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 

wwPDB Validation 3D Report Full Report


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

  • 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 po ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-phosphoseryl-tRNA(Sec) selenium transferase
A, B, C, D
501Homo sapiensMutation(s): 0 
Gene Names: SEPSECS (TRNP48)
EC: 2.9.1.2
Find proteins for Q9HD40 (Homo sapiens)
Go to Gene View: SEPSECS
Go to UniProtKB:  Q9HD40
Entity ID: 2
MoleculeChainsLengthOrganism
tRNASecE90Homo sapiens
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SEP
Query on SEP

Download SDF File 
Download CCD File 
B, D
PHOSPHOSERINE
PHOSPHONOSERINE
C3 H8 N O6 P
BZQFBWGGLXLEPQ-REOHCLBHSA-N
 Ligand Interaction
TS6
Query on TS6

Download SDF File 
Download CCD File 
A, C
Monothiophosphate
phosphorothioic O,O,S-acid
H3 O3 P S
RYYWUUFWQRZTIU-UHFFFAOYSA-N
 Ligand Interaction
PLR
Query on PLR

Download SDF File 
Download CCD File 
A, B, C, D
(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
4'-DEOXYPYRIDOXINE PHOSPHATE
C8 H12 N O5 P
RBCOYOYDYNXAFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 166.818α = 90.00
b = 166.818β = 90.00
c = 236.322γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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