1RDS

CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of ribonuclease Ms (as a ribonuclease T1 homologue) complexed with a guanylyl-3',5'-cytidine analogue.

Nonaka, T.Nakamura, K.T.Uesugi, S.Ikehara, M.Irie, M.Mitsui, Y.

(1993) Biochemistry 32: 11825-11837

  • DOI: 10.1021/bi00095a011
  • Primary Citation of Related Structures:  
    1RDS, 1RMS

  • PubMed Abstract: 
  • A ribonuclease T1 homologue, ribonuclease Ms (RNase Ms) from Aspergillus saitoi, has been crystallized as a complex with a substrate analogue GfpC where the 2'-hydroxyl (2'-OH) group of guanosine in guanylyl-3',5'-cytidine (GpC) is replaced by the 2'-fluorine (2'-F) atom to prevent transesterification ...

    A ribonuclease T1 homologue, ribonuclease Ms (RNase Ms) from Aspergillus saitoi, has been crystallized as a complex with a substrate analogue GfpC where the 2'-hydroxyl (2'-OH) group of guanosine in guanylyl-3',5'-cytidine (GpC) is replaced by the 2'-fluorine (2'-F) atom to prevent transesterification. The crystal structure of the complex was solved at 1.8-A resolution to a final R-factor of 0.204. The role of His92 (RNase T1 numbering) as the general acid catalyst was confirmed. Of the two alternative candidates for a general base to abstract a proton from the 2'-OH group, His40 and Glu58 were found close to the 2'-F atom, making the decision between the two groups difficult. We then superposed the active site of the RNase Ms/GfpC complex with that of pancreatic ribonuclease S (RNase S) complexed with a substrate analogue UpcA, a phosphonate analogue of uridylyl-3',5'-adenosine (UpA), and found that His12 and His119 of RNase A almost exactly coincided with Glu58 and His92, respectively, of RNase Ms. Similar superposition with a prokaryotic microbial ribonuclease, RNase St [Nakamura, K. T., Iwahashi, K., Yamamoto, Y., Iitaka, Y., Yoshida, N., & Mitsui, Y. (1982) Nature 299, 564-566], also indicated Glu58 as a general base. Thus the present comparative geometrical studies consistently favor, albeit indirectly, the traditional as well as the most recent notion [Steyaert, J., Hallenga, K., Wyns, L., & Stanssens, P. (1990) Biochemistry 29, 9064-9072] that Glu58, rather than His40, must be the general base catalyst in the intact enzymes of the RNase T1 family.


    Related Citations: 
    • Three-Dimensional Structure of Ribonuclease Ms(Asterisk)3'-Guanylic Acid Complex at 2.5 Angstroms Resolution
      Nonaka, T., Mitsui, Y., Irie, M., Nakamura, K.T.
      (1991) FEBS Lett 283: 207
    • Histidine-40 of Ribonuclease T1 Acts as Base Catalyst When the True Catalytic Base, Glutamic Acid-58,is Replaced by Alanine
      Steyaert, J., Hallenga, K., Syns, L., Stanssens, P.
      (1990) Biochemistry 29: 9064
    • Crystallization of a Complex between Ribonuclease Ms and 3'-Guanylic Acid
      Nonaka, T., Mitsui, Y., Nakamura, K.T., Watanabe, H., Ohgi, K., Irie, M.
      (1989) J Mol Biol 207: 853

    Organizational Affiliation

    Department of BioEngineering, Nagaoka University of Technology, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE MSA105Aspergillus phoenicisMutation(s): 0 
EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
Find proteins for P00653 (Aspergillus phoenicis)
Explore P00653 
Go to UniProtKB:  P00653
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GPC
Query on GPC

Download Ideal Coordinates CCD File 
B [auth A]2'-FLUOROGUANYLYL-(3'-5')-PHOSPHOCYTIDINE
C19 H24 F N8 O11 P
ZSBUMMSBXYRQAK-FOJQSULLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.52α = 90
b = 60.57β = 90
c = 34.95γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other