1R5D

X-ray structure of bovine seminal ribonuclease swapping dimer from a new crystal form

Summary for 1R5D

• Entry DOI: 10.2210/pdb1r5d/pdb
• Related: 1R5C
• Descriptor: Ribonuclease, seminal (2 entities in total)
• Functional Keywords: ribonucleases, protein dynamics, protein structure-function, ligand binding, population shift, 3d domain swapping, hydrolase
• Biological source: Bos taurus (cattle)
• Cellular location: Secreted: P00669
• Total number of polymer chains: 2
• Total formula weight: 27265.28

Authors

Merlino, A.,Vitagliano, L.,Sica, F.,Zagari, A.,Mazzarella, L. (deposition date: 2003-10-10, release date: 2004-04-13, Last modification date: 2024-10-09)

Primary citation

Merlino, A.,Vitagliano, L.,Sica, F.,Zagari, A.,Mazzarella, L.
Population shift vs induced fit: The case of bovine seminal ribonuclease swapping dimer
Biopolymers, 73:689-695, 2004

PubMed Abstract: Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. This enzyme exists as two conformational isomers with distinctive biological properties. The structure of the major isomer is characterized by the swapping of the N-terminal segment (MxM BS-RNase). In this article, the crystal structures of the ligand-free MxM BS-RNase and its complex with 2'-deoxycitidylyl(3',5')-2'-deoxyadenosine derived from isomorphous crystals have been refined. Interestingly, the comparison between this novel ligand-free form and the previously published sulfate-bound structure reveals significant differences. In particular, the ligand-free MxM BS-RNase is closer to the structure of MxM BS-RNase productive complexes than to the sulfate-bound form. These results reveal that MxM BS-RNase presents a remarkable flexibility, despite the structural constraints of the interchain disulfide bridges and the swapping of the N-terminal helices. These findings have important implications to the ligand binding mechanism of MxM BS-RNase. Indeed, a population shift rather than a substrate-induced conformational transition may occur in the MxM BS-RNase ligand binding process.

PubMed: 15048772
DOI: 10.1002/bip.20016

Experimental method

X-RAY DIFFRACTION (2.5 Å)