9QOF | pdb_00009qof

E.coli seryl-tRNA synthetase (Arm deletion mutant) bound to sulphamoyl seryl-adenylate analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.163 (Depositor), 0.163 (DCC) 
  • R-Value Work: 
    0.130 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 
    0.131 (Depositor) 

Starting Model: experimental
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Literature

Seryl-tRNA synthetase from Escherichia coli,implication of its N-terminal domain in aminoacylation activity and specificity.

Borel, F.Vincent, C.Leberman, R.Hartlein, M.

(1994) Nucleic Acids Res 22: 2963-2969

  • DOI: https://doi.org/10.1093/nar/22.15.2963
  • Primary Citation of Related Structures:  
    9QOF

  • PubMed Abstract: 

    Escherichia coli seryl-tRNA synthetase (SerRS) a dimeric class II aminoacyl-tRNA synthetase with two structural domains charges specifically the five iso-acceptor tRNA(ser) as well as the tRNA(sec) (selC product) of E. coli. The N-terminal domain is a 60 A long arm-like coiled coil structure built of 2 long antiparallel a-h helices, whereas the C-terminal domain is a alpha-beta structure. A deletion of the N-terminal arm of the enzyme does not affect the amino acid activation step of the reaction, but reduces dramatically amino-acylation activity. The Kcat/Km value for the mutant enzyme is reduced by more than 4 orders of magnitude, with a nearly 30 fold increased Km value for tRNA(ser). An only slightly truncated mutant form (16 amino acids of the tip of the arm replaced by a glycine) has an intermediate aminoacylation activity. Both mutant synthetases have lost their specificity for tRNA(ser) and charge also non-cognate type 1 tRNA(s). Our results support the hypothesis that class II synthetases have evolved from an ancestral catalytic core enzyme by adding non-catalytic N-terminal or C-terminal tRNA binding (specificity) domains which act as determinants for cognate and anti-determinants for non-cognate tRNAs.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine--tRNA ligase
A, B
368Escherichia coli K-12Mutation(s): 0 
Gene Names: serSb0893JW0876
EC: 6.1.1.11
UniProt
Find proteins for P0A8L1 (Escherichia coli (strain K12))
Explore P0A8L1 
Go to UniProtKB:  P0A8L1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8L1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.163 (Depositor), 0.163 (DCC) 
  • R-Value Work:  0.130 (Depositor), 0.130 (DCC) 
  • R-Value Observed: 0.131 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.615α = 90
b = 92.901β = 90
c = 171.691γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release