1M07

RESIDUES INVOLVED IN THE CATALYSIS AND BASE SPECIFICITY OF CYTOTOXIC RIBONUCLEASE FROM BULLFROG (RANA CATESBEIANA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Residues involved in the catalysis, base specificity, and cytotoxicity of ribonuclease from Rana catesbeiana based upon mutagenesis and X-ray crystallography

Leu, Y.-J.Chern, S.-S.Wang, S.-C.Hsiao, Y.-Y.Amiraslanov, I.Liaw, Y.-C.Liao, Y.-D.

(2003) J.Biol.Chem. 278: 7300-7309

  • DOI: 10.1074/jbc.M206701200

  • PubMed Abstract: 
  • The Rana catesbeiana (bullfrog) ribonucleases, which belong to the RNase A superfamily, exert cytotoxicity toward tumor cells. RC-RNase, the most active among frog ribonucleases, has a unique base preference for pyrimidine-guanine rather than pyrimid ...

    The Rana catesbeiana (bullfrog) ribonucleases, which belong to the RNase A superfamily, exert cytotoxicity toward tumor cells. RC-RNase, the most active among frog ribonucleases, has a unique base preference for pyrimidine-guanine rather than pyrimidine-adenine in RNase A. Residues of RC-RNase involved in base specificity and catalytic activity were determined by site-directed mutagenesis, k(cat)/K(m) analysis toward dinucleotides, and cleavage site analysis of RNA substrate. The results show that Pyr-1 (N-terminal pyroglutamate), Lys-9, and Asn-38 along with His-10, Lys-35, and His-103 are involved in catalytic activity, whereas Pyr-1, Thr-39, Thr-70, Lys-95, and Glu-97 are involved in base specificity. The cytotoxicity of RC-RNase is correlated, but not proportional to, its catalytic activity. The crystal structure of the RC-RNase.d(ACGA) complex was determined at 1.80 A resolution. Residues Lys-9, His-10, Lys-35, and His-103 interacted directly with catalytic phosphate at the P(1) site, and Lys-9 was stabilized by hydrogen bonds contributed by Pyr-1, Tyr-28, and Asn-38. Thr-70 acts as a hydrogen bond donor for cytosine through Thr-39 and determines B(1) base specificity. Interestingly, Pyr-1 along with Lys-95 and Glu-97 form four hydrogen bonds with guanine at B(2) site and determine B(2) base specificity.


    Related Citations: 
    • PURIFICATION AND CLONING OF CYTOTOXIC RIBONUCLEASE FROM RANA CATESBEIANA (BULLFROG)
      Liao, Y.D.,Huang, H.C.,Leu, Y.J.,Wei, C.W.,Tang, P.C.,Wang, S.C.
      (2000) Nucleic Acids Res. 28: 4097
    • THE CRYSTAL STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTE OF RANA CATESBEIANA
      Leu, Y.-J.,Chern, S.-S.,Wang, S.-C.,Hsiao, Y.-Y.,Amiraslanov, I.R.,Liaw, Y.-C.,Liao, Y.-D.
      () TO BE PUBLISHED --: --
    • THE SECONDARY STRUCTURE OF A PYRIMIDINE-GUANINE SEQUENCE-SPECIFIC RIBONUCLEASE POSSESSING CYTOTOXIC ACTIVITY FROM THE OOCYTE OF RANA CATESBEIANA
      Chen, C.,Hom, K.,Huang, R.F.,Chou, P.J.,Liao, Y.D.,Huang, T.
      (1996) J.BIOMOL.NMR 8: 331
    • THE RANA CATESBEIANA RCR GENE ENCODING A CYTOTOXIC RIBONUCLEASE : TISSUE DISTRIBUTION, CLONING, PURIFICATION, CYTOTOXICITY, AND ACTIVE RESIDUES FOR RNASE ACTIVITY
      Huang, H.C.,Wang, S.C.,Leu, Y.J.,Lu, S.C.,Liao, Y.D.
      (1998) J.Biol.Chem. 273: 6395
    • THE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTE OF RANA CATESBEIANA (BULLFROG)
      Chang, C.F.,Chen, C.,Chen, Y.C.,Hom, K.,Huang, R.F.,Huang, T.H.
      (1998) J.Mol.Biol. 283: 231


    Organizational Affiliation

    Institute of Biomedical Sciences and the Institute of Molecular Biology, Academia Sinica, Taipei 115, and the Department of Life Science, National Tsing-Hua University, Hsin-Chu 300, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease
A, B
111Lithobates catesbeianaGene Names: RCR
EC: 3.1.27.-
Find proteins for P11916 (Lithobates catesbeiana)
Go to UniProtKB:  P11916
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*CP*GP*A)-3'C,D4N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 28.629α = 90.00
b = 53.566β = 98.31
c = 72.203γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-21
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-11-19
    Type: Other