1RCN

CRYSTAL STRUCTURE OF THE RIBONUCLEASE A D(APTPAPAPG) COMPLEX : DIRECT EVIDENCE FOR EXTENDED SUBSTRATE RECOGNITION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition.

Fontecilla-Camps, J.C.de Llorens, R.le Du, M.H.Cuchillo, C.M.

(1994) J Biol Chem 269: 21526-21531

  • DOI: 10.2210/pdb1rcn/pdb
  • Primary Citation of Related Structures:  
    1RCN

  • PubMed Abstract: 
  • The crystal structure of the complex between ribonuclease A and d(ApTpApApG) has been solved by x-ray crystallography using the molecular replacement method. The model includes, besides the enzyme, the d(ApTpApA) 5'-segment (A1T2A3A4) and 68 solvent molecules ...

    The crystal structure of the complex between ribonuclease A and d(ApTpApApG) has been solved by x-ray crystallography using the molecular replacement method. The model includes, besides the enzyme, the d(ApTpApA) 5'-segment (A1T2A3A4) and 68 solvent molecules. The R-factor for the strongest 87% of the measured data that partially extends to 2.3-A resolution is 0.207. The A1 position is well defined; the 5'-O of the deoxyribose establishes a hydrogen bond with a solvent molecule that is, in turn, bonded to the epsilon-amino group of Lys66. The base (B0 site) is well ordered; it interacts with a symmetry-related enzyme molecule. In the crystal, the phosphate group at the p0 site has no direct charge compensation. However, Lys66 is not too far, and, in solution, it could bind to it. The T2 (R1B1p1) site is occupied as in other complex structures, and it is defined by very good electron density. The A3 site shows that the adenine moiety interacts with Asn71 and Gln69 and that the phosphate at p2 forms a salt bridge with Lys7. The most consistent model for the base of A4 (B3), both in terms of electron density and stereochemistry, shows that it forms a hydrogen bond with Gln69 and a g-g- array with the base at B2. The stacking of B2 and B3 may be a general feature of the binding of polyribonucleotides to ribonuclease A. The side chains of Gln69, Asn71, and Glu111 may thus constitute a malleable binding site capable of establishing various hydrogen bonds depending on the nature of the stacked bases. There is no evidence for the 3' G5 site in the electron density map.


    Organizational Affiliation

    Laboratoire de Cristallographie et de Cristallogénèse des Protéines, Institut de Biologie Structurale, Grenoble, France.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RIBONUCLEASE A (E.C.3.1.27.5))B [auth E]124Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*TP*AP*A)-3')A [auth D]4N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.32 Å
    • R-Value Work: 0.172 
    • R-Value Observed: 0.172 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 71.86α = 90
    b = 43.2β = 90
    c = 43.83γ = 90
    Software Package:
    Software NamePurpose
    X-PLORrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1994-09-30
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance