2ODR

Methanococcus Maripaludis Phosphoseryl-tRNA synthetase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.292 
  • R-Value Observed: 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 U S A 104: 2620-2625

  • DOI: 10.1073/pnas.0611504104
  • Primary Citation of Related Structures:  
    2ODR

  • 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 Methanococcus maripaludis phosphoseryl-tRNA synthetase (SepRS), which catalyzes the first step of this pathway ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
phosphoseryl-tRNA synthetaseA665Methanococcus maripaludis S2Mutation(s): 0 
Gene Names: MMP0688, sepS
EC: 6.1.1 (PDB Primary Data), 6.1.1.27 (UniProt)
UniProt
Find proteins for Q6LZE1 (Methanococcus maripaludis (strain S2 / LL))
Explore Q6LZE1 
Go to UniProtKB:  Q6LZE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6LZE1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
phosphoseryl-tRNA synthetaseB648Methanococcus maripaludis S2Mutation(s): 0 
Gene Names: MMP0688, sepS
EC: 6.1.1 (PDB Primary Data), 6.1.1.27 (UniProt)
UniProt
Find proteins for Q6LZE1 (Methanococcus maripaludis (strain S2 / LL))
Explore Q6LZE1 
Go to UniProtKB:  Q6LZE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6LZE1
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
phosphoseryl-tRNA synthetaseC701Methanococcus maripaludis S2Mutation(s): 0 
Gene Names: MMP0688, sepS
EC: 6.1.1 (PDB Primary Data), 6.1.1.27 (UniProt)
UniProt
Find proteins for Q6LZE1 (Methanococcus maripaludis (strain S2 / LL))
Explore Q6LZE1 
Go to UniProtKB:  Q6LZE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6LZE1
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
phosphoseryl-tRNA synthetaseD685Methanococcus maripaludis S2Mutation(s): 0 
Gene Names: MMP0688, sepS
EC: 6.1.1 (PDB Primary Data), 6.1.1.27 (UniProt)
UniProt
Find proteins for Q6LZE1 (Methanococcus maripaludis (strain S2 / LL))
Explore Q6LZE1 
Go to UniProtKB:  Q6LZE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6LZE1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.292 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.172α = 90
b = 133.943β = 90
c = 208.382γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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