2ODR

Methanococcus Maripaludis Phosphoseryl-tRNA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.228 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.292 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Toward understanding phosphoseryl-tRNACys formation: the crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase.

Kamtekar, S.Hohn, M.J.Park, H.S.Schnitzbauer, M.Sauerwald, A.Soll, D.Steitz, T.A.

(2007) Proc.Natl.Acad.Sci.Usa 104: 2620-2625

  • DOI: 10.1073/pnas.0611504104

  • PubMed Abstract: 
  • A number of archaeal organisms generate Cys-tRNA(Cys) in a two-step pathway, first charging phosphoserine (Sep) onto tRNA(Cys) and subsequently converting it to Cys-tRNA(Cys). We have determined, at 3.2-A resolution, the structure of the Methanococcu ...

    A number of archaeal organisms generate Cys-tRNA(Cys) in a two-step pathway, first charging phosphoserine (Sep) onto tRNA(Cys) and subsequently converting it to Cys-tRNA(Cys). We have determined, at 3.2-A resolution, the structure of the Methanococcus maripaludis phosphoseryl-tRNA synthetase (SepRS), which catalyzes the first step of this pathway. The structure shows that SepRS is a class II, alpha(4) synthetase whose quaternary structure arrangement of subunits closely resembles that of the heterotetrameric (alphabeta)(2) phenylalanyl-tRNA synthetase (PheRS). Homology modeling of a tRNA complex indicates that, in contrast to PheRS, a single monomer in the SepRS tetramer may recognize both the acceptor terminus and anticodon of a tRNA substrate. Using a complex with tungstate as a marker for the position of the phosphate moiety of Sep, we suggest that SepRS and PheRS bind their respective amino acid substrates in dissimilar orientations by using different residues.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry and Chemistry and Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phosphoseryl-tRNA synthetase
A
665Methanococcus maripaludis (strain S2 / LL)Mutation(s): 0 
Gene Names: sepS
EC: 6.1.1.27
Find proteins for Q6LZE1 (Methanococcus maripaludis (strain S2 / LL))
Go to UniProtKB:  Q6LZE1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
phosphoseryl-tRNA synthetase
B
648Methanococcus maripaludis (strain S2 / LL)Mutation(s): 0 
Gene Names: sepS
EC: 6.1.1.27
Find proteins for Q6LZE1 (Methanococcus maripaludis (strain S2 / LL))
Go to UniProtKB:  Q6LZE1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
phosphoseryl-tRNA synthetase
C
701Methanococcus maripaludis (strain S2 / LL)Mutation(s): 0 
Gene Names: sepS
EC: 6.1.1.27
Find proteins for Q6LZE1 (Methanococcus maripaludis (strain S2 / LL))
Go to UniProtKB:  Q6LZE1
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
phosphoseryl-tRNA synthetase
D
685Methanococcus maripaludis (strain S2 / LL)Mutation(s): 0 
Gene Names: sepS
EC: 6.1.1.27
Find proteins for Q6LZE1 (Methanococcus maripaludis (strain S2 / LL))
Go to UniProtKB:  Q6LZE1
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, B, C, D
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.228 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.292 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 119.172α = 90.00
b = 133.943β = 90.00
c = 208.382γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description