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

    Biology II, Ulm University, 89069 Ulm, Germany.,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.,UMR8261 (CNRS-University of Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, 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