7V5H

VcOrn native structure with N terminal tag

Summary for 7V5H

• Entry DOI: 10.2210/pdb7v5h/pdb
• Descriptor: Oligoribonuclease (2 entities in total)
• Functional Keywords: vcorn, active pocket, n terminal tag., hydrolase
• Biological source: Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
• Total number of polymer chains: 1
• Total formula weight: 22711.72

Authors

Zhang, J.,Zhang, Q.,Bartlam, M. (deposition date: 2021-08-17, release date: 2021-12-15, Last modification date: 2023-11-29)

Primary citation

Zhang, J.,Sun, L.,Zhang, Q.,Bartlam, M.
Crystal structure of oligoribonuclease from Vibrio cholerae O1 El Tor with bound peptide.
Acta Crystallogr.,Sect.F, 77:437-443, 2021

PubMed Abstract: Oligoribonuclease (Orn), a member of the DEDDh superfamily, can hydrolyse 2-5 nt nanoRNAs to mononucleotides. It is involved in maintaining the intracellular levels of RNA, c-di-GMP signalling and transcription initiation in many bacterial species. Here, the crystal structure of Orn from Vibrio cholerae O1 El Tor (VcOrn) is reported at a resolution of 1.7 Å. VcOrn, which consists of nine α-helices and six β-strands, crystallizes with a single monomer in the asymmetric unit but forms a homodimer via crystallographic twofold symmetry. Electron density is observed in the active pocket that corresponds to an intersubunit N-terminal expression tag with sequence GPLGSHHH. The positively charged N-terminal tag binds in the negatively charged nucleotide-binding pocket with a buried surface area of ∼500 Å. The N-terminal tag interacts with VcOrn via π-π stacking with two conserved residues involved in nucleotide binding, as well as via salt bridges and hydrogen bonds. The structure reported here reveals that the active pocket can accommodate polypeptides in addition to nucleotides, thus providing an important starting point for investigation into substrate modification and inhibitor design targeting VcOrn.

PubMed: 34866598
DOI: 10.1107/S2053230X21011043

Experimental method

X-RAY DIFFRACTION (1.7 Å)