3T7R | pdb_00003t7r

Crystal structure of apo BVU_3255, a methyltransferase from Bacteroides vulgatus ATCC 8482

• PDB DOI: https://doi.org/10.2210/pdb3T7R/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: 2.90 Å
• R-Value Free: 
  0.265 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.224 (DCC) 

Starting Model: experimental

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 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.

Macromolecule Content 

• Total Structure Weight: 61.71 kDa 
• Atom Count: 4,119 
• Modeled Residue Count: 496 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase	A, B	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
6PP	C [auth A], D [auth B]	3-[(2Z)-3-methylpent-2-en-1-yl]benzene-1,2-diol C12 H16 O2 HZIMMWSOLFBHHZ-CLFYSBASSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.265 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.224 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.063	α = 90
b = 72.14	β = 90
c = 55.893	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	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