PDBsum entry: 11ba

Hydrolase

PDB id: 11ba

Contents

Protein chains

124 a.a. *

Ligands

SO4 ×3

UPA ×2

Waters ×108

* Residue conservation analysis

PDB id:

11ba

Name:

Hydrolase

Title:

Binding of a substrate analogue to a domain swapping protein complex of bovine seminal ribonuclease with uridylyl-2',5'-

Structure:

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

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Secretion: seminal fluid

Biol. unit:

Dimer (from PQS)

Resolution:

2.06Å R-factor: 0.184

Authors:

L.Vitagliano,S.Adinolfi,A.Riccio,F.Sica,A.Zagari,L.Mazzarell

Key ref:

L.Vitagliano et al. (1998). Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine. Protein Sci, 7, 1691-1699. PubMed id: 10082366 Ref: Full text

Date:

17-Mar-99 Release date: 26-Mar-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)

Full text	Protein Sci 7:1691-1699 (1998)
PubMed id: 10082366

Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine.

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

ABSTRACT

Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. The native enzyme is a mixture of two dimeric forms with distinct structural features. The most abundant form is characterized by the swapping of N-terminal fragments. In this paper, the crystal structure of the complex between the swapping dimer and uridylyl(2',5')adenosine is reported at 2.06 A resolution. The refined model has a crystallographic R-factor of 0.184 and good stereochemistry. The quality of the electron density maps enables the structure of both the inhibitor and active site residues to be unambiguously determined. The overall architecture of the active site is similar to that of RNase A. The dinucleotide adopts an extended conformation with the pyrimidine and purine base interacting with Thr45 and Asn71, respectively. Several residues (Gln11, His12, Lys41, His119, and Phe120) bind the oxygens of the phosphate group. The structural similarity of the active sites of BS-RNase and RNase A includes some specific water molecules believed to be relevant to catalytic activity. Upon binding of the dinucleotide, small but significant modifications of the tertiary and quaternary structure of the protein are observed. The ensuing correlation of these modifications with the catalytic activity of the enzyme is discussed.

Selected figure(s)

Figure 2.
Fig. 2. - 2Fc omitmapsoftheregion 16-22. (A) Subunit SA showingthe two alternativeconformationsofthe HP and B) subunit SB. The mapswerecontoured at la. Figure continues n next page.)

Figure 3.
Fig. 3. o - , omit map contoured at u of thebounddinucleotide n one of the two active ites. heelectrondensity for hesecond ite is equallywelldefined.

The above figures are reprinted by permission from the Protein Society: Protein Sci (1998, 7, 1691-1699) copyright 1998.

Figures were selected by an automated process.