1Q9E

RNase T1 variant with adenine specificity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

RNase T1 Variant RV Cleaves Single-Stranded RNA after Purines Due to Specific Recognition by the Asn46 Side Chain Amide.

Czaja, R.Struhalla, M.Saenger, W.Hahn, U.

(2004) Biochemistry 43: 2854-2862

  • DOI: 10.1021/bi035961f

  • PubMed Abstract: 
  • Attempts to alter the guanine specificity of ribonuclease T1 (RNase T1) by rational or random mutagenesis have failed so far. The RNase T1 variant RV (Lys41Glu, Tyr42Phe, Asn43Arg, Tyr45Trp, and Glu46Asn) designed by combination of a random and a rat ...

    Attempts to alter the guanine specificity of ribonuclease T1 (RNase T1) by rational or random mutagenesis have failed so far. The RNase T1 variant RV (Lys41Glu, Tyr42Phe, Asn43Arg, Tyr45Trp, and Glu46Asn) designed by combination of a random and a rational mutagenesis approach, however, exhibits a stronger preference toward adenosine residues than wild-type RNase T1. Steady state kinetics of the cleavage reaction of the two dinucleoside phosphate substrates adenylyl-3',5'-cytidine and guanylyl-3',5'-cytidine revealed that the ApC/GpC ratio of the specificity coefficient (k(cat)/K(m)) was increased approximately 7250-fold compared to that of the wild-type. The crystal structure of the nucleotide-free RV variant has been refined in space group P6(1) to a crystallographic R-factor of 19.9% at 1.7 A resolution. The primary recognition site of the RV variant adopts a similar conformation as already known from crystal structures of RNase T1 not complexed to any nucleotide. Noteworthy is a high flexibility of Trp45 and Asn46 within the three individual molecules in the asymmetric unit. In addition to the kinetic studies, these data indicate the participation of Asn46 in the specific recognition of the base and therefore a specific binding of adenosine.


    Related Citations: 
    • Crystallography & NMR System
      Brunger, A.T.,Adams, P.D.,Clore, G.M.,DeLano, W.L.,Gros, P.,Grosse-Kunstleve, R.W.,Jiang, J.S.,Kuszewski, J.,Nilges, M.,Pannu, N.S.,Read, R.J.,Rice, L.M.,Simonson, T.,Warren, G.L.
      (1998) Acta Crystallogr.,Sect.D 54: 905


    Organizational Affiliation

    Department of Chemistry, Division of Biochemistry and Molecular Biology, Hamburg University, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Guanyl-specific ribonuclease T1 precursor
A, B, C
104Aspergillus oryzae (strain ATCC 42149 / RIB 40)Mutation(s): 5 
Gene Names: rntA
EC: 3.1.27.3
Find proteins for P00651 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Go to UniProtKB:  P00651
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, C
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.199 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 56.500α = 90.00
b = 56.500β = 90.00
c = 158.700γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance