1LRA

CRYSTALLOGRAPHIC STUDY OF GLU 58 ALA RNASE T1(ASTERISK)2'-GUANOSINE MONOPHOSPHATE AT 1.9 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystallographic study of Glu58Ala RNase T1 x 2'-guanosine monophosphate at 1.9-A resolution.

Pletinckx, J.Steyaert, J.Zegers, I.Choe, H.W.Heinemann, U.Wyns, L.

(1994) Biochemistry 33: 1654-1662

  • DOI: 10.1021/bi00173a006
  • Primary Citation of Related Structures:  
    1LRA

  • PubMed Abstract: 
  • Glu58 is known to participate in phosphodiester transesterification catalyzed by the enzyme RNase T1. For Glu58 RNase T1, an altered mechanism has been proposed in which His40 replaces Glu58 as the base catalyst [Steyaert, J., Hallenga, K., Wyns, L., & Stanssens, P ...

    Glu58 is known to participate in phosphodiester transesterification catalyzed by the enzyme RNase T1. For Glu58 RNase T1, an altered mechanism has been proposed in which His40 replaces Glu58 as the base catalyst [Steyaert, J., Hallenga, K., Wyns, L., & Stanssens, P. (1990) Biochemistry 29, 9064-9072]. Glu58Ala Rnase T1 has been cocrystallized with guanosine 2'-monophosphate (2'-GMP). The crystals are of space group P2(1), with one molecule per asymmetric unit (a = 32.44 A, b = 49.64 A, c = 26.09 A, beta = 99.17 degrees). The three-dimensional structure of the enzyme was determined to a nominal resolution of 1.9 A, yielding a crystallographic R factor of 0.178 for all X-ray data. Comparison of this structure with wild-type structures leads to the following conclusions. The minor changes apparent in the tertiary structure can be explained by either the mutation of Glu58 or by the change in the space group. In the active site, the extra space available through the mutation of Glu58 is occupied by the phosphate group (after a reorientation) and by a solvent molecule replacing a carboxylate oxygen of Glu58. This solvent molecule is a candidate for participation in the altered mechanism of this mutant enzyme. Following up on a study of conserved water sites in RNase T1 crystallized in space group P2(1)2(1)2(1) [Malin, R., Zielenkiewicz, P., & Saenger, W. (1991) J. Mol. Biol. 266, 4848-4852], we investigated the hydration structure for four different packing modes of RNase T1.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • Three-Dimensional Structure of Ribonuclease T1 Complexed with Guanylyl-2',5'-Guanosine at 1.8 Angstroms Resolution
      Koepke, J., Maslowska, M., Heinemann, U., Saenger, W.
      (1989) J Mol Biol 206: 475
    • Three-Dimensional Structure of the Ribonuclease T1(Asterisk)2'-Gmp Complex at 1.9-Angstroms Resolution
      Arni, R., Heinemann, U., Tokuoka, R., Saenger, W.
      (1988) J Biol Chem 263: 15358
    • Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1(Asterisk)2'-Guanylic Acid Complex at 1.9 Angstroms Resolution
      Arni, R., Heinemann, U., Maslowska, M., Tokuoka, R., Saenger, W.
      (1987) Acta Crystallogr B 43: 549
    • The Structural and Sequence Homology of a Family of Microbial Ribonucleases
      Hill, C., Dodson, G., Heinemann, U., Saenger, W., Mitsui, Y., Nakamura, K., Borisov, S., Tischenko, G., Polyakov, K., Pavlovsky, S.
      (1983) Trends Biochem Sci (pers Ed ) 8: 364
    • Crystallographic Study of Mechanism of Ribonuclease T1-Catalysed Specific RNA Hydrolysis
      Heinemann, U., Saenger, W.
      (1983) J Biomol Struct Dyn 1: 523
    • Specific Protein-Nucleic Acid Recognition in Ribonuclease T1-2'-Guanylic Acid Complex. An X-Ray Study
      Heinemann, U., Saenger, W.
      (1982) Nature 299: 27
    • Crystallization of a Complex between Ribonuclease T1 and 2'-Guanylic Acid
      Heinemann, U., Wernitz, M., Paehler, A., Saenger, W., Menke, G., Rueterjans, H.
      (1980) Eur J Biochem 109: 109
    • Ribonuclease T1 with Free Recognition and Catalytic Site: Crystal Structure Analysis at 1.5 Angstroms
      Martinez-Oyanedel, J., Choe, H.-W., Heinemann, U., Saenger, W.
      (1991) J Mol Biol 222: 335
    • Histidine-40 of Ribonuclease T1Acts as Base Catalyst When the True Catalytic Base, Glutamic Acid 58 is Replaced by Alanine
      Steyaert, J., Hallenga, K., Wyns, L., Stanssens, P.
      (1990) Biochemistry 29: 9064

    Organizational Affiliation

    Instituut voor Moleculaire Biologie, Vrije Universiteit Brussel, Belgium.



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
Query on 2GP

Download Ideal Coordinates CCD File 
C [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]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.44α = 90
b = 49.64β = 99.75
c = 26.09γ = 90
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other