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PDBsum entry 1h8x

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protein Protein-protein interface(s) links
Hydrolase PDB id
1h8x
Jmol
Contents
Protein chain
126 a.a. *
Waters ×340
* Residue conservation analysis
PDB id:
1h8x
Name: Hydrolase
Title: Domain-swapped dimer of a human pancreatic ribonuclease variant
Structure: Ribonuclease 1. Chain: a, b. Fragment: rnase 1, hp-rnase. Engineered: yes. Mutation: yes. Other_details: residie 100 is a formilmethionine (fme)
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: pancreas. Plasmid: pm8. Gene: pm8. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: synthetic gene
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.196     R-free:   0.242
Authors: A.Canals,J.Pous,A.Guasch,A.Benito,M.Ribo,M.Vilanova,M.Coll
Key ref:
A.Canals et al. (2001). The structure of an engineered domain-swapped ribonuclease dimer and its implications for the evolution of proteins toward oligomerization. Structure, 9, 967-976. PubMed id: 11591351 DOI: 10.1016/S0969-2126(01)00659-1
Date:
16-Feb-01     Release date:   14-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07998  (RNAS1_HUMAN) -  Ribonuclease pancreatic
Seq:
Struc:
156 a.a.
126 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 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   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
DOI no: 10.1016/S0969-2126(01)00659-1 Structure 9:967-976 (2001)
PubMed id: 11591351  
 
 
The structure of an engineered domain-swapped ribonuclease dimer and its implications for the evolution of proteins toward oligomerization.
A.Canals, J.Pous, A.Guasch, A.Benito, M.Ribó, M.Vilanova, M.Coll.
 
  ABSTRACT  
 
BACKGROUND: Domain swapping has been proposed as a mechanism that explains the evolution from monomeric to oligomeric proteins. Bovine and human pancreatic ribonucleases are monomers with no biological properties other than their RNA cleavage ability. In contrast, the closely related bovine seminal ribonuclease is a natural domain-swapped dimer that has special biological properties, such as cytotoxicity to tumour cells. Several recombinant ribonuclease variants are domain-swapped dimers, but a structure of this kind has not yet been reported for the human enzyme. RESULTS: The crystal structure at 2 A resolution of an engineered ribonuclease variant called PM8 reveals a new kind of domain-swapped dimer, based on the change of N-terminal domains between the two subunits. The swapping is fastened at both hinge peptides by the newly introduced Gln101, involved in two intermolecular hydrogen bonds and in a stacking interaction between residues of different chains. Two antiparallel salt bridges and water-mediated hydrogen bonds complete a new interface between subunits, while the hinge loop becomes organized in a 3(10) helix structure. CONCLUSIONS: Proteins capable of domain swapping may quickly evolve toward an oligomeric form. As shown in the present structure, a single residue substitution reinforces the quaternary structure by forming an open interface. An evolutionary advantage derived from the new oligomeric state will fix the mutation and favour others, leading to a more extended complementary dimerization surface, until domain swapping is no longer necessary for dimer formation. The newly engineered swapped dimer reported here follows this hypothetical pathway for the rapid evolution of proteins.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Structure of the Hinge Peptide and Interaction with Gln101Stereo views of (a) the hinge peptide in chain A forming a 3[10] helix structure and (b) the H bonds and stacking interactions between Gln101 and residues Pro19 and Ser20 (see text). The final sA 2F[o] - F[c] electron density maps (contoured at 1.0 s) and the refined model are presented in both images. Red dashed lines indicate hydrogen bonds. Chains A and B are colored green and purple, respectively

 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 967-976) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21087800 Y.Yu, and S.Lutz (2011).
Circular permutation: a different way to engineer enzyme structure and function.
  Trends Biotechnol, 29, 18-25.  
  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
18478031 C.S.Weirich, J.P.Erzberger, and Y.Barral (2008).
The septin family of GTPases: architecture and dynamics.
  Nat Rev Mol Cell Biol, 9, 478-489.  
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.  
17295322 L.Lin, H.Nakano, S.Nakamura, S.Uchiyama, S.Fujimoto, S.Matsunaga, Y.Kobayashi, T.Ohkubo, and K.Fukui (2007).
Crystal structure of Pyrococcus horikoshii PPC protein at 1.60 A resolution.
  Proteins, 67, 505-507.
PDB code: 2dt4
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.  
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.  
15995211 C.Montella, L.Bellsolell, R.Pérez-Luque, J.Badía, L.Baldoma, M.Coll, and J.Aguilar (2005).
Crystal structure of an iron-dependent group III dehydrogenase that interconverts L-lactaldehyde and L-1,2-propanediol in Escherichia coli.
  J Bacteriol, 187, 4957-4966.
PDB codes: 2bi4 2bl4
16096724 M.Amani, A.A.Moosavi-Movahedi, G.Floris, S.Longu, A.Mura, S.Z.Moosavi-Nejad, A.A.Saboury, and F.Ahmad (2005).
Comparative study of the conformational lock, dissociative thermal inactivation and stability of euphorbia latex and lentil seedling amine oxidases.
  Protein J, 24, 183-191.  
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.  
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
14622261 C.Ercole, F.Avitabile, P.Del Vecchio, O.Crescenzi, T.Tancredi, and D.Picone (2003).
Role of the hinge peptide and the intersubunit interface in the swapping of N-termini in dimeric bovine seminal RNase.
  Eur J Biochem, 270, 4729-4735.  
12382322 C.E.Morris (2002).
How did cells get their size?
  Anat Rec, 268, 239-251.  
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
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.