4RQF

human Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

SerRS-tRNASec 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 43: 10534-10545

  • DOI: https://doi.org/10.1093/nar/gkv996
  • Primary Citation of Related Structures:  
    4RQE, 4RQF

  • 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 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.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine--tRNA ligase, cytoplasmicB [auth A],
C [auth B]
522Homo sapiensMutation(s): 1 
Gene Names: SARSSERS
EC: 6.1.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P49591 (Homo sapiens)
Explore P49591 
Go to UniProtKB:  P49591
PHAROS:  P49591
GTEx:  ENSG00000031698 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49591
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
selenocysteine tRNAA [auth C]90Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.377α = 90
b = 108.894β = 90
c = 89.491γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Derived calculations
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description