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Hydrolase PDB id
1bk7
Jmol
Contents
Protein chain
190 a.a. *
Waters ×187
* Residue conservation analysis
PDB id:
1bk7
Name: Hydrolase
Title: Ribonuclease mc1 from the seeds of bitter gourd
Structure: Protein (ribonuclease mc1). Chain: a. Synonym: rnase mc1. Ec: 3.1.27.1
Source: Momordica charantia. Balsam pear. Organism_taxid: 3673. Tissue: seed
Resolution:
1.75Å     R-factor:   0.192     R-free:   0.241
Authors: A.Nakagawa,I.Tanaka
Key ref: A.Nakagawa et al. (1999). Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution. Biochim Biophys Acta, 1433, 253-260. PubMed id: 10446375 DOI: 10.1016/S0167-4838(99)00126-0
Date:
15-Jul-98     Release date:   23-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P23540  (RNMC_MOMCH) -  Ribonuclease MC
Seq:
Struc: 		191 a.a.
190 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.1  - Ribonuclease T(2).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     hydrolase activity     5 terms  

 

 
DOI no: 10.1016/S0167-4838(99)00126-0 Biochim Biophys Acta 1433:253-260 (1999)
PubMed id: 10446375  
 
 
Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution.
A.Nakagawa, I.Tanaka, R.Sakai, T.Nakashima, G.Funatsu, M.Kimura.
 
  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 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20810747 M.Lin, H.McRae, H.Dan, E.Tangorra, A.Laverdiere, and J.Pasick (2010).
High-resolution epitope mapping for monoclonal antibodies to the structural protein Erns of classical swine fever virus using peptide array and random peptide phage display approaches.
  J Gen Virol, 91, 2928-2940.  
18305191 S.M.Rodriguez, S.Panjikar, K.Van Belle, L.Wyns, J.Messens, and R.Loris (2008).
Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli.
  Protein Sci, 17, 681-690.
PDB code: 2z70
  17671376 M.de Leeuw, L.Roiz, P.Smirnoff, B.Schwartz, O.Shoseyov, and O.Almog (2007).
Binding assay and preliminary X-ray crystallographic analysis of ACTIBIND, a protein with anticarcinogenic and antiangiogenic activities.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 716-719.  
15274921 J.H.Gan, L.Yu, J.Wu, H.Xu, J.S.Choudhary, W.P.Blackstock, W.Y.Liu, and Z.X.Xia (2004).
The three-dimensional structure and X-ray sequence reveal that trichomaglin is a novel S-like ribonuclease.
  Structure, 12, 1015-1025.
PDB code: 1sgl
11914487 A.Rabijns, C.Verboven, P.Rougé, A.Barre, E.J.Van Damme, W.J.Peumans, and C.J.De Ranter (2002).
Structure of an RNase-related protein from Calystegia sepium.
  Acta Crystallogr D Biol Crystallogr, 58, 627-633.
PDB code: 1jy5
12239315 J.P.Langedijk, P.A.van Veelen, W.M.Schaaper, A.H.de Ru, R.H.Meloen, and M.M.Hulst (2002).
A structural model of pestivirus E(rns) based on disulfide bond connectivity and homology modeling reveals an extremely rare vicinal disulfide.
  J Virol, 76, 10383-10392.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.