enzyme in oxidized and reduced forms, respectively. In the latter, C1 of the substrate is 3.6 A from the nucleophilic flavin N5 position. This orientation is consistent with covalent catalysis by flavin.

Organizational Affiliation

Department of Biochemistry, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Macromolecule Content

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable UDP-galactopyranose mutase	A, B	390	Klebsiella pneumoniae	Mutation(s): 1 Gene Names: glf, rfbD EC: 5.4.99.9
UniProt
Find proteins for Q48485 (Klebsiella pneumoniae) Explore Q48485 Go to UniProtKB: Q48485
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q48485
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDA Query on FDA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE C₂₇ H₃₅ N₉ O₁₅ P₂ YPZRHBJKEMOYQH-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GDU Query on GDU Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GALACTOSE-URIDINE-5'-DIPHOSPHATE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-ABVWGUQPSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]