PDBsum entry: 1h8x

Hydrolase

PDB id: 1h8x

Contents

Protein chains

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

Protein chains

P07998  (RNAS1_HUMAN) -  Ribonuclease pancreatic

Seq: 156 a.a.

Struc: 126 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.27.5 - Pancreatic ribonuclease.
• 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 

• Cellular component: extracellular region (1 term)
• Biochemical function: nucleic acid binding (5 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.