ISDA

Deposition Date 2016-06-03

Release Date 2017-03-22

Last Version Date 2024-11-06

Entry Detail

PDB ID:

5L7V

Keywords:

HYDROLASE

Title:

Crystal Structure of BvGH123 with bond transition state analog Galthiazoline.

Biological Source:

Source Organism:

Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / NBRC 14291 / NCTC 11154) (Taxon ID: 435590)

Host Organism:

Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.30 Å

R-Value Free:

0.22

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:glycoside hydrolase
Gene (Uniprot):BVU_2198
Chain IDs:A, B
Chain Length:563
Number of Molecules:2
Biological Source:Bacteroides vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / NBRC 14291 / NCTC 11154)

UniProt ID:A6L2E5 Pfam ID:PF22680, PF13320

Ligand Molecules

GNL

Primary Citation

Structural and mechanistic insights into a Bacteroides vulgatus retaining N-acetyl-beta-galactosaminidase that uses neighbouring group participation.

Roth, C, Petricevic, M, John, A, Goddard-Borger, E.D, Davies, G.J, Williams, S.J.Show

Chem. Commun. (Camb.) 52 11096 11099 (2016)

PMID: 27546776 DOI: 10.1039/c6cc04649e

Abstact

Bacteroides vulgatus is a member of the human microbiota whose abundance is increased in patients with Crohn's disease. We show that a B. vulgatus glycoside hydrolase from the carbohydrate active enzyme family GH123, BvGH123, is an N-acetyl-β-galactosaminidase that acts with retention of stereochemistry, and, through a 3-D structure in complex with Gal-thiazoline, provide evidence in support of a neighbouring group participation mechanism.

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Protein

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Disease

Primary Citation of related structures