title: Crystal structures of a type-1 ribosome inactivating protein from Momordica balsamina in the bound and unbound states.
abstract: The ribosome inactivating proteins (RIPs) of type 1 are plant toxins that eliminate adenine base selectively from the single stranded loop of rRNA. We report six crystal structures, type 1 RIP from Momordica balsamina (A), three in complexed states with ribose (B), guanine (C) and adenine (D) and two structures of MbRIP-1 when crystallized with adenosine triphosphate (ATP) (E) and 2'-deoxyadenosine triphosphate (2'-dATP) (F). These were determined at 1.67Å, 1.60Å, 2.20Å, 1.70Å, 2.07Å and 1.90Å resolutions respectively. The structures contained, (A) unbound protein molecule, (B) one protein molecule and one ribose sugar, (C) one protein molecule and one guanine base, (D) one protein molecule and one adenine base, (E) one protein molecule and one ATP-product adenine molecule and (F) one protein molecule and one 2'-dATP-product adenine molecule. Three distinct conformations of the side chain of Tyr70 were observed with (i) χ(1)=-66°and χ(2)=165° in structures (A) and (B); (ii) χ(1)=-95° and χ(2)=70° in structures (C), (D) and (E); and (iii) χ(1)=-163° and χ(2)=87° in structure (F). The conformation of Tyr70 in (F) corresponds to the structure of a conformational intermediate. This is the first structure which demonstrates that the slow conversion of DNA substrates by RIPs can be trapped during crystallization.
authors.affiliation: Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
authors.forename: Gajraj Singh
authors.initials: GS
authors.lastname: Kushwaha
authors.forename: Nisha
authors.initials: N
authors.lastname: Pandey
authors.forename: Mau
authors.initials: M
authors.lastname: Sinha
authors.forename: S Baskar
authors.initials: SB
authors.lastname: Singh
authors.forename: Punit
authors.initials: P
authors.lastname: Kaur
authors.forename: Sujata
authors.initials: S
authors.lastname: Sharma
authors.forename: Tej P
authors.initials: TP
authors.lastname: Singh
mesh_terms: D000225:Adenine / Q000737:chemistry; D000255:Adenosine Triphosphate / Q000737:chemistry; D000595:Amino Acid Sequence; D000818:Animals; D020134:Catalytic Domain; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D003838:Deoxyadenine Nucleotides / Q000737:chemistry; D006147:Guanine / Q000737:chemistry; D018054:Hydrobromic Acid; D008958:Models, Molecular; D008969:Molecular Sequence Data; D029775:Momordica; D010940:Plant Proteins / Q000737:chemistry*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D012329:RNA, Bacterial / Q000737:chemistry; D012335:RNA, Ribosomal / Q000737:chemistry; D051381:Rats; D012266:Ribose / Q000737:chemistry; D054789:Ribosome Inactivating Proteins, Type 1 / Q000737:chemistry*; D012270:Ribosomes / Q000737:chemistry; D040681:Structural Homology, Protein
chemical_list: D003838:Deoxyadenine Nucleotides; D010940:Plant Proteins; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D054789:Ribosome Inactivating Proteins, Type 1; D018054:Hydrobromic Acid; D006147:Guanine; D012266:Ribose; D000255:Adenosine Triphosphate; D000225:Adenine; C026600:2'-deoxyadenosine triphosphate