3T7S

Crystal structure of complex of SAM and BVU_3255, a methyltransferase from Bacteroides vulgatus ATCC 8482

• PDB DOI: https://doi.org/10.2210/pdb3T7S/pdb

• Classification: TRANSFERASE
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-31 Released: 2011-10-12 
• Deposition Author(s): Kumar, V., Sivaraman, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.267 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Literature

Structural characterization of BVU_3255, a methyltransferase from human intestine antibiotic resistant pathogen Bacteroides vulgatus

Kumar, V., Sivaraman, J.

(2011) J Struct Biol 

• PubMed: 21872662 
• DOI: https://doi.org/10.1016/j.jsb.2011.08.007
• Primary Citation of Related Structures:  
  3T7R, 3T7S, 3T7T


• PubMed Abstract: 
  

  Methylation is important for various cellular activities. To date, there is no report of any methyltransferase structure from the human intestine antibiotic resistant pathogen Bacteroides vulgatus. The protein BVU_3255 from B. vulgatus ATCC 8482 belongs to a SAM-dependent methyltransferase. Here, we report the crystal structure of apo BVU_3255, and its complexes with SAM and SAH, which revealed a typical class I Rossmann Fold Methyltransferase. Isothermal titration calorimetric studies showed that both SAM and SAH bind with equal affinity. The structural and sequence analysis suggested that BVU_3255 is a small molecule methyltransferase and involved in methylating the intermediates in ubiquinone biosynthesis pathway.

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Organizational Affiliation: 

Department of Biological Sciences, National University of Singapore, Singapore, Republic of Singapore.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 124.25 kDa 
• Atom Count: 8,176 
• Modelled Residue Count: 965 
• Deposited Residue Count: 1,072 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase	A, B, C, D	268	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_3255
UniProt
Find proteins for A6L5C0 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L5C0  Go to UniProtKB:  A6L5C0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	E [auth A], F [auth B], G [auth C], H [auth D]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SAM	Binding MOAD:  3T7S	Ka: 4.45e+4 (M^-1) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.267 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.419	α = 90
b = 106.648	β = 90
c = 133.004	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Kumar, V., Sivaraman, J.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description