3WKR

Crystal structure of the SepCysS-SepCysE complex from Methanocaldococcus jannaschii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea.

Liu, Y.Nakamura, A.Nakazawa, Y.Asano, N.Ford, K.A.Hohn, M.J.Tanaka, I.Yao, M.Soll, D.

(2014) Proc Natl Acad Sci U S A 111: 10520-10525

  • DOI: 10.1073/pnas.1411267111
  • Primary Citation of Related Structures:  
    3WKR, 3WKS

  • PubMed Abstract: 
  • Methanogenic archaea lack cysteinyl-tRNA synthetase; they synthesize Cys-tRNA and cysteine in a tRNA-dependent manner. Two enzymes are required: Phosphoseryl-tRNA synthetase (SepRS) forms phosphoseryl-tRNA(Cys) (Sep-tRNA(Cys)), which is converted to Cys-tRNA(Cys) by Sep-tRNA:Cys-tRNA synthase (SepCysS) ...

    Methanogenic archaea lack cysteinyl-tRNA synthetase; they synthesize Cys-tRNA and cysteine in a tRNA-dependent manner. Two enzymes are required: Phosphoseryl-tRNA synthetase (SepRS) forms phosphoseryl-tRNA(Cys) (Sep-tRNA(Cys)), which is converted to Cys-tRNA(Cys) by Sep-tRNA:Cys-tRNA synthase (SepCysS). This represents the ancestral pathway of Cys biosynthesis and coding in archaea. Here we report a translation factor, SepCysE, essential for methanococcal Cys biosynthesis; its deletion in Methanococcus maripaludis causes Cys auxotrophy. SepCysE acts as a scaffold for SepRS and SepCysS to form a stable high-affinity complex for tRNA(Cys) causing a 14-fold increase in the initial rate of Cys-tRNA(Cys) formation. Based on our crystal structure (2.8-Å resolution) of a SepCysS⋅SepCysE complex, a SepRS⋅SepCysE⋅SepCysS structure model suggests that this ternary complex enables substrate channeling of Sep-tRNA(Cys). A phylogenetic analysis suggests coevolution of SepCysE with SepRS and SepCysS in the last universal common ancestral state. Our findings suggest that the tRNA-dependent Cys biosynthesis proceeds in a multienzyme complex without release of the intermediate and this mechanism may have facilitated the addition of Cys to the genetic code.


    Organizational Affiliation

    Departments of Molecular Biophysics and Biochemistry andChemistry, Yale University, New Haven, CT 06520; and dieter.soll@yale.edu yao@castor.sci.hokudai.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
O-phospho-L-seryl-tRNA:Cys-tRNA synthaseA, B, E, F416Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: MJ1678pscS
EC: 2.5.1.73
UniProt
Find proteins for Q59072 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q59072 
Go to UniProtKB:  Q59072
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59072
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein MJ1481C, D, G, H216Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: MJ1481
UniProt
Find proteins for Q58876 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58876 
Go to UniProtKB:  Q58876
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58876
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B, E, F L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.230 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.88α = 90
b = 106.88β = 90
c = 495.253γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2022-08-24
    Changes: Database references, Derived calculations