5X6B | pdb_00005x6b

Crystal structure of SepCysE-SepCysS in complex with tRNACys from Methanocaldococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb5X6B/pdb
• NAKB: 5X6B

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-21 Released: 2017-12-06 
• Deposition Author(s): Chen, M., Kato, K., Yao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.261 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Models: experimental

Literature

Structural basis for tRNA-dependent cysteine biosynthesis

Chen, M., Kato, K., Kubo, Y., Tanaka, Y., Liu, Y., Long, F., Whitman, W.B., Lill, P., Gatsogiannis, C., Raunser, S., Shimizu, N., Shinoda, A., Nakamura, A., Tanaka, I., Yao, M.

(2017) Nat Commun 8: 1521-1521

• PubMed: 29142195 
• DOI: https://doi.org/10.1038/s41467-017-01543-y
• Primary Citation Related Structures: 
  5X6B, 5X6C


• PubMed Abstract: 
  

  Cysteine can be synthesized by tRNA-dependent mechanism using a two-step indirect pathway, where O-phosphoseryl-tRNA synthetase (SepRS) catalyzes the ligation of a mismatching O-phosphoserine (Sep) to tRNA ^Cys followed by the conversion of tRNA-bounded Sep into cysteine by Sep-tRNA:Cys-tRNA synthase (SepCysS). In ancestral methanogens, a third protein SepCysE forms a bridge between the two enzymes to create a ternary complex named the transsulfursome. By combination of X-ray crystallography, SAXS and EM, together with biochemical evidences, here we show that the three domains of SepCysE each bind SepRS, SepCysS, and tRNA ^Cys , respectively, which mediates the dynamic architecture of the transsulfursome and thus enables a global long-range channeling of tRNA ^Cys between SepRS and SepCysS distant active sites. This channeling mechanism could facilitate the consecutive reactions of the two-step indirect pathway of Cys-tRNA ^Cys synthesis (tRNA-dependent cysteine biosynthesis) to prevent challenge of translational fidelity, and may reflect the mechanism that cysteine was originally added into genetic code.

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Organizational Affiliation: 
• Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.
Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan.
Japan Science and Technology Agency, PRESTO, Sapporo, 060-0810, Japan.
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany.
Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, 305-0801, Japan.
Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.
Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan. [e-mail].
Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 169.88 kDa 
• Atom Count: 9,621 
• Modeled Residue Count: 1,064 
• Deposited Residue Count: 1,341 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-phospho-L-seryl-tRNA:Cys-tRNA synthase	A [auth I], B [auth J]	417	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 [auth E], D [auth F]	216	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

Entity ID: 3
Molecule	Chains	Length	Organism	Image
tRNACys	E [auth P]	75	Methanocaldococcus jannaschii DSM 2661

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.261 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.252	α = 90
b = 107.252	β = 90
c = 551.102	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Chen, M., Kato, K., Yao, M.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description