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PDBsum entry 1n1x

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protein links
Hydrolase PDB id
1n1x
Jmol
Contents
Protein chain
119 a.a. *
Waters ×146
* Residue conservation analysis
PDB id:
1n1x
Name: Hydrolase
Title: Crystal structure analysis of the monomeric [s- carboxyamidomethyl-cys31, s-carboxyamidomethyl-cys32] bovine seminal ribonuclease
Structure: Ribonuclease, seminal. Chain: a. Synonym: seminal rnase, ribonuclease bs-1. Ec: 3.1.27.5
Source: Bos taurus. Cattle. Organism_taxid: 9913. Other_details: seminal fluid
Resolution:
1.45Å     R-factor:   0.205     R-free:   0.258
Authors: F.Sica,A.Di Fiore,A.Zagari,L.Mazzarella
Key ref:
F.Sica et al. (2003). The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative. Proteins, 52, 263-271. PubMed id: 12833549 DOI: 10.1002/prot.10407
Date:
21-Oct-02     Release date:   26-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00669  (RNS_BOVIN) -  Seminal ribonuclease
Seq:
Struc:
150 a.a.
119 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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   3 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
DOI no: 10.1002/prot.10407 Proteins 52:263-271 (2003)
PubMed id: 12833549  
 
 
The unswapped chain of bovine seminal ribonuclease: Crystal structure of the free and liganded monomeric derivative.
F.Sica, A.Di Fiore, A.Zagari, L.Mazzarella.
 
  ABSTRACT  
 
Bovine seminal ribonuclease, a homodimeric enzyme joined covalently by two interchain disulphide bonds, is an equilibrium mixture of two conformational isomers, MxM and M=M. The major form, MxM, whose crystal structure has been previously determined at 1.9 A resolution, presents the swapping of the N-terminal segments (residues 1-15) and composite active sites formed by residues of different chains. The three-dimensional domain swapping does not occur in the M=M form. The different fold of each N-terminal tail is directed by the hinge loop (residue 16-22) connecting the swapping domain to the body of the protein. Reduction and alkylation of interchain disulphide bridges produce a monomeric derivative and a noncovalent swapped dimer, which are both active. The free and nucleotide-bound forms of the monomer have been crystallized at an alkaline pH and refined at 1.45 and 1.65 A resolution, respectively. In both cases, the N-terminal fragment is folded on the main body of the protein to produce an intact active site and a chain architecture very similar to that of bovine pancreatic ribonuclease. In this new fold of the seminal chain, the hinge loop is disordered. Despite the difference between the tertiary structure of the monomer and that of the chains in the MxM form, the active sites of the two enzymes are virtually indistinguishable. Furthermore, the structure of the liganded enzyme represents the first example of a ribonuclease complex studied at an alkaline pH and provides new information on the binding of a nucleotide when the catalytic histidines are deprotonated.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Ribbon representation of the MCAM peptide fold. The carboxamidomethylated sidechains of Cys31 and Cys32 are drawn in ball-and-stick.
Figure 3.
Figure 3. The active site region in the liganded MCAM. (a) Isomorphous difference map (see text) contoured at 2.0 for 3 -UMP. (b) Isomorphous difference map contoured at 1.8 for adenosine. (c) Hydrogen-bonding network (dotted lines) between 3 -UMP and the protein matrix. (d) Superimposed structures of the 3 -UMP complexes with MCAM (cyan) and with a RNase A mutant (magenta; PDB code: 4RSK). The His119 sidechain adopts the A conformation in MCAM and the B conformation in the RNase A mutant. The H-bond distances are given in angstrom units. The figure was drawn with BOBSCRIPT[22] (a and b) and MOLSCRIPT[21] (c and d).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2003, 52, 263-271) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  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
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.  
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
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
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.