Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 145.46 kDa 
• Atom Count: 9117 
• Modelled Residue Count: 1002 
• Deposited Residue Count: 1139 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2DU4

Crystal structure of Archaeoglobus fulgidus O-phosphoseryl-tRNA synthetase complexed with tRNACys

• PDB DOI: 10.2210/pdb2DU4/pdb
• NDB: PR0220

• Classification: LIGASE/RNA
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-20 Released: 2007-03-13 
• Deposition Author(s): Fukunaga, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Literature

Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea.

Fukunaga, R., Yokoyama, S.

(2007) Nat Struct Mol Biol 14: 272-279

• PubMed: 17351629 
• DOI: 10.1038/nsmb1219
• Primary Citation of Related Structures:  
  2DU3, 2DU4, 2DU5, 2DU6, 2DU7


• PubMed Abstract: 
  

Cysteine is ligated to tRNA(Cys) by cysteinyl-tRNA synthetase in most organisms. However, in methanogenic archaea lacking cysteinyl-tRNA synthetase, O-phosphoserine is ligated to tRNA(Cys) by O-phosphoseryl-tRNA synthetase (SepRS), and the phosphoseryl-tRNA(Cys) is converted to cysteinyl-tRNA(Cys). In this study, we determined the crystal structure of the SepRS tetramer in complex with tRNA(Cys) and O-phosphoserine at 2.6-A resolution. The catalytic domain of SepRS recognizes the negatively charged side chain of O-phosphoserine at a noncanonical site, using the dipole moment of a conserved alpha-helix. The unique C-terminal domain specifically recognizes the anticodon GCA of tRNA(Cys). On the basis of the structure, we engineered SepRS to recognize tRNA(Cys) mutants with the anticodons UCA and CUA and clarified the anticodon recognition mechanism by crystallography. The mutant SepRS-tRNA pairs may be useful for translational incorporation of O-phosphoserine into proteins in response to the stop codons UGA and UAG.

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Organizational Affiliation: 

Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
O-phosphoseryl-tRNA synthetase	B [auth A], C [auth B]	534	Archaeoglobus fulgidus	Mutation(s): 0  EC: 6.1.1 (PDB Primary Data), 6.1.1.27 (UniProt)
UniProt
Find proteins for O30126 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O30126  Go to UniProtKB:  O30126

Entity ID: 1
Molecule	Chains	Length	Organism	Image
tRNA	A [auth C]	71	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.269 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.433	α = 90
b = 148.433	β = 90
c = 151.532	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-20 
• Released Date: 2007-03-13 
Deposition Author(s): Fukunaga, R.

Revision History  

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance