PDBsum entry 3bco

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Hydrolase PDB id
Protein chains
124 a.a. *
Waters ×87
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of the swapped form of p19a/l28q/n67d bs- rnase
Structure: Seminal ribonuclease. Chain: a, b. Synonym: seminal rnase, s-rnase, ribonuclease bs-1. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Gene: srn. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.25Å     R-factor:   0.218     R-free:   0.250
Authors: A.Merlino,C.Ercole,D.Picone,E.Pizzo,L.Mazzarella,F.Sica
Key ref:
A.Merlino et al. (2008). The buried diversity of bovine seminal ribonuclease: shape and cytotoxicity of the swapped non-covalent form of the enzyme. J Mol Biol, 376, 427-437. PubMed id: 18164315 DOI: 10.1016/j.jmb.2007.11.008
13-Nov-07     Release date:   12-Feb-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P00669  (RNS_BOVIN) -  Seminal ribonuclease
150 a.a.
124 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     8 terms  


DOI no: 10.1016/j.jmb.2007.11.008 J Mol Biol 376:427-437 (2008)
PubMed id: 18164315  
The buried diversity of bovine seminal ribonuclease: shape and cytotoxicity of the swapped non-covalent form of the enzyme.
A.Merlino, C.Ercole, D.Picone, E.Pizzo, L.Mazzarella, F.Sica.
Bovine seminal ribonuclease exists in the native state as an equilibrium mixture of a swapped and an unswapped dimer. The molecular envelope and the exposed surface of the two isomers are practically indistinguishable and their diversity is almost completely buried in the interior of the protein. Surprisingly, the cytotoxic and antitumor activity of the enzyme is a peculiar property of the swapped dimer. This buried diversity comes into light in the reducing environment of the cytosol, where the unswapped dimer dissociates into monomers, whereas the swapped one generates a metastable dimeric form (NCD-BS) with a quaternary assembly that allows the molecule to escape the protein inhibitor of ribonucleases. The stability of this quaternary shape was mainly attributed to the combined presence of Pro19 and Leu28. We have prepared and fully characterized by X-ray diffraction the double mutant P19A/L28Q (PALQ) of the seminal enzyme. While the swapped and unswapped forms of the mutant have structures very similar to that of the corresponding wild-type forms, the non-covalent form (NCD-PALQ) adopts an opened quaternary structure, different from that of NCD-BS. Moreover, model building clearly indicates that NCD-PALQ can be easily sequestered by the protein inhibitor. In agreement with these results, cytotoxic assays have revealed that PALQ has limited activity, whereas the single mutants P19A and L28Q display cytotoxic activity against malignant cells almost as large as the wild-type enzyme. The significant increase in the antitumor activity, brought about by the substitution of just two residues in going from the double mutant to the wild-type enzyme, suggests a new strategy to improve this important biological property by strengthening the interface that stabilizes the quaternary structure of NCD-BS.
  Selected figure(s)  
Figure 5.
Fig. 5. NCD-PALQ quaternary structure (green) compared with that of NCD-BS (red). One subunit was used for the superimposition of the dimers. The side chains of residues in position 28 are shown as ball and stick drawings.
Figure 6.
Fig. 6. Stereo view of the complex between (a) NCD-PALQ and RI, (b) NCD-BS and RI. In NCD-PALQ, the carboxyamidomethylated side chains of Cys31 and Cys32 and the Gln28 are shown as ball-and stick drawings.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 376, 427-437) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21322759 C.Andrady, S.K.Sharma, and K.A.Chester (2011).
Antibody-enzyme fusion proteins for cancer therapy.
  Immunotherapy, 3, 193-211.  
21122069 C.Giancola, C.Ercole, I.Fotticchia, R.Spadaccini, E.Pizzo, G.D'Alessio, and D.Picone (2011).
Structure-cytotoxicity relationships in bovine seminal ribonuclease: new insights from heat and chemical denaturation studies on variants.
  FEBS J, 278, 111-122.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20136512 J.F.Collet, and J.Messens (2010).
Structure, function, and mechanism of thioredoxin proteins.
  Antioxid Redox Signal, 13, 1205-1216.  
  19177350 A.Merlino, G.Avella, S.Di Gaetano, A.Arciello, R.Piccoli, L.Mazzarella, and F.Sica (2009).
Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant.
  Protein Sci, 18, 50-57.
PDB code: 3f8g
19280639 A.Merlino, I.Russo Krauss, M.Perillo, C.A.Mattia, C.Ercole, D.Picone, A.Vergara, and F.Sica (2009).
Toward an antitumor form of bovine pancreatic ribonuclease: The crystal structure of three noncovalent dimeric mutants.
  Biopolymers, 91, 1029-1037.
PDB codes: 3fkz 3fl0 3fl1 3fl3
19603492 A.Zagari (2009).
The four cysteines ring motif in proteins.
  Biopolymers, 91, 1048-1055.  
19263489 C.Ercole, R.A.Colamarino, E.Pizzo, F.Fogolari, R.Spadaccini, and D.Picone (2009).
Comparison of the structural and functional properties of RNase A and BS-RNase: A stepwise mutagenesis approach.
  Biopolymers, 91, 1009-1017.  
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.