5MTZ

Crystal structure of a long form RNase Z from yeast


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of Trz1, the long form RNase Z from yeast.

Ma, M.Li de la Sierra-Gallay, I.Lazar, N.Pellegrini, O.Durand, D.Marchfelder, A.Condon, C.van Tilbeurgh, H.

(2017) Nucleic Acids Res. 45: 6209-6216

  • DOI: 10.1093/nar/gkx216

  • PubMed Abstract: 
  • tRNAs are synthesized as precursor RNAs that have to undergo processing steps to become functional. Yeast Trz1 is a key endoribonuclease involved in the 3΄ maturation of tRNAs in all domains of life. It is a member of the β-lactamase family of RNases ...

    tRNAs are synthesized as precursor RNAs that have to undergo processing steps to become functional. Yeast Trz1 is a key endoribonuclease involved in the 3΄ maturation of tRNAs in all domains of life. It is a member of the β-lactamase family of RNases, characterized by an HxHxDH sequence motif involved in coordination of catalytic Zn-ions. The RNase Z family consists of two subfamilies: the short (250-400 residues) and the long forms (about double in size). Short form RNase Z enzymes act as homodimers: one subunit embraces tRNA with a protruding arm, while the other provides the catalytic site. The long form is thought to contain two fused β-lactamase domains within a single polypeptide. Only structures of short form RNase Z enzymes are known. Here we present the 3.1 Å crystal structure of the long-form Trz1 from Saccharomyces cerevisiae. Trz1 is organized into two β-lactamase domains connected by a long linker. The N-terminal domain has lost its catalytic residues, but retains the long flexible arm that is important for tRNA binding, while it is the other way around in the C-terminal domain. Trz1 likely evolved from a duplication and fusion of the gene encoding the monomeric short form RNase Z.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease Z
A, B
874Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TRZ1
EC: 3.1.26.11
Find proteins for P36159 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36159
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.181 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 136.000α = 90.00
b = 136.000β = 90.00
c = 115.810γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
BUCCANEERmodel building
SHELXCDphasing
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China Scholarship CouncilChina201206180025
French Infrastructure for Integrates Structural Biology (FRISBI)FranceANR-10-INSB-05

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Structure summary
  • Version 1.2: 2018-01-31
    Type: Database references