PDBsum entry: 1a2w

Endonuclease

PDB id: 1a2w

Contents

Protein chains

124 a.a. *

Ligands

SO4

Metals

_CL ×2

Waters ×92

* Residue conservation analysis

PDB id:

1a2w

Name:

Endonuclease

Title:

Crystal structure of a 3d domain-swapped dimer of bovine pancreatic ribonuclease a

Structure:

Ribonuclease a. Chain: a, b. Fragment: swapped helical domain. Other_details: swapped helical domain contains residues 1- 15, hinge loops contain residues 16-22, major domain contains residues 23-124

Source:

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

Biol. unit:

Monomer (from PDB file)

Resolution:

2.10Å R-factor: 0.192 R-free: 0.256

Authors:

Y.Liu,P.J.Hart,M.P.Schlunegger,D.S.Eisenberg

Key ref:

Y.Liu et al. (1998). The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution. Proc Natl Acad Sci U S A, 95, 3437-3442. PubMed id: 9520384 DOI: 10.1073/pnas.95.7.3437

Date:

12-Jan-98 Release date: 29-Apr-98

Protein chains

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic

Seq: 150 a.a.

Struc: 124 a.a.

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 (6 terms)

DOI no: 10.1073/pnas.95.7.3437

Proc Natl Acad Sci U S A 95:3437-3442 (1998)

PubMed id: 9520384

The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution.

Y.Liu, P.J.Hart, M.P.Schlunegger, D.Eisenberg.

ABSTRACT

The dimer of bovine pancreatic ribonuclease A (RNase A) discovered by Crestfield, Stein, and Moore in 1962 has been crystallized and its structure determined and refined to a 2.1-A resolution. The dimer is 3D domain-swapped. The N-terminal helix (residues 1-15) of each subunit is swapped into the major domain (residues 23-124) of the other subunit. The dimer of bull seminal ribonuclease (BS-RNase) is also known to be domain-swapped, but the relationship of the subunits within the two dimers is strikingly different. In the RNase A dimer, the 3-stranded beta sheets of the two subunits are hydrogen-bonded at their edges to form a continuous 6-stranded sheet across the dimer interface; in the BS-RNase dimer, it is instead the two helices that abut. Whereas the BS-RNase dimer has 2-fold molecular symmetry, the two subunits of the RNase A dimer are related by a rotation of approximately 160 degrees. Taken together, these structures show that intersubunit adhesion comes mainly from the swapped helical domain binding to the other subunit in the "closed interface" but that the overall architecture of the domain-swapped oligomer depends on the interactions in the second type of interface, the "open interface." The RNase A dimer crystals take up the dye Congo Red, but the structure of a Congo Red-stained crystal reveals no bound dye molecule. Dimer formation is inhibited by excess amounts of the swapped helical domain. The possible implications for amyloid formation are discussed.

Selected figure(s)

Figure 1.
Fig. 1. Stereo view of the electron density superimposed on the model of the hinge loops of the RNase A dimer. These loops link the swapped helix (residues 1-15) to the major domain (residues 23-124). The electron density is a simulated annealing omit Fo-Fc map (32), contoured at 2.5 using the graphical program SETOR (33). Loop 1 (Upper, residues 16-22) is extended, whereas loop 2 (Lower, residues 216-222) forms a helix. These hinge loops are shown with the same orientation as those in Fig. 2C.

Figure 2.
Fig. 2. The structures of three RNase molecules, with red domains all in the same orientation. The hinge loops (residues 16-22) are shown in green. (A) The RNase A monomer (Protein Data Bank code: 1RTB) (28). The helix to be swapped (residues 1-15) is shown in blue; the major domain (residues 23-124) is shown in red. The "closed interface" is that between the blue helix and the red major domain. (B) The BS-RNase domain-swapped dimer (Protein Data Bank code: 1BSR) (2). The two intersubunit disulfide bonds are shown in yellow. The "open interface" here is between the adjacent red and blue helices. (C) The RNase A dimer. Subunit 1 (blue, residues 1-124) and subunit 2 (red, residues 201-324) are related by a ~160-degree rotation about an axis roughly perpendicular to the page. The hinge loops are in the same orientation as those in Fig. 1. Notice the 6-stranded beta-sheet formed from three strands of each subunit. The open interface here is between the adjacent red and blue strands of the beta-sheet. Notice also that the open interfaces in B and C differ but that the closed interfaces in A, B, and C are the same. Functional unit 1 (see Table 3) consists of the blue swapped helix and the red major domain. The diagrams are made with the program MOLSCRIPT (37).

Figures were selected by an automated process.