PDBsum entry 1jvt

Go to PDB code: 
protein Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
124 a.a. *
Waters ×69
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of ribonuclease a (ligand-free form)
Structure: Ribonuclease a. Chain: a, b. Synonym: rnase 1. Rnase a. Ec:
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Biol. unit: Not given
2.05Å     R-factor:   0.170     R-free:   0.240
Authors: L.Vitagliano,A.Merlino,A.Zagari,L.Mazzarella
Key ref:
L.Vitagliano et al. (2002). Reversible substrate-induced domain motions in ribonuclease A. Proteins, 46, 97. PubMed id: 11746706 DOI: 10.1002/prot.10033
31-Aug-01     Release date:   05-Jun-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
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     nucleic acid binding     7 terms  


DOI no: 10.1002/prot.10033 Proteins 46:97 (2002)
PubMed id: 11746706  
Reversible substrate-induced domain motions in ribonuclease A.
L.Vitagliano, A.Merlino, A.Zagari, L.Mazzarella.
Despite the increasing number of successful determinations of complex protein structures the understanding of their dynamics properties is still rather limited. Using X-ray crystallography, we demonstrate that ribonuclease A (RNase A) undergoes significant domain motions upon ligand binding. In particular, when cytidine 2'-monophosphate binds to RNase A, the structure of the enzyme becomes more compact. Interestingly, our data also show that these structural alterations are fully reversible in the crystal state. These findings provide structural bases for the dynamic behavior of RNase A in the binding of the substrate shown by Petsko and coworkers (Rasmussen et al. Nature 1992;357:423-424). These subtle domain motions may assume functional relevance for more complex system and may play a significant role in the cooperativity of oligomeric enzymes.
  Selected figure(s)  
Figure 1.
Figure 1. Omit F[o]-F[c] map (2.5 ) of the active site region. The electron density of catalytically important residues is shown in gray. a: Molecule A of lf-RNase A. b: Molecule A of RNase A-CMP. c: Molecule B of RNase A-CMP. d: Molecule A of rs-RNase A; a molecule of 2 -CMP in the expected position is also shown.
Figure 3.
Figure 3. C^ atom drawing of molecules A of RNase A-CMP (black line) and lf-RNase A (gray line) superimposed on the V[1] -sheet. The ligand in the RNase A-CMP complex is also shown.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2002, 46, 97-0) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20730777 B.Alakent, S.Baskan, and P.Doruker (2011).
Effect of ligand binding on the intraminimum dynamics of proteins.
  J Comput Chem, 32, 483-496.  
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
18565758 S.Yin, Y.Xie, and J.A.Loo (2008).
Mass spectrometry of protein-ligand complexes: enhanced gas-phase stability of ribonuclease-nucleotide complexes.
  J Am Soc Mass Spectrom, 19, 1199-1208.  
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.  
15772084 M.A.Seeliger, M.Spichty, S.E.Kelly, M.Bycroft, S.M.Freund, M.Karplus, and L.S.Itzhaki (2005).
Role of conformational heterogeneity in domain swapping and adapter function of the Cks proteins.
  J Biol Chem, 280, 30448-30459.  
16849163 N.J.Marianayagam, and S.E.Jackson (2005).
Native-state dynamics of the ubiquitin family: implications for function and evolution.
  J R Soc Interface, 2, 47-54.  
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
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
14645226 V.Y.Gorbatyuk, C.K.Tsai, C.F.Chang, and T.H.Huang (2004).
Effect of N-terminal and Met23 mutations on the structure and dynamics of onconase.
  J Biol Chem, 279, 5772-5780.
PDB code: 1pu3
12945053 A.Merlino, L.Vitagliano, M.A.Ceruso, and L.Mazzarella (2003).
Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin.
  Proteins, 53, 101-110.  
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
12377788 A.Russo, A.Antignani, C.Giancola, and G.D'Alessio (2002).
Engineering the refolding pathway and the quaternary structure of seminal ribonuclease by newly introduced disulfide bridges.
  J Biol Chem, 277, 48643-48649.  
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
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.