4OJM

Crystal structure of a C-terminally truncated CYT-18 protein including N-terminal residues


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.171 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

An in Vitro Peptide Complementation Assay for CYT-18-Dependent Group I Intron Splicing Reveals a New Role for the N-Terminus.

Geng, C.Paukstelis, P.J.

(2014) Biochemistry 53: 1311-1319

  • DOI: https://doi.org/10.1021/bi401614h
  • Primary Citation of Related Structures:  
    4OJM

  • PubMed Abstract: 

    The mitochondrial tyrosyl tRNA synthetase from Neurospora crassa (CYT-18 protein) is a bifunctional group I intron splicing cofactor. CYT-18 is capable of splicing multiple group I introns from a wide variety of sources by stabilizing the catalytically active intron structures. CYT-18 and mt TyrRSs from related fungal species have evolved to assist in group I intron splicing in part by the accumulation of three N-terminal domain insertions. Biochemical and structural analysis indicate that the N-terminal insertions serve primarily to create a structure-stabilizing scaffold for critical tertiary interactions between the two major RNA domains of group I introns. Previous studies concluded that the primarily α-helical N-terminal insertion, H0, contributes to protein stability and is necessary for splicing the N. crassa ND1 intron but is dispensable for splicing the N. crassa mitochondrial LSU intron. Here, we show that CYT-18 with a complete H0 deletion retains residual ND1 intron splicing activity and that addition of the missing N-terminus in trans is capable of restoring a significant portion of its splicing activity. The development of this peptide complementation assay has allowed us to explore important characteristics of the CYT-18/group I intron interaction including the stoichiometry of H0 in intron splicing and the importance of specific H0 residues. Evaluation of truncated H0 peptides in this assay and a re-examination of the CYT-18 crystal structure suggest a previously unknown structural role of the first five N-terminal residues of CYT-18. These residues interact directly with another splicing insertion, making H0 a central structural element responsible for connecting all three N-terminal splicing insertions.


  • Organizational Affiliation

    University of Maryland , Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, College Park, Maryland 20742, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine--tRNA ligase, mitochondrialA [auth X]392Neurospora crassa OR74AMutation(s): 0 
Gene Names: cyt-18B18P24.070NCU03030
EC: 6.1.1.1
UniProt
Find proteins for P12063 (Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987))
Explore P12063 
Go to UniProtKB:  P12063
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12063
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TYR
Query on TYR

Download Ideal Coordinates CCD File 
B [auth X]TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.88α = 90
b = 73.21β = 111.35
c = 56.79γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description