5X6C

Crystal structure of SepRS-SepCysE from Methanocaldococcus jannaschii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.101 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.185 

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 tRNA <sup>Cys </sup> followed by the conversion o ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-phosphoserine--tRNA(Cys) ligase
A, B
553Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: sepS
EC: 6.1.1.27
Find proteins for Q59054 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q59054
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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.101 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.185 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 279.821α = 90.00
b = 279.821β = 90.00
c = 279.821γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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