3HL2

The crystal structure of the human SepSecS-tRNASec complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history


Literature

The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation.

Palioura, S.Sherrer, R.L.Steitz, T.A.Soll, D.Simonovic, M.

(2009) Science 325: 321-325

  • DOI: 10.1126/science.1173755
  • Primary Citation of Related Structures:  
    3HL2

  • PubMed Abstract: 
  • Selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) catalyzes the final step of selenocysteine formation by a poorly understood tRNA-dependent mechanism ...

    Selenocysteine is the only genetically encoded amino acid in humans whose biosynthesis occurs on its cognate transfer RNA (tRNA). O-Phosphoseryl-tRNA:selenocysteinyl-tRNA synthase (SepSecS) catalyzes the final step of selenocysteine formation by a poorly understood tRNA-dependent mechanism. The crystal structure of human tRNA(Sec) in complex with SepSecS, phosphoserine, and thiophosphate, together with in vivo and in vitro enzyme assays, supports a pyridoxal phosphate-dependent mechanism of Sec-tRNA(Sec) formation. Two tRNA(Sec) molecules, with a fold distinct from other canonical tRNAs, bind to each SepSecS tetramer through their 13-base pair acceptor-TPsiC arm (where Psi indicates pseudouridine). The tRNA binding is likely to induce a conformational change in the enzyme's active site that allows a phosphoserine covalently attached to tRNA(Sec), but not free phosphoserine, to be oriented properly for the reaction to occur.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
O-phosphoseryl-tRNA(Sec) selenium transferaseA, B, C, D501Homo sapiensMutation(s): 0 
Gene Names: SEPSECSTRNP48
EC: 2.9.1.1 (PDB Primary Data), 2.9.1.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HD40 (Homo sapiens)
Explore Q9HD40 
Go to UniProtKB:  Q9HD40
PHAROS:  Q9HD40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HD40
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
tRNASecE 90Homo sapiens
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.818α = 90
b = 166.818β = 90
c = 236.322γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary