4LE5 | pdb_00004le5

Structure of an Unusual S-adenosylmethionine synthetase from Campylobacter jejuni

• PDB DOI: https://doi.org/10.2210/pdb4LE5/pdb

• Classification: TRANSFERASE
• Organism(s): Campylobacter jejuni RM1221
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-25 Released: 2014-02-12 
• Deposition Author(s): Zano, S.P., Pavlovsky, A.G., Viola, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.263 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Structure of an unusual S-adenosylmethionine synthetase from Campylobacter jejuni.

Zano, S.P., Pavlovsky, A.G., Viola, R.E.

(2014) Acta Crystallogr D Biol Crystallogr 70: 442-450

• PubMed: 24531478 
• DOI: https://doi.org/10.1107/S139900471303023X
• Primary Citation Related Structures: 
  4LE5


• PubMed Abstract: 
  

  S-Adenosylmethionine (AdoMet) participates in a wide range of methylation and other group-transfer reactions and also serves as the precursor for two groups of quorum-sensing molecules that function as regulators of the production of virulence factors in Gram-negative bacteria. The synthesis of AdoMet is catalyzed by AdoMet synthetases (MATs), a ubiquitous family of enzymes found in species ranging from microorganisms to mammals. The AdoMet synthetase from the bacterium Campylobacter jejuni (cjMAT) is an outlier among this homologous enzyme family, with lower sequence identity, numerous insertions and substitutions, and higher catalytic activity compared with other bacterial MATs. Alterations in the structure of this enzyme provide an explanation for its unusual dimeric quaternary structure relative to the other MATs. Taken together with several active-site substitutions, this new structure provides insights into its improved kinetic properties with alternative substrates.

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Organizational Affiliation: 
• Department of Chemistry, The University of Toledo, Toledo, OH 43606, USA.

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: 94.51 kDa 
• Atom Count: 6,166 
• Modeled Residue Count: 774 
• Deposited Residue Count: 860 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine synthetase	A, B	430	Campylobacter jejuni RM1221	Mutation(s): 0  Gene Names: CJE1239, metK EC: 2.5.1.6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.263 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.655	α = 90
b = 113.075	β = 116.49
c = 62.179	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Zano, S.P., Pavlovsky, A.G., Viola, R.E.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2014-11-12
  Changes: Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description