1DET

RIBONUCLEASE T1 CARBOXYMETHYLATED AT GLU 58 IN COMPLEX WITH 2'GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 3SYU


Literature

Crystal structure of ribonuclease T1 carboxymethylated at Glu58 in complex with 2'-GMP.

Ishikawa, K.Suzuki, E.Tanokura, M.Takahashi, K.

(1996) Biochemistry 35: 8329-8334

  • DOI: 10.1021/bi960493d
  • Primary Citation of Related Structures:  
    1DET

  • PubMed Abstract: 
  • The carboxymethylation of RNase T1 at the gamma-carboxyl group of Glu58 leads to a complete loss of the enzymatic activity while it retains substrate-binding ability. Accompanying the carboxymethylation, RNase T1 undergoes a remarkable thermal stabilization of 9 degrees C in the melting temperature (Tm) ...

    The carboxymethylation of RNase T1 at the gamma-carboxyl group of Glu58 leads to a complete loss of the enzymatic activity while it retains substrate-binding ability. Accompanying the carboxymethylation, RNase T1 undergoes a remarkable thermal stabilization of 9 degrees C in the melting temperature (Tm). In order to clarify the inactivation and stabilization mechanisms of RNase T1 by carboxymethylation, the crystal structure of carboxymethylated RNase T1 (CM-RNase T1) complexed with 2'-GMP was determined at 1.8 A resolution. The structure, including 79 water molecules and two Na+, was refined to an R factor of 0.194 with 10 354 reflections > 1 sigma (F). The carboxyl group of CM-Glu58, which locates in the active site, occupies almost the same position as the phosphate group of 2'-GMP in the crystal structure of intact RNase T1.2'-GMP complex. Therefore, the phosphate group of 2'-GMP cannot locate in the active site but protrudes toward the solvent. This forces 2'-GMP to adopt an anti form, which contrasts with the syn form in the crystal of the intact RNase T1.2'-GMP complex. The inaccessibility of the phosphate group to the active site can account for the lack of the enzymatic activity in CM-RNase T1. One of the carboxyl oxygen atoms of CM-Glu58 forms two hydrogen bonds with the side-chains of Tyr38 and His40. These hydrogen bonds are considered to mainly contribute to the higher thermal stability of CM-RNase T1. Another carboxyl oxygen atoms of CM-Glu58 is situated nearby His40 and Arg77. This may provide additional electrostatic stabilization.


    Related Citations: 
    • Three-Dimensional Structure of the Ternary Complex between Ribonuclease T1, Guanosine 3',5'-Bisphosphate and Inorganic Phosphate at 0.19 Nm Resolution
      Lenz, A., Choe, H.W., Granzin, J., Heinemann, U., Saenger, W.
      (1993) Eur J Biochem 211: 311
    • X-Ray Analysis of Cubic Crystals of the Complex Formed between Ribonuclease T1 and Guanosine-3',5'-Bisphosphate
      Lenz, A., Heinemann, U., Maslowska, M., Saenger, W.
      (1991) Acta Crystallogr B 47: 521
    • Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2'-Guanylic Acid Complex: An X-Ray Study
      Heinemann, U., Saenger, W.
      (1982) Nature 299: 27

    Organizational Affiliation

    Central Research Laboratories, Ajinomoto Company, Inc., Kawasaki, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE T1A104Aspergillus oryzaeMutation(s): 0 
EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
UniProt
Find proteins for P00651 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore P00651 
Go to UniProtKB:  P00651
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2GP (Subject of Investigation/LOI)
Query on 2GP

Download Ideal Coordinates CCD File 
D [auth A]GUANOSINE-2'-MONOPHOSPHATE
C10 H14 N5 O8 P
WTIFIAZWCCBCGE-UUOKFMHZSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGA
Query on CGA
AL-PEPTIDE LINKINGC7 H11 N O6GLU
Binding Affinity Annotations 
IDSourceBinding Affinity
2GP Binding MOAD:  1DET Kd: 5.00e+4 (nM) from 1 assay(s)
PDBBind:  1DET Kd: 5.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.69α = 90
b = 88.69β = 90
c = 88.69γ = 90
Software Package:
Software NamePurpose
WEISdata collection
PROLSQrefinement
WEISdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance