4PON | pdb_00004pon

The crystal structure of a putative SAM-dependent methyltransferase, YtqB, from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb4PON/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus spizizenii str. W23
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-26 Released: 2014-04-02 
• Deposition Author(s): Park, S.C., Song, W.S., Yoon, S.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of a putative SAM-dependent methyltransferase, YtqB, from Bacillus subtilis

Park, S.C., Song, W.S., Yoon, S.I.

(2014) Biochem Biophys Res Commun 446: 921-926

• PubMed: 24637210 
• DOI: https://doi.org/10.1016/j.bbrc.2014.03.026
• Primary Citation Related Structures: 
  4PON, 4POO


• PubMed Abstract: 
  

  S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTases) methylate diverse biological molecules using a SAM cofactor. The ytqB gene of Bacillus subtilis encodes a putative MTase and its biological function has never been characterized. To reveal the structural features and the cofactor binding mode of YtqB, we have determined the crystal structures of YtqB alone and in complex with its cofactor, SAM, at 1.9 Å and 2.2 Å resolutions, respectively. YtqB folds into a β-sheet sandwiched by two α-helical layers, and assembles into a dimeric form. Each YtqB monomer contains one SAM binding site, which shapes SAM into a slightly curved conformation and exposes the reactive methyl group of SAM potentially to a substrate. Our comparative structural analysis of YtqB and its homologues indicates that YtqB is a SAM-dependent class I MTase, and provides insights into the substrate binding site of YtqB.

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Organizational Affiliation: 
• Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701, Republic of Korea.
Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701, Republic of Korea; Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 200-701, Republic of Korea. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 43.58 kDa 
• Atom Count: 2,800 
• Modeled Residue Count: 343 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative RNA methylase	A, B	200	Bacillus spizizenii str. W23	Mutation(s): 0  Gene Names: BSUW23_14785, ytqB
UniProt
Find proteins for E0TY72 (Bacillus spizizenii (strain ATCC 23059 / NRRL B-14472 / W23)) Explore E0TY72  Go to UniProtKB:  E0TY72

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.859	α = 90
b = 76.57	β = 90
c = 100.951	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Park, S.C., Song, W.S., Yoon, S.I.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2014-09-17
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description