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: 1.9 Å

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


  • 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., ...

    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: 
    • 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
    • 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
    • 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
    • Crystallographic Study of Mechanism of Ribonuclease T1-Catalysed Specific RNA Hydrolysis
      Heinemann, U.,Saenger, W.
      (1983) J.Biomol.Struct.Dyn. 1: 523
    • 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.,Sect.B 43: 549
    • 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
    • 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
    • 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

    Instituut voor Moleculaire Biologie, Vrije Universiteit Brussel, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE T1
A
104Aspergillus oryzae (strain ATCC 42149 / RIB 40)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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
2GP
Query on 2GP

Download SDF File 
Download CCD File 
A
GUANOSINE-2'-MONOPHOSPHATE
C10 H14 N5 O8 P
WTIFIAZWCCBCGE-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 32.440α = 90.00
b = 49.640β = 99.75
c = 26.090γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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