PDBsum entry 11bg

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Hydrolase PDB id
Protein chains
124 a.a. *
SO4 ×8
U2G ×4
Waters ×124
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: A potential allosteric subsite generated by domain swapping seminal ribonuclease
Structure: Protein (bovine seminal ribonuclease). Chain: a, b. Other_details: complexed with 2',5'-upg
Source: Bos taurus. Cattle. Organism_taxid: 9913. Other_details: bovine (bos taurus) seminal fluid
Biol. unit: Dimer (from PQS)
1.90Å     R-factor:   0.189    
Authors: L.Vitagliano,S.Adinolfi,F.Sica,A.Merlino,A.Zagari,L.Mazzarel
Key ref:
L.Vitagliano et al. (1999). A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease. J Mol Biol, 293, 569-577. PubMed id: 10543951 DOI: 10.1006/jmbi.1999.3158
11-Mar-99     Release date:   05-Nov-99    
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

 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: 10.1006/jmbi.1999.3158 J Mol Biol 293:569-577 (1999)
PubMed id: 10543951  
A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease.
L.Vitagliano, S.Adinolfi, F.Sica, A.Merlino, A.Zagari, L.Mazzarella.
Bovine seminal ribonuclease (BS-RNase) is a peculiar member of the pancreatic-like ribonuclease superfamily endowed with unique biological functions. It has been shown that native BS-RNase is a mixture of two distinct dimeric forms. The most abundant form is characterised by the swapping of the N-terminal helix. Kinetic studies have shown that this dimer is allosterically regulated, whereas the minor component, in which no swapping occurs, exhibits typical Michaelian kinetics. In order to correlate the catalytic properties with the structural features of BS-RNase, we have determined the crystal structure of the BS-RNase swapping dimer complexed with uridylyl(2'-5')guanosine. The structure of the complex was refined to an R value of 0.189 at 1.9 A resolution. Surprisingly, the enzyme binds four dinucleotide molecules, all in a non-productive way. In the two active sites, the guanine base is located in the subsite that is specific for pyrimidines. This unusual binding has been observed also in complexes of RNase A with guanine-containing nucleotides (retro-binding). One of the two additional dinucleotide molecules bound to the enzyme is located on the surface of the protein in a pocket generated by crystal packing; the second was found in a cavity at the interface between the two subunits of the swapping dimer. There are indications that the interface site plays a role in the allosteric regulation exhibited by BS-RNase. This finding suggests that domain swapping may not merely be a mechanism that proteins adopt for the transition from a monomeric to oligomeric state but can be used to achieve modulations in catalytic function.
  Selected figure(s)  
Figure 1.
Figure 1. Omit electron density map calculated with Fourier coefficients Fo - Fc of the dinucleotide bound at one active site contoured to 2.2s. This picture was generated using the program O (Jones et al., 1991).
Figure 6.
Figure 6. Space-filling representation of the dimer and the substrate analogue bound at the interface site.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 293, 569-577) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
18423397 A.T.Torelli, R.C.Spitale, J.Krucinska, and J.E.Wedekind (2008).
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.
  Biochem Biophys Res Commun, 371, 154-158.
PDB code: 3cqs
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
15048772 A.Merlino, L.Vitagliano, F.Sica, A.Zagari, and L.Mazzarella (2004).
Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer.
  Biopolymers, 73, 689-695.
PDB codes: 1r5c 1r5d
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.  
14755576 D.Peters, and J.Peters (2004).
The ribbon of hydrogen bonds in globular proteins. IV. The example of the papain family.
  Biopolymers, 73, 178-191.  
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
12623012 F.Rousseau, J.W.Schymkowitz, and L.S.Itzhaki (2003).
The unfolding story of three-dimensional domain swapping.
  Structure, 11, 243-251.  
12833549 F.Sica, A.Di Fiore, A.Zagari, and L.Mazzarella (2003).
The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative.
  Proteins, 52, 263-271.
PDB codes: 1n1x 1n3z
12382288 A.Merlino, L.Vitagliano, M.A.Ceruso, A.Di Nola, and L.Mazzarella (2002).
Global and local motions in ribonuclease A: a molecular dynamics study.
  Biopolymers, 65, 274-283.  
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
11856829 R.Berisio, F.Sica, V.S.Lamzin, K.S.Wilson, A.Zagari, and L.Mazzarella (2002).
Atomic resolution structures of ribonuclease A at six pH values.
  Acta Crystallogr D Biol Crystallogr, 58, 441-450.
PDB codes: 1kf2 1kf3 1kf4 1kf5 1kf7 1kf8
11344301 F.Rousseau, J.W.Schymkowitz, H.R.Wilkinson, and L.S.Itzhaki (2001).
Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues.
  Proc Natl Acad Sci U S A, 98, 5596-5601.  
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
11573096 J.W.Schymkowitz, F.Rousseau, H.R.Wilkinson, A.Friedler, and L.S.Itzhaki (2001).
Observation of signal transduction in three-dimensional domain swapping.
  Nat Struct Biol, 8, 888-892.  
11296285 N.E.Robinson, and A.B.Robinson (2001).
Prediction of protein deamidation rates from primary and three-dimensional structure.
  Proc Natl Acad Sci U S A, 98, 4367-4372.  
  10892814 L.Vitagliano, A.Merlino, A.Zagari, and L.Mazzarella (2000).
Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine.
  Protein Sci, 9, 1217-1225.
PDB codes: 1eos 1eow
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.