1RMS

CRYSTAL STRUCTURES OF RIBONUCLEASE MS COMPLEXED WITH 3'-GUANYLIC ACID A GP*C ANALOGUE, 2'-DEOXY-2'-FLUOROGUANYLYL-3',5'-CYTIDINE

DOI: 10.2210/pdb1RMS/pdb

Classification: HYDROLASE(ENDORIBONUCLEASE)
Organism(s): Aspergillus phoenicis
Mutation(s): No

Deposited: 1991-12-02 Released: 1992-07-15
Deposition Author(s): Nonaka, T., Mitsui, Y., Nakamura, K.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Observed: 0.185

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

PubMed: 8218254 Search on PubMed
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. 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 2.5A Resolution
Nonaka, T., Mitsui, Y., Irie, M., Nakamura, K.T.
(1991) FEBS Lett 283: 207

Crystallization of a Complex between Ribonuclease Ms and 3'-Guanylic Acid
Mitsui, T.Nonaka Y., Nakamura, K.T., Watanabe, H., Ohgi, K., Irie, M.
(1989) J Mol Biol 207: 853

Three-Dimensional Structure of the Ribonuclease T1(Asterisk)2'-Gmp Complex at 1.9-A Resolution
Arni, R., Heinemann, U., Tokuoka, R., Saenger, W.
(1988) J Biol Chem 263: 15358

Organizational Affiliation:

Department of BioEngineering, Nagaoka University of Technology, Japan.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE MS	A	105	Aspergillus phoenicis	Mutation(s): 0 EC: 3.1.4.23 (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
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3GP Query on 3GP Download Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	GUANOSINE-3'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P ZDPUTNZENXVHJC-UUOKFMHZSA-N		Ligand Interaction