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Hydrolase(phosphoric diester,RNA) PDB id
1bsr
Jmol
Contents
Protein chains
124 a.a. *
Ligands
SO4 ×7
Waters ×113
* Residue conservation analysis
PDB id:
1bsr
Name: Hydrolase(phosphoric diester,RNA)
Title: Bovine seminal ribonuclease structure at 1.9 angstroms resol
Structure: Bovine seminal ribonuclease. Chain: a, b. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
1.90Å     R-factor:   0.177    
Authors: L.Mazzarella
Key ref:
L.Mazzarella et al. (1993). Bovine seminal ribonuclease: structure at 1.9 A resolution. Acta Crystallogr D Biol Crystallogr, 49, 389-402. PubMed id: 15299514 DOI: 10.1107/S0907444993003403
Date:
28-Apr-93     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00669  (RNS_BOVIN) -  Seminal ribonuclease
Seq:
Struc: 		150 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.5  - 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   1 term 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1107/S0907444993003403 Acta Crystallogr D Biol Crystallogr 49:389-402 (1993)
PubMed id: 15299514  
 
 
Bovine seminal ribonuclease: structure at 1.9 A resolution.
L.Mazzarella, S.Capasso, D.Demasi, G.Di Lorenzo, C.A.Mattia, A.Zagari.
 
  ABSTRACT  
 
The crystal structure of bovine seminal ribonuclease, a homodimeric enzyme closely related to pancreatic ribonuclease, has been refined at a nominal resolution of 1.9 A employing data collected on an electronic area detector. The final model consists of two chains containing 1990 non-H atoms, seven sulfate anions and 113 water molecules per asymmetric unit. The unit-cell parameters are a = 36.5 (1), b = 66.7 (1) and c = 107.5 (2) A, space group P22(1)2(1). The R factor is 0.177 for 16 492 reflections in the resolution range 6.0-1.9 A and the deviations from ideal values of bond lengths and bond angles are 0.020 A and 3.7 degrees, respectively. The molecule is formed by two pancreatic like chains, which have their N-terminal segments interchanged so that each active site is formed by residues from both subunits. The two chains are related by a non-crystallographic twofold symmetry and are covalently linked by two consecutive disulfide bridges, which form an unusual sixteen-membered ring across the dimer interface. The deviations from the molecular symmetry, the hydration shell and the sulfate-binding sites are also discussed in relation to the known structure of the pancreatic enzyme.
 
  Selected figure(s)  
 
Figure 13.
Fig. 13. Histogram showing the distribution of the thermal factors for water molecules. 		Figure 14.
Fig. 14. A group of highly conserved water molecules for S1. Broken lines indicate hydrogen bonds involving water molecules. The same pattern is also observed for $2 and for RNase A.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 389-402) copyright 1993.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
21050179 E.Pizzo, A.Merlino, M.Turano, I.Russo Krauss, F.Coscia, A.Zanfardino, M.Varcamonti, A.Furia, C.Giancola, L.Mazzarella, F.Sica, and G.D'Alessio (2010).
A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish.
  Biochem J, 433, 345-355.
PDB codes: 3ljd 3lje 3ln8
  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.  
19825371 W.Ardelt, B.Ardelt, and Z.Darzynkiewicz (2009).
Ribonucleases as potential modalities in anticancer therapy.
  Eur J Pharmacol, 625, 181-189.  
18673284 T.J.Rutkoski, and R.T.Raines (2008).
Evasion of ribonuclease inhibitor as a determinant of ribonuclease cytotoxicity.
  Curr Pharm Biotechnol, 9, 185-189.  
17044066 B.L.Simons, H.Kaplan, S.M.Fournier, T.Cyr, and M.A.Hefford (2007).
A novel cross-linked RNase A dimer with enhanced enzymatic properties.
  Proteins, 66, 183-195.  
16519682 M.Rodríguez, A.Benito, M.Ribó, and M.Vilanova (2006).
Characterization of the dimerization process of a domain-swapped dimeric variant of human pancreatic ribonuclease.
  FEBS J, 273, 1166-1176.  
16933205 M.V.Anissimova, W.O.Baek, V.P.Varlamov, N.T.Mrabet, and M.A.Vijayalakshmi (2006).
Natural and chemically induced oligomeric ribonucleases: structural study by immobilized metal ion affinity electrophoresis and their functional relationship.
  J Mol Recognit, 19, 287-298.  
16739492 P.V.Zelenikhin, G.V.Cherepnev, F.Kern, and O.N.Ilinskaia (2006).
Binase does not induce polyclonal T-cell response.
  Dokl Biol Sci, 407, 195-197.  
15728177 A.Merlino, L.Mazzarella, A.Carannante, A.Di Fiore, A.Di Donato, E.Notomista, and F.Sica (2005).
The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase mutants.
  J Biol Chem, 280, 17953-17960.
PDB codes: 1yv4 1yv6 1yv7
15596505 A.Merlino, M.A.Ceruso, L.Vitagliano, and L.Mazzarella (2005).
Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A.
  Biophys J, 88, 2003-2012.  
15647261 D.Picone, A.Di Fiore, C.Ercole, M.Franzese, F.Sica, S.Tomaselli, and L.Mazzarella (2005).
The role of the hinge loop in domain swapping. The special case of bovine seminal ribonuclease.
  J Biol Chem, 280, 13771-13778.
PDB codes: 1y92 1y94
16045769 G.N.Hatzopoulos, D.D.Leonidas, R.Kardakaris, J.Kobe, and N.G.Oikonomakos (2005).
The binding of IMP to ribonuclease A.
  FEBS J, 272, 3988-4001.
PDB codes: 1z6d 1z6s
15041676 A.Merlino, L.Vitagliano, M.A.Ceruso, and L.Mazzarella (2004).
Dynamic properties of the N-terminal swapped dimer of ribonuclease A.
  Biophys J, 86, 2383-2391.  
15192098 F.Sica, A.Di Fiore, A.Merlino, and L.Mazzarella (2004).
Structure and stability of the non-covalent swapped dimer of bovine seminal ribonuclease: an enzyme tailored to evade ribonuclease protein inhibitor.
  J Biol Chem, 279, 36753-36760.
PDB code: 1tq9
14622261 C.Ercole, F.Avitabile, P.Del Vecchio, O.Crescenzi, T.Tancredi, and D.Picone (2003).
Role of the hinge peptide and the intersubunit interface in the swapping of N-termini in dimeric bovine seminal RNase.
  Eur J Biochem, 270, 4729-4735.  
  12623012 F.Rousseau, J.W.Schymkowitz, and L.S.Itzhaki (2003).
The unfolding story of three-dimensional domain swapping.
  Structure, 11, 243-251.  
12966091 G.Gotte, M.Libonati, and D.V.Laurents (2003).
Glycosylation and specific deamidation of ribonuclease B affect the formation of three-dimensional domain-swapped oligomers.
  J Biol Chem, 278, 46241-46251.  
11746706 L.Vitagliano, A.Merlino, A.Zagari, and L.Mazzarella (2002).
Reversible substrate-induced domain motions in ribonuclease A.
  Proteins, 46, 97.
PDB codes: 1jvt 1jvu 1jvv
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
  11709166 J.W.O'Neill, D.E.Kim, K.Johnsen, D.Baker, and K.Y.Zhang (2001).
Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus.
  Structure, 9, 1017-1027.
PDB codes: 1k50 1k51 1k52 1k53
  11106177 C.Park, and R.T.Raines (2000).
Dimer formation by a "monomeric" protein.
  Protein Sci, 9, 2026-2033.  
10713119 R.Piccoli, C.De Lorenzo, F.Dal Piaz, P.Pucci, and G.D'Alessio (2000).
Trypsin sheds light on the singular case of seminal RNase, a dimer with two quaternary conformations.
  J Biol Chem, 275, 8000-8006.  
  10997903 Y.Bourne, M.H.Watson, A.S.Arvai, S.L.Bernstein, S.I.Reed, and J.A.Tainer (2000).
Crystal structure and mutational analysis of the Saccharomyces cerevisiae cell cycle regulatory protein Cks1: implications for domain swapping, anion binding and protein interactions.
  Structure, 8, 841-850.
PDB code: 1qb3
10091597 E.H.Vatzaki, S.C.Allen, D.D.Leonidas, K.Trautwein-Fritz, J.Stackhouse, S.A.Benner, and K.R.Acharya (1999).
Crystal structure of a hybrid between ribonuclease A and bovine seminal ribonuclease--the basic surface, at 2.0 A resolution.
  Eur J Biochem, 260, 176-182.
PDB code: 1b6v
10583363 G.D'alessio (1999).
Evolution of oligomeric proteins. The unusual case of a dimeric ribonuclease.
  Eur J Biochem, 266, 699-708.  
10393896 R.Piccoli, S.Di Gaetano, C.De Lorenzo, M.Grauso, C.Monaco, D.Spalletti-Cernia, P.Laccetti, J.Cinátl, J.Matousek, and G.D'Alessio (1999).
A dimeric mutant of human pancreatic ribonuclease with selective cytotoxicity toward malignant cells.
  Proc Natl Acad Sci U S A, 96, 7768-7773.  
10090281 V.Gupta, S.Muyldermans, L.Wyns, and D.M.Salunke (1999).
The crystal structure of recombinant rat pancreatic RNase A.
  Proteins, 35, 1.
PDB code: 1rra
  9865960 C.De Lorenzo, F.Dal Piaz, R.Piccoli, A.Di Maro, P.Pucci, and G.D'Alessio (1998).
Selective and asymmetric action of trypsin on the dimeric forms of seminal RNase.
  Protein Sci, 7, 2653-2658.  
  10082366 L.Vitagliano, S.Adinolfi, A.Riccio, F.Sica, A.Zagari, and L.Mazzarella (1998).
Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine.
  Protein Sci, 7, 1691-1699.
PDB code: 11ba
9893950 V.Cafaro, A.Bracale, F.Formiggini, E.Notomista, G.D'Alessio, and A.Di Donato (1998).
Protein engineering of ribonucleases.
  Biochimie, 80, 905-909.  
9520384 Y.Liu, P.J.Hart, M.P.Schlunegger, and D.Eisenberg (1998).
The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution.
  Proc Natl Acad Sci U S A, 95, 3437-3442.
PDB code: 1a2w
  9083108 M.Bergdoll, M.H.Remy, C.Cagnon, J.M.Masson, and P.Dumas (1997).
Proline-dependent oligomerization with arm exchange.
  Structure, 5, 391-401.  
  8805536 N.Khazanovich, K.Bateman, M.Chernaia, M.Michalak, and M.James (1996).
Crystal structure of the yeast cell-cycle control protein, p13suc1, in a strand-exchanged dimer.
  Structure, 4, 299-309.
PDB code: 1puc
7744072 A.D'Ursi, H.Oschkinat, C.Cieslar, D.Picone, G.D'Alessio, P.Amodeo, and P.A.Temussi (1995).
Assignment and secondary-structure determination of monomeric bovine seminal ribonuclease employing computer-assisted evaluation of homonuclear three-dimensional 1H-NMR spectra.
  Eur J Biochem, 229, 494-502.  
  8520472 A.Di Donato, V.Cafaro, I.Romeo, and G.D'Alessio (1995).
Hints on the evolutionary design of a dimeric RNase with special bioactions.
  Protein Sci, 4, 1470-1477.  
7731986 K.Mazzarella, L.Vitagliano, and A.Zagari (1995).
Swapping structural determinants of ribonucleases: an energetic analysis of the hinge peptide 16-22.
  Proc Natl Acad Sci U S A, 92, 3799-3803.  
  8580836 M.J.Bennett, M.P.Schlunegger, and D.Eisenberg (1995).
3D domain swapping: a mechanism for oligomer assembly.
  Protein Sci, 4, 2455-2468.  
8159715 M.J.Bennett, S.Choe, and D.Eisenberg (1994).
Domain swapping: entangling alliances between proteins.
  Proc Natl Acad Sci U S A, 91, 3127-3131.  
8016107 R.J.Youle, Y.N.Wu, S.M.Mikulski, K.Shogen, R.S.Hamilton, D.Newton, G.D'Alessio, and M.Gravell (1994).
RNase inhibition of human immunodeficiency virus infection of H9 cells.
  Proc Natl Acad Sci U S A, 91, 6012-6016.  
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 codes are shown on the right.