PDBsum entry 1r5d

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protein Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
124 a.a. *
Waters ×63
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: X-ray structure of bovine seminal ribonuclease swapping dimer from a new crystal form
Structure: Ribonuclease, seminal. Chain: a, b. Synonym: seminal rnase, s-rnase, ribonuclease bs-1. Ec:
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
2.50Å     R-factor:   0.185     R-free:   0.255
Authors: A.Merlino,L.Vitagliano,F.Sica,A.Zagari,L.Mazzarella
Key ref: A.Merlino et al. (2004). Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer. Biopolymers, 73, 689-695. PubMed id: 15048772
10-Oct-03     Release date:   13-Apr-04    
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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     7 terms  


Biopolymers 73:689-695 (2004)
PubMed id: 15048772  
Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer.
A.Merlino, L.Vitagliano, F.Sica, A.Zagari, L.Mazzarella.
Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. This enzyme exists as two conformational isomers with distinctive biological properties. The structure of the major isomer is characterized by the swapping of the N-terminal segment (MxM BS-RNase). In this article, the crystal structures of the ligand-free MxM BS-RNase and its complex with 2'-deoxycitidylyl(3',5')-2'-deoxyadenosine derived from isomorphous crystals have been refined. Interestingly, the comparison between this novel ligand-free form and the previously published sulfate-bound structure reveals significant differences. In particular, the ligand-free MxM BS-RNase is closer to the structure of MxM BS-RNase productive complexes than to the sulfate-bound form. These results reveal that MxM BS-RNase presents a remarkable flexibility, despite the structural constraints of the interchain disulfide bridges and the swapping of the N-terminal helices. These findings have important implications to the ligand binding mechanism of MxM BS-RNase. Indeed, a population shift rather than a substrate-induced conformational transition may occur in the MxM BS-RNase ligand binding process.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205197 N.Thiyagarajan, B.D.Smith, R.T.Raines, and K.R.Acharya (2011).
Functional and structural analyses of N-acylsulfonamide-linked dinucleoside inhibitors of RNase A.
  FEBS J, 278, 541-549.
PDB codes: 2xog 2xoi
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
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.  
18161991 E.D.Merkley, B.Bernard, and V.Daggett (2008).
Conformational changes below the Tm: molecular dynamics studies of the thermal pretransition of ribonuclease A.
  Biochemistry, 47, 880-892.  
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
16280619 T.Mamonova, B.Hespenheide, R.Straub, M.F.Thorpe, and M.Kurnikova (2005).
Protein flexibility using constraints from molecular dynamics simulations.
  Phys Biol, 2, S137-S147.  
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
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