PDBsum entry: 11bg

Hydrolase

PDB id: 11bg

Contents

Protein chains

124 a.a. *

Ligands

SO4 ×8

U2G ×4

Waters ×124

* Residue conservation analysis

PDB id:

11bg

Name:

Hydrolase

Title:

A potential allosteric subsite generated by domain swapping seminal ribonuclease

Structure:

Protein (bovine seminal ribonuclease). Chain: a, b. Other_details: complexed with 2',5'-upg

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Other_details: bovine (bos taurus) seminal fluid

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.189

Authors:

L.Vitagliano,S.Adinolfi,F.Sica,A.Merlino,A.Zagari,L.Mazzarel

Key ref:

L.Vitagliano et al. (1999). A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease. J Mol Biol, 293, 569-577. PubMed id: 10543951 DOI: 10.1006/jmbi.1999.3158

Date:

11-Mar-99 Release date: 05-Nov-99

Protein chains

P00669  (RNS_BOVIN) -  Seminal ribonuclease

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)
• Biological process: metabolic process (1 term)
• Biochemical function: catalytic activity (6 terms)

DOI no: 10.1006/jmbi.1999.3158

J Mol Biol 293:569-577 (1999)

PubMed id: 10543951

A potential allosteric subsite generated by domain swapping in bovine seminal ribonuclease.

L.Vitagliano, S.Adinolfi, F.Sica, A.Merlino, A.Zagari, L.Mazzarella.

ABSTRACT

Bovine seminal ribonuclease (BS-RNase) is a peculiar member of the pancreatic-like ribonuclease superfamily endowed with unique biological functions. It has been shown that native BS-RNase is a mixture of two distinct dimeric forms. The most abundant form is characterised by the swapping of the N-terminal helix. Kinetic studies have shown that this dimer is allosterically regulated, whereas the minor component, in which no swapping occurs, exhibits typical Michaelian kinetics. In order to correlate the catalytic properties with the structural features of BS-RNase, we have determined the crystal structure of the BS-RNase swapping dimer complexed with uridylyl(2'-5')guanosine. The structure of the complex was refined to an R value of 0.189 at 1.9 A resolution. Surprisingly, the enzyme binds four dinucleotide molecules, all in a non-productive way. In the two active sites, the guanine base is located in the subsite that is specific for pyrimidines. This unusual binding has been observed also in complexes of RNase A with guanine-containing nucleotides (retro-binding). One of the two additional dinucleotide molecules bound to the enzyme is located on the surface of the protein in a pocket generated by crystal packing; the second was found in a cavity at the interface between the two subunits of the swapping dimer. There are indications that the interface site plays a role in the allosteric regulation exhibited by BS-RNase. This finding suggests that domain swapping may not merely be a mechanism that proteins adopt for the transition from a monomeric to oligomeric state but can be used to achieve modulations in catalytic function.

Selected figure(s)

Figure 1.
Figure 1. Omit electron density map calculated with Fourier coefficients Fo - Fc of the dinucleotide bound at one active site contoured to 2.2s. This picture was generated using the program O (Jones et al., 1991).

Figure 6.
Figure 6. Space-filling representation of the dimer and the substrate analogue bound at the interface site.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 293, 569-577) copyright 1999.

Figures were selected by an automated process.