Macromolecule Content

Total Structure Weight: 213.64 kDa
Atom Count: 16024
Modelled Residue Count: 1821
Deposited Residue Count: 1912
Unique protein chains: 1

2Y0E

BceC and the final step of UGDs reaction

PDB DOI: 10.2210/pdb2Y0E/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia cepacia
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-02 Released: 2011-07-27
Deposition Author(s): Rocha, J., Popescu, A.O., Borges, P., Mil-Homens, D., Sa-Correia, I., Fialho, A.M., Frazao, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.197
R-Value Work: 0.163
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of Burkholderia Cepacia Udp-Glucose Dehydrogenase (Ugd) Bcec and Role of Tyr10 in Final Hydrolysis of Ugd Thioester Intermediate.

Rocha, J., Popescu, A.O., Borges, P., Mil-Homens, D., Moreira, L.M., Sa-Correia, I., Fialho, A.M., Frazao, C.

(2011) J Bacteriol 193: 3978

PubMed: 21602353 Search on PubMedSearch on PubMed Central
DOI: 10.1128/JB.01076-10
Primary Citation of Related Structures:
2Y0C, 2Y0D, 2Y0E

PubMed Abstract:

Members of the Burkholderia cepacia complex (BCC) are serious respiratory pathogens in immunocompromised individuals and in patients with cystic fibrosis (CF). They are exceptionally resistant to many antimicrobial agents and have the capacity to spread between patients, leading to a decline in lung function and necrotizing pneumonia. BCC members often express a mucoid phenotype associated with the secretion of the exopolysaccharide (EPS) cepacian. There is much evidence supporting the fact that cepacian is a major virulence factor of BCC. UDP-glucose dehydrogenase (UGD) is responsible for the NAD-dependent 2-fold oxidation of UDP-glucose (UDP-Glc) to UDP-glucuronic acid (UDP-GlcA), which is a key step in cepacian biosynthesis. Here, we report the structure of BceC, determined at 1.75-Å resolution. Mutagenic studies were performed on the active sites of UGDs, and together with the crystallographic structures, they elucidate the molecular mechanism of this family of sugar nucleotide-modifying enzymes. Superposition with the structures of human and other bacterial UGDs showed an active site with high structural homology. This family contains a strictly conserved tyrosine residue (Y10 in BceC; shown in italics) within the glycine-rich motif (GXGYXG) of its N-terminal Rossmann-like domain. We constructed several BceC Y10 mutants, revealing only residual dehydrogenase activity and thus highlighting the importance of this conserved residue in the catalytic activity of BceC. Based on the literature of the UGD/GMD nucleotide sugar 6-dehydrogenase family and the kinetic and structural data we obtained for BceC, we determined Y10 as a key catalytic residue in a UGD rate-determining step, the final hydrolysis of the enzymatic thioester intermediate.

Related Citations:

Cloning, Expression, Purification, Crystallization and Preliminary Crystallographic Studies of Bcec, a Udp-Glucose Dehydrogenase from Burkholderia Cepacia Ist408.
Rocha, J., Popescu, A.O., Sa-Correia, I., Fialho, A.M., Frazao, C.
(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 269

Cloning, Expression, Purification, Crystallization and Preliminary Crystallographic Studies of Ugdg, an Udp-Glucose Dehydrogenase from Sphingomonas Elodea Atcc 31461.
Rocha, J., Granja, A.T., Sa-Correia, I., Fialho, A., Frazao, C.
(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 69

Organizational Affiliation:

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, P-2781-901 Oeiras, Portugal.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-GLUCOSE DEHYDROGENASE	A, B, C, D	478	Burkholderia cepacia	Mutation(s): 0 EC: 1.1.1.22
UniProt
Find proteins for C9E261 (Burkholderia cepacia) Explore C9E261 Go to UniProtKB: C9E261
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C9E261
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UGA Query on UGA Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C]	AA [auth D], E [auth A], M [auth B], T [auth C]	URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID C₁₅ H₂₂ N₂ O₁₈ P₂ HDYANYHVCAPMJV-LXQIFKJMSA-N		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C]	BA [auth D], CA [auth D], DA [auth D], F [auth A], G [auth A], BA [auth D], CA [auth D], DA [auth D], F [auth A], G [auth A], H [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	FA [auth D], J [auth A], K [auth A], L [auth A], Y [auth C], FA [auth D], J [auth A], K [auth A], L [auth A], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain S [auth B] SDF format, chain X [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C]	EA [auth D], I [auth A], S [auth B], X [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.197
R-Value Work: 0.163
R-Value Observed: 0.165
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.631	α = 90
b = 108.933	β = 90
c = 187.708	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2010-12-02
Released Date: 2011-07-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-07-27
Type: Initial release
Version 1.1: 2019-03-06
Changes: Data collection, Experimental preparation, Other
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation