title: Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins.
abstract: NanoRNase (Nrn) specifically degrades nucleoside 3',5'-bisphosphate and the very short RNA, nanoRNA, during the final step of mRNA degradation. The crystal structure of Nrn in complex with a reaction product GMP was determined. The overall structure consists of two domains that are interconnected by a flexible loop and form a cleft. Two Mn²⁺ ions are coordinated by conserved residues in the DHH motif of the N-terminal domain. GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables us to predict the substrate-bound form of Nrn as well as other DHH/DHHA1 phosphoesterase family proteins.
authors.affiliation: Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.
authors.forename: Yuri
authors.initials: Y
authors.lastname: Uemura
authors.forename: Noriko
authors.initials: N
authors.lastname: Nakagawa
authors.forename: Taisuke
authors.initials: T
authors.lastname: Wakamatsu
authors.forename: Kwang
authors.initials: K
authors.lastname: Kim
authors.forename: Gaetano Thomas
authors.initials: GT
authors.lastname: Montelione
authors.forename: John Francis
authors.initials: JF
authors.lastname: Hunt
authors.forename: Seiki
authors.initials: S
authors.lastname: Kuramitsu
authors.forename: Ryoji
authors.initials: R
authors.lastname: Masui
mesh_terms: D020816:Amino Acid Motifs; D001426:Bacterial Proteins / Q000737:chemistry*; D001439:Bacteroides / Q000201:enzymology*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000378:metabolism; D008024:Ligands; D008345:Manganese / Q000737:chemistry; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry; D012333:RNA, Messenger / Q000378:metabolism; D012260:Ribonucleases / Q000737:chemistry*; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D008024:Ligands; D012333:RNA, Messenger; D008345:Manganese; D012313:RNA; D012260:Ribonucleases; C583898:nanoRNase, Bacteroides fragilis
keywords: Crystal structure; DHH/DHHA1 family; Nrn; RecJ exonuclease of T. thermophilus HB8; adenosine 3′,5′-bisphosphate; bfNrn; guanosine 3′,5′-bisphosphate; mRNA degradation; nanoRNA; nanoRNase; nanoRNase of Bacteroides fragilis; nanoRNase of Staphylococcus haemolyticus; nanoRNase of Thermus thermophilus HB8; pAp; pGp; shNrn; ttNrn; ttRecJ