3WKS | pdb_00003wks

Crystal structure of the SepCysS-SepCysE N-terminal domain complex from

• PDB DOI: https://doi.org/10.2210/pdb3WKS/pdb

• Classification: TRANSFERASE
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-30 Released: 2014-07-30 
• Deposition Author(s): Nakazawa, Y., Asano, N., Nakamura, A., Yao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.03 Å
• R-Value Free: 
  0.240 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Ancient translation factor is essential for tRNA-dependent cysteine biosynthesis in methanogenic archaea.

Liu, Y., Nakamura, A., Nakazawa, Y., Asano, N., Ford, K.A., Hohn, M.J., Tanaka, I., Yao, M., Soll, D.

(2014) Proc Natl Acad Sci U S A 111: 10520-10525

• PubMed: 25002468 
• DOI: https://doi.org/10.1073/pnas.1411267111
• Primary Citation Related Structures: 
  3WKR, 3WKS


• PubMed Abstract: 
  

  Methanogenic archaea lack cysteinyl-tRNA synthetase; they synthesize Cys-tRNA and cysteine in a tRNA-dependent manner. Two enzymes are required: Phosphoseryl-tRNA synthetase (SepRS) forms phosphoseryl-tRNA(Cys) (Sep-tRNA(Cys)), which is converted to Cys-tRNA(Cys) by Sep-tRNA:Cys-tRNA synthase (SepCysS). This represents the ancestral pathway of Cys biosynthesis and coding in archaea. Here we report a translation factor, SepCysE, essential for methanococcal Cys biosynthesis; its deletion in Methanococcus maripaludis causes Cys auxotrophy. SepCysE acts as a scaffold for SepRS and SepCysS to form a stable high-affinity complex for tRNA(Cys) causing a 14-fold increase in the initial rate of Cys-tRNA(Cys) formation. Based on our crystal structure (2.8-Å resolution) of a SepCysS⋅SepCysE complex, a SepRS⋅SepCysE⋅SepCysS structure model suggests that this ternary complex enables substrate channeling of Sep-tRNA(Cys). A phylogenetic analysis suggests coevolution of SepCysE with SepRS and SepCysS in the last universal common ancestral state. Our findings suggest that the tRNA-dependent Cys biosynthesis proceeds in a multienzyme complex without release of the intermediate and this mechanism may have facilitated the addition of Cys to the genetic code.

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Organizational Affiliation: 
• Departments of Molecular Biophysics and Biochemistry and.
Departments of Molecular Biophysics and Biochemistry andFaculty of Advanced Life Science and.
Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.
Faculty of Advanced Life Science and.
Faculty of Advanced Life Science andGraduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan [e-mail] [e-mail].
Departments of Molecular Biophysics and Biochemistry andChemistry, Yale University, New Haven, CT 06520; and [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 119.94 kDa 
• Atom Count: 7,055 
• Modeled Residue Count: 873 
• Deposited Residue Count: 1,044 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-phospho-L-seryl-tRNA:Cys-tRNA synthase	A, B	416	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: MJ1678 EC: 2.5.1.73
UniProt
Find proteins for Q59072 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q59072  Go to UniProtKB:  Q59072

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein MJ1481	C, D	106	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: MJ1481
UniProt
Find proteins for Q58876 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58876  Go to UniProtKB:  Q58876

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.03 Å
• R-Value Free:  0.240 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.073	α = 90
b = 107.135	β = 90
c = 110.762	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-30 
Deposition Author(s): Nakazawa, Y., Asano, N., Nakamura, A., Yao, M.

Revision History  

• Version 1.0: 2014-07-30
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2022-08-24
  Changes: Database references, Derived calculations