4RQE

human Seryl-tRNA synthetase dimer complexed with two molecules of tRNAsec


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

SerRS-tRNA Sec complex structures reveal mechanism of the first step in selenocysteine biosynthesis

Wang, C.Guo, Y.Tian, Q.Jia, Q.Gao, Y.Zhang, Q.Zhou, C.Xie, W.

(2015) Nucleic Acids Res 

  • DOI: 10.1093/nar/gkv996
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Selenocysteine (Sec) is found in the catalytic centers of many selenoproteins and plays important roles in living organisms. Malfunctions of selenoproteins lead to various human disorders including cancer. Known as the 21st amino acid, the biosynthes ...

    Selenocysteine (Sec) is found in the catalytic centers of many selenoproteins and plays important roles in living organisms. Malfunctions of selenoproteins lead to various human disorders including cancer. Known as the 21st amino acid, the biosynthesis of Sec involves unusual pathways consisting of several stages. While the later stages of the pathways are well elucidated, the molecular basis of the first stage-the serylation of Sec-specific tRNA (tRNA(Sec)) catalyzed by seryl-tRNA synthetase (SerRS)-is unclear. Here we present two cocrystal structures of human SerRS bound with tRNA(Sec) in different stoichiometry and confirm the formation of both complexes in solution by various characterization techniques. We discovered that the enzyme mainly recognizes the backbone of the long variable arm of tRNA(Sec) with few base-specific contacts. The N-terminal coiled-coil region works like a long-range lever to precisely direct tRNA 3' end to the other protein subunit for aminoacylation in a conformation-dependent manner. Restraints of the flexibility of the coiled-coil greatly reduce serylation efficiencies. Lastly, modeling studies suggest that the local differences present in the D- and T-regions as well as the characteristic U20:G19:C56 base triple in tRNA(Sec) may allow SerRS to distinguish tRNA(Sec) from closely related tRNA(Ser) substrate.


    Organizational Affiliation

    State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510275, People's Republic of China Center for Cellular & Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou, Guangdong 510006, People's Republic of China xiewei6@mail.sysu.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine--tRNA ligase, cytoplasmic
A, C
522Homo sapiensMutation(s): 2 
Gene Names: SARSSERSSARS1
EC: 6.1.1.11
Find proteins for P49591 (Homo sapiens)
Go to UniProtKB:  P49591
NIH Common Fund Data Resources
PHAROS  P49591

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
selenocysteine tRNAB, D90Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download CCD File 
A, C
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
SER
Query on SER

Download CCD File 
A, C
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.276 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.809α = 90
b = 142.023β = 101.95
c = 115.456γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Derived calculations