1M07

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report



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
  • Primary Citation of Related Structures:  
    1M07

  • 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: 
    • 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 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
    • 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
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RibonucleaseAB111Lithobates catesbeianusMutation(s): 0 
Gene Names: RCR
EC: 3.1.27.5 (PDB Primary Data), 3.1.27 (UniProt)
Find proteins for P11916 (Lithobates catesbeianus)
Explore P11916 
Go to UniProtKB:  P11916
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*CP*GP*A)-3'C, D4N/A
    Small Molecules
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    PCA
    Query on PCA
    A,BL-PEPTIDE LINKINGC5 H7 N O3GLN
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.80 Å
    • R-Value Free: 0.228 
    • R-Value Work: 0.189 
    • R-Value Observed: 0.227 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 28.629α = 90
    b = 53.566β = 98.31
    c = 72.203γ = 90
    Software Package:
    Software NamePurpose
    CNSrefinement
    ADSCdata collection
    SCALEPACKdata scaling
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2003-01-21
      Type: Initial release
    • Version 1.1: 2008-04-28
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2014-11-19
      Changes: Other
    • Version 2.0: 2019-12-25
      Changes: Database references, Derived calculations, Polymer sequence