4N2P

Structure of Archease from Pyrococcus horikoshii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation.

Desai, K.K.Cheng, C.L.Bingman, C.A.Phillips Jr., G.N.Raines, R.T.

(2014) Nucleic Acids Res 42: 3931-3942

  • DOI: 10.1093/nar/gkt1375
  • Primary Citation of Related Structures:  
    4N2P

  • PubMed Abstract: 
  • Archease is a 16-kDa protein that is conserved in all three domains of life. In diverse bacteria and archaea, the genes encoding Archease and the tRNA ligase RtcB are localized into an operon. Here we provide a rationale for this operon organization by showing that Archease and RtcB from Pyrococcus horikoshii function in tandem, with Archease altering the catalytic properties of the RNA ligase ...

    Archease is a 16-kDa protein that is conserved in all three domains of life. In diverse bacteria and archaea, the genes encoding Archease and the tRNA ligase RtcB are localized into an operon. Here we provide a rationale for this operon organization by showing that Archease and RtcB from Pyrococcus horikoshii function in tandem, with Archease altering the catalytic properties of the RNA ligase. RtcB catalyzes the GTP and Mn(II)-dependent joining of either 2',3'-cyclic phosphate or 3'-phosphate termini to 5'-hydroxyl termini. We find that catalytic concentrations of Archease are sufficient to activate RtcB, and that Archease accelerates both the RNA 3'-P guanylylation and ligation steps. In addition, we show that Archease can alter the NTP specificity of RtcB such that ATP, dGTP or ITP is used efficiently. Moreover, RtcB variants that have inactivating substitutions in the guanine-binding pocket can be rescued by the addition of Archease. We also present a 1.4 Å-resolution crystal structure of P. horikoshii Archease that reveals a metal-binding site consisting of conserved carboxylates located at the protein tip. Substitution of the Archease metal-binding residues drastically reduced Archease-dependent activation of RtcB. Thus, evolution has sought to co-express archease and rtcB by creating a tRNA splicing operon.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA, Department of Biochemistry and Cell Biology and Department of Chemistry, Rice University, Houston, TX 77005, USA and Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein archeaseA, B, C, D143Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH1536
Find proteins for O59205 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O59205 
Go to UniProtKB:  O59205
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.219α = 90
b = 55.386β = 91.13
c = 87.085γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
ARP/wARPmodel building
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-01
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references
  • Version 1.2: 2020-09-23
    Changes: Database references, Derived calculations, Structure summary