Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.55 kDa 
• Atom Count: 1656 
• Modelled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique protein chains: 1

1UCA

Crystal structure of the Ribonuclease MC1 from bitter gourd seeds complexed with 2'-UMP

• PDB DOI: 10.2210/pdb1UCA/pdb

• Classification: HYDROLASE
• Organism(s): Momordica charantia
• Mutation(s): No 


• Deposited: 2003-04-10 Released: 2003-04-29 
• Deposition Author(s): Suzuki, A., Yao, M., Tanaka, I., Numata, T., Kikukawa, S., Yamasaki, N., Kimura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.213 
• R-Value Work: 0.194 

Literature

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: 572-576

• PubMed: 10964705 
• DOI: 10.1006/bbrc.2000.3318
• Primary Citation of Related Structures:  
  1UCA, 1UCC


• PubMed Abstract: 
  

Ribonuclease MC1 (RNase MC1) isolated from seeds of bitter gourd (Momordica charantia) consists of 190 amino acids and is characterized by a preferential cleavage at the 5'-side of uridine. This uridine specificity distinguishes RNase MC1 from other enzymes belonging to the RNase T2 family. The three-dimensional structures of RNase MC1, in a complex with either 2'-UMP or 3'-UMP, were determined at 1.48 and 1.77 A resolutions, respectively. The side chains of Gln9 and Asn71 interact with O4 and N3, respectively, of the uracil base by hydrogen bondings. In addition, the uracil base is sandwiched by the hydrophobic side chains of Leu73 and Phe80. Compared with these amino acid residues and corresponding residues in RNases in the RNase T2 family, Gln9 and Phe80 are highly conserved in the RNases in T2 family, while Asn71 and Leu73 in RNase MC1 are variant in sequences. It is thus likely that interactions of the side chains of Asn71 and Leu73 with the uracil base are responsible for the absolute uridine specificity of RNase MC1. Site-directed mutagenesis experiments showed that replacement of Asn by Thr decreased both the catalytic efficiency and the binding affinity by 2.3- and 7.0-fold, respectively, and substitution of Leu73 for Ala predominantly decreased the binding affinity by 14. 5-fold, compared with findings in case of wild-type RNase MC1. It is thus demonstrated that Asn71 and Leu73 play an essential role in uridine preference for RNase MC1.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease MC	A	190	Momordica charantia	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U2P	B [auth A]	PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER C9 H13 N2 O9 P HQIDPEYTETUCNF-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.213 
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.81	α = 90
b = 67.94	β = 90
c = 75.61	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-10 
• Released Date: 2003-04-29 
Deposition Author(s): Suzuki, A., Yao, M., Tanaka, I., Numata, T., Kikukawa, S., Yamasaki, N., Kimura, M.

Revision History  

• Version 1.0: 2003-04-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance