2CNM

RimI - Ribosomal S18 N-alpha-protein acetyltransferase in complex with a bisubstrate inhibitor (Cterm-Arg-Arg-Phe-Tyr-Arg-Ala-N-alpha- acetyl-S-CoA).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

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This is version 1.5 of the entry. See complete history


Literature

Crystal Structure of Rimi from Salmonella Typhimurium Lt2, the Gnat Responsible for N{Alpha}- Acetylation of Ribosomal Protein S18.

Vetting, M.W.Bareich, D.C.Yu, M.Blanchard, J.S.

(2008) Protein Sci 17: 1781-1790

  • DOI: https://doi.org/10.1110/ps.035899.108
  • Primary Citation of Related Structures:  
    2CNM, 2CNS, 2CNT

  • PubMed Abstract: 

    The three ribosomal proteins L7, S5, and S18 are included in the rare subset of prokaryotic proteins that are known to be N(alpha)-acetylated. The GCN5-related N-acetyltransferase (GNAT) protein RimI, responsible for the N(alpha)-acetylation of the ribosomal protein S18, was cloned from Salmonella typhimurium LT2 (RimI(ST)), overexpressed, and purified to homogeneity. Steady-state kinetic parameters for RimI(ST) were determined for AcCoA and a peptide substrate consisting of the first six amino acids of the target protein S18. The crystal structure of RimI(ST) was determined in complex with CoA, AcCoA, and a CoA-S-acetyl-ARYFRR bisubstrate inhibitor. The structures are consistent with a direct nucleophilic addition-elimination mechanism with Glu103 and Tyr115 acting as the catalytic base and acid, respectively. The RimI(ST)-bisubstrate complex suggests that several residues change conformation upon interacting with the N terminus of S18, including Glu103, the proposed active site base, facilitating proton exchange and catalysis.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
A, B, C
160Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
EC: 2.3.1.128
UniProt
Find proteins for Q8ZJW4 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZJW4 
Go to UniProtKB:  Q8ZJW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZJW4
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18
D, E, F
7Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 1 
UniProt
Find proteins for Q8ZK81 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZK81 
Go to UniProtKB:  Q8ZK81
Entity Groups  
UniProt GroupQ8ZK81
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.127α = 90
b = 133.127β = 90
c = 190.986γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-02-08
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2017-02-15
    Changes: Derived calculations
  • Version 1.4: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.5: 2019-10-23
    Changes: Data collection, Database references, Derived calculations, Other