PDBsum entry: 1js0

Hydrolase

PDB-id: 1js0

Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

124 a.a. *

Ligands

SO4 ×4

Waters ×267

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1js0

Name:

Hydrolase

Title:

Crystal structure of 3d domain-swapped rnase a minor trimer

Structure:

Ribonuclease a. Chain: a, b, c. Synonym: rnase 1, rnase a, ribonuclease pancreatic. Ec: 3.1.27.5

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas

Biological unit:

Trimer (from PQS)

UniProt:

Chains A, B, C: P61823 (RNAS1_BOVIN)

Seq:

150 a.a.

Struc:

124 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.3.1.27.5   [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.

Resolution:

2.20Å

R-factor:

0.184

R-free:

0.257

Authors:

Y.Liu,G.Gotte,M.Libonati,D.Eisenberg

Key ref:

Y.Liu et al. (2002). Structures of the two 3D domain-swapped RNase A trimers.. Protein Sci, 11, 371-380. [PubMed id: 11790847] [DOI: 10.1110/ps.36602]

Date:

15-Aug-01

Release date:

13-Mar-02

Related entries:

1a2w
crystal structure of 3d domain-swapped minor dimer of rnase
a
1f0v
crystal structure of 3d domain-swapped major dimer of rnase
a

Quick_links

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Surface

Key reference

DOI no: 10.1110/ps.36602

Protein Sci 11:371-380 (2002)

PubMed id: 11790847

Structures of the two 3D domain-swapped RNase A trimers.

Y.Liu, G.Gotte, M.Libonati, D.Eisenberg.

ABSTRACT

When concentrated in mildly acidic solutions, bovine pancreatic ribonuclease (RNase A) forms long-lived oligomers including two types of dimer, two types of trimer, and higher oligomers. In previous crystallographic work, we found that the major dimeric component forms by a swapping of the C-terminal beta-strands between the monomers, and that the minor dimeric component forms by swapping the N-terminal alpha-helices of the monomers. On the basis of these structures, we proposed that a linear RNase A trimer can form from a central molecule that simultaneously swaps its N-terminal helix with a second RNase A molecule and its C-terminal strand with a third molecule. Studies by dissociation are consistent with this model for the major trimeric component: the major trimer dissociates into both the major and the minor dimers, as well as monomers. In contrast, the minor trimer component dissociates into the monomer and the major dimer. This suggests that the minor trimer is cyclic, formed from three monomers that swap their C-terminal beta-strands into identical molecules. These conclusions are supported by cross-linking of lysyl residues, showing that the major trimer swaps its N-terminal helix, and the minor trimer does not. We verified by X-ray crystallography the proposed cyclic structure for the minor trimer, with swapping of the C-terminal beta-strands. This study thus expands the variety of domain-swapped oligomers by revealing the first example of a protein that can form both a linear and a cyclic domain-swapped oligomer. These structures permit interpretation of the enzymatic activities of the RNase A oligomers on double-stranded RNA.

Selected figure(s)

Figure 1.
Fig. 1. Speculative dissociation pathways of the model of RNase A linear trimer. The proposed model of a trimer (A) can dissociate in two ways. (Top pathway) The blue subunit dissociates from the trimer and refolds to form the monomer (B). The remaining two subunits (red and green) refold to form the major dimer (C). (Bottom pathway) The red subunit dissociates from the trimer and refolds to form the monomer (B). The remaining two subunits (green and blue) refold to form the minor dimer (D). The figure was created using Raster 3D (Merritt and Bacon 1997).

Figure 6.
Fig. 6. The trap for a sulfate ion at the open interface of the RNase A minor trimer. The sulfate ion and the water molecules are in red and purple, respectively. The protein chains from the three subunits of the minor trimer are in cyan, green, and yellow, respectively. The protein atoms and residues that hydrogen bond with the water molecules and sulfate ion are indicated. There is an intricate hydrogen bond network in the trap. The waters in the trap are aligned in three layers as labeled. The structure is viewed perpendicular to the threefold axis of the minor trimer. For clarity, the sidechains of Cys 110, Glu 111, and Asn 113 are omitted. The figure was created using SETOR (Evans 1993).

The above figures are reprinted by permission from the Protein Society: Protein Sci (2002, 11, 371-380) copyright 2002.

Figures were selected by an automated process.