5X6B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

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:  
    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) ...

    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.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
O-phospho-L-seryl-tRNA:Cys-tRNA synthaseA [auth I],
B [auth J]
417Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: MJ1678pscS
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59072
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein MJ1481C [auth E],
D [auth F]
216Methanocaldococcus jannaschii DSM 2661Mutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58876
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
tRNACysE [auth P]75Methanocaldococcus jannaschii DSM 2661
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A [auth I],
B [auth J]
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.252α = 90
b = 107.252β = 90
c = 551.102γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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