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


This is version 2.0 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
  • 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 pyrimidine-adenine in RNase A ...

    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
RibonucleaseC [auth A], D [auth B]111Lithobates 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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*CP*GP*A)-3'A [auth C], B [auth D]4N/A
    Small Molecules
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    PCA
    Query on PCA
    C [auth A], D [auth B]L-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  (Full details and data files)

    • 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