5L7V

Crystal Structure of BvGH123 with bond transition state analog Galthiazoline.

• PDB DOI: https://doi.org/10.2210/pdb5L7V/pdb

• Classification: HYDROLASE
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-06-03 Released: 2017-03-22 
• Deposition Author(s): Roth, C., Petricevic, M., John, A., Goddard-Borger, E.D., Davies, G.J., Williams, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.221 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

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.

(2016) Chem Commun (Camb) 52: 11096-11099

• PubMed: 27546776 
• DOI: https://doi.org/10.1039/c6cc04649e
• Primary Citation of Related Structures:  
  5L7R, 5L7V


• PubMed Abstract: 
  

  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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Organizational Affiliation: 

Department of Chemistry, University of York, Heslington, York, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 129.4 kDa 
• Atom Count: 9,132 
• Modelled Residue Count: 1,125 
• Deposited Residue Count: 1,126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycoside hydrolase	A, B	563	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_2198
UniProt
Find proteins for A6L2E5 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L2E5  Go to UniProtKB:  A6L2E5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNL	C [auth A], D [auth B]	(3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol C8 H13 N O4 S DRHXTSWSUAJOJZ-JAJWTYFOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GNL	Binding MOAD:  5L7V	Kd: 9.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.221 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.504	α = 90
b = 148.386	β = 90
c = 147.659	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Roth, C., Petricevic, M., John, A., Goddard-Borger, E.D., Davies, G.J., Williams, S.J.

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description