PDBsum entry 3f8g

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Hydrolase PDB id
Protein chain
125 a.a. *
SO4 ×5
Waters ×162
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: The x-ray structure of a dimeric variant of human pancreatic ribonuclease with high cytotoxic and antitumor activities
Structure: Ribonuclease pancreatic. Chain: a, b. Synonym: rnase 1, rnase a, rnase upi-1, rib-1, hp-rnase. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: rnase1, rib1, rns1. Expressed in: escherichia coli. Expression_system_taxid: 562
2.60Å     R-factor:   0.215     R-free:   0.306
Authors: A.Merlino,G.Avella,L.Mazzarella,F.Sica
Key ref:
A.Merlino et al. (2009). Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant. Protein Sci, 18, 50-57. PubMed id: 19177350 DOI: 10.1002/pro.6
12-Nov-08     Release date:   10-Feb-09    
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Protein chains
Pfam   ArchSchema ?
P07998  (RNAS1_HUMAN) -  Ribonuclease pancreatic
156 a.a.
125 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 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   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  


DOI no: 10.1002/pro.6 Protein Sci 18:50-57 (2009)
PubMed id: 19177350  
Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant.
A.Merlino, G.Avella, S.Di Gaetano, A.Arciello, R.Piccoli, L.Mazzarella, F.Sica.
A specialized class of RNases shows a high cytotoxicity toward tumor cell lines, which is critically dependent on their ability to reach the cytosol and to evade the action of the ribonuclease inhibitor (RI). The cytotoxicity and antitumor activity of bovine seminal ribonuclease (BSRNase), which exists in the native state as an equilibrium mixture of a swapped and an unswapped dimer, are peculiar properties of the swapped form. A dimeric variant (HHP2-RNase) of human pancreatic RNase, in which the enzyme has been engineered to reproduce the sequence of BSRNase helix-II (Gln28-->Leu, Arg31-->Cys, Arg32-->Cys, and Asn34-->Lys) and to eliminate a negative charge on the surface (Glu111-->Gly), is also extremely cytotoxic. Surprisingly, this activity is associated also to the unswapped form of the protein. The crystal structure reveals that on this molecule the hinge regions, which are highly disordered in the unswapped form of BSRNase, adopt a very well-defined conformation in both subunits. The results suggest that the two hinge peptides and the two Leu28 side chains may provide an anchorage to a transient noncovalent dimer, which maintains Cys31 and Cys32 of the two subunits in proximity, thus stabilizing a quaternary structure, similar to that found for the noncovalent swapped dimer of BSRNase, that allows the molecule to escape RI and/or to enhance the formation of the interchain disulfides.
  Selected figure(s)  
Figure 1.
(A) A ribbon diagram showing the secondary structural elements in M=M-HHP2. The intersubunit disulphide bridges are drawn in ball-and-stick representation. (B) Superimposition of active site region of the two subunits of M=M-HHP2: the groups adopting a different conformation in B subunit are drawn in cyan. (C) Omit Fo-Fc map of the two hinge peptides (first subunit on the top) contoured at 3.5 [sigma](I). (D) Space-filled model of the putative noncovalent unswapped dimer obtained by reduction of intersubunit disulphide bridges of M=M-HHP2. In this representation, the two subunits are colored in cyan, the hinge peptides in blue, the two Leu28 in red, and the Cys31 and 32 of the two subunits in yellow. [Color figure can be viewed in the online issue, which is available at].
  The above figure is reprinted from an Open Access publication published by the Protein Society: Protein Sci (2009, 18, 50-57) copyright 2009.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21322759 C.Andrady, S.K.Sharma, and K.A.Chester (2011).
Antibody-enzyme fusion proteins for cancer therapy.
  Immunotherapy, 3, 193-211.  
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.  
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