1J1F

Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-GMP: Structural Basis for Alterations in Substrate Specificity

Numata, T.Suzuki, A.Kakuta, Y.Kimura, K.Yao, M.Tanaka, I.Yoshida, Y.Ueda, T.Kimura, M.

(2003) Biochemistry 42: 5270-5278

  • DOI: 10.1021/bi034103g
  • Primary Citation of Related Structures:  
    1J1F, 1J1G, 1UCG

  • PubMed Abstract: 
  • Ribonuclease MC1 (RNase MC1), isolated from bitter gourd seeds, is a uridine specific RNase belonging to the RNase T2 family. Mutations of Asn71 in RNase MC1 to the amino acids Thr (N71T) and Ser (N71S) in guanosine preferential RNases altered the substrate specificity from uridine specific to guanosine specific, as shown by the transphosphorylation of diribonucleoside monophosphates [Numata, T ...

    Ribonuclease MC1 (RNase MC1), isolated from bitter gourd seeds, is a uridine specific RNase belonging to the RNase T2 family. Mutations of Asn71 in RNase MC1 to the amino acids Thr (N71T) and Ser (N71S) in guanosine preferential RNases altered the substrate specificity from uridine specific to guanosine specific, as shown by the transphosphorylation of diribonucleoside monophosphates [Numata, T., et al. (2001) Biochemistry 40, 524-530]. To elucidate the structural basis for the alteration of substrate specificity, crystal structures of the RNase MC1 mutants N71T and N71S, free or complexed with 5'-GMP, were determined at resolutions higher than 2 A. In the N71T-5'-GMP and N71S-5'-GMP complexes, the guanine moiety was, as in the case of the uracil moiety bound to wild-type RNase MC1, firmly stabilized in the B2 site by an extensive network of hydrogen bonds and hydrophobic interactions. Structure comparisons showed that mutations of Asn71 to Thr or Ser cause an enlargement of the B2 site, which then make it feasible to insert a guanine base into the B2 site of mutants N71T and N71S. This binding further allows for hydrogen bonding interaction of the side chain hydroxyl groups of Thr71 or Ser71 with the N7 atom of the guanine base. The mode of guanine binding of mutants N71T and N71S was found to be essentially identical to that of a guanosine preferential RNase NW from Nicotiana glutinosa. In particular, hydrogen bonds between the N7 atom of the guanine base and the hydroxyl groups of the amino acids at position 71 (RNase MC1 numbering) were completely conserved in three guanosine preferential enzymes, thereby indicating that the hydrogen bond may play an essential role in guanine binding in guanosine preferential RNases in the RNase T2 family. Consequently, it can be concluded that amino acids at position 71 (RNase MC1 numbering) serve as one of the determinants for substrate specificity (or preference) in the RNase T2 fimily by changing the size and shape of the B2 site.


    Related Citations: 
    • Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution
      Nakagawa, A., Tanaka, I., Sakai, R., Nakashima, T., Funatsu, G., Kimura, M.
      (1999) Biochim Biophys Acta 1433: 253
    • Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity
      Suzuki, A., Yao, M., Tanaka, I., Numata, T., Kikukawa, S., Yamasaki, N., Kimura, M.
      (2000) Biochem Biophys Res Commun 275: 572
    • Amino acid residues in ribonuclease MC1 from bitter gourd seeds which are essential for uridine specificity
      Numata, T., Suzuki, A., Yao, M., Tanaka, I., Kimura, M.
      (2001) Biochemistry 40: 524

    Organizational Affiliation

    Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan. rinsei@agr.kyushu-u.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE MC1A191Momordica charantiaMutation(s): 1 
EC: 3.1.27.1 (PDB Primary Data), 4.6.1.19 (UniProt)
UniProt
Find proteins for P23540 (Momordica charantia)
Explore P23540 
Go to UniProtKB:  P23540
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23540
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5GP
Query on 5GP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.375α = 90
b = 65.777β = 90
c = 75.882γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations