1BK7

RIBONUCLEASE MC1 FROM THE SEEDS OF BITTER GOURD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

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This is version 1.3 of the entry. See complete history


Literature

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: 253-260

  • DOI: 10.1016/s0167-4838(99)00126-0
  • Primary Citation of Related Structures:  
    1BK7

  • PubMed Abstract: 
  • The ribonuclease MC1 (RNase MC1) from seeds of bitter gourd (Momordica charantia) consists of 190 amino acid residues with four disulfide bridges and belongs to the RNase T(2) family, including fungal RNases typified by RNase Rh from Rhizopus niveus and RNase T(2) from Aspergillus oryzae ...

    The ribonuclease MC1 (RNase MC1) from seeds of bitter gourd (Momordica charantia) consists of 190 amino acid residues with four disulfide bridges and belongs to the RNase T(2) family, including fungal RNases typified by RNase Rh from Rhizopus niveus and RNase T(2) from Aspergillus oryzae. The crystal structure of RNase MC1 has been determined at 1.75 A resolution with an R-factor of 19.7% using the single isomorphous replacement method. RNase MC1 structurally belongs to the (alpha+beta) class of proteins, having ten helices (six alpha-helices and four 3(10)-helices) and eight beta-strands. When the structures of RNase MC1 and RNase Rh are superposed, the close agreement between the alpha-carbon positions for the total structure is obvious: the root mean square deviations calculated only for structurally related 151 alpha-carbon atoms of RNase MC1 and RNase Rh molecules was 1.76 A. Furthermore, the conformation of the catalytic residues His-46, Glu-105, and His-109 in RNase Rh can be easily superposed with that of the possible catalytic residues His-34, Glu-84, and His-88 in RNase MC1. This observation strongly indicates that RNase MC1 from a plant origin catalyzes RNA degradation in a similar manner as fungal RNases.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Analysis of a Plant Ribonuclease from the Seeds of the Bitter Gourd Momordica Charantia
      De, A., Funatsu, G.
      (1992) J Mol Biol 228: 1271
    • The Complete Amino Acid Sequence of Ribonuclease from the Seeds of Bitter Gourd
      Ide, H., Kimura, M., Arai, M., Funatsu, G.
      (1991) FEBS Lett 284: 161
    • The Complete Amino Acid Sequence of Ribonuclease from the Seeds of Bitter Gourd
      Ide, H., Kimura, M., Arai, M., Funatsu, G.
      (1991) FEBS Lett 289: 126

    Organizational Affiliation

    Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RIBONUCLEASE MC1)A190Momordica charantiaMutation(s): 0 
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
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.8α = 90
b = 67.97β = 90
c = 75.43γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
SHARPphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-23
    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: 2018-04-04
    Changes: Data collection