5X6B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.596 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • DOI: 10.1038/s41467-017-01543-y
  • Primary Citation of Related Structures:  

  • 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 tRNACys followed by the conversion of tRNA-bounde ...

    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 tRNACys 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 tRNACys, respectively, which mediates the dynamic architecture of the transsulfursome and thus enables a global long-range channeling of tRNACys between SepRS and SepCysS distant active sites. This channeling mechanism could facilitate the consecutive reactions of the two-step indirect pathway of Cys-tRNACys synthesis (tRNA-dependent cysteine biosynthesis) to prevent challenge of translational fidelity, and may reflect the mechanism that cysteine was originally added into genetic code.


    Organizational Affiliation

    Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-phospho-L-seryl-tRNA:Cys-tRNA synthase
I, J
417Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
EC: 2.5.1.73
Find proteins for Q59072 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q59072
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein MJ1481
E, F
216Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Find proteins for Q58876 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58876
Entity ID: 3
MoleculeChainsLengthOrganism
tRNACysP75Methanocaldococcus jannaschii DSM 2661
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
I, J
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.596 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.225 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 107.252α = 90.00
b = 107.252β = 90.00
c = 551.102γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release