3N1N: Crystal Structure Of The Complex Of Type I Ribosome Inactivating Protein With Guanine At 2.2a Resolution

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 1.67A, 1.60A, 2.20A, 1.70A, 2.07A and 1.90A 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) chi(1)=-66 degrees and chi(2)=165 degrees in structures (A) and (B); (ii) chi(1)=-95 degrees and chi(2)=70 degrees in structures (C), (D) and (E); and (iii) chi(1)=-163 degrees and chi(2)=87 degrees 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.
PDB ID: 3N1NDownload
MMDB ID: 83370
PDB Deposition Date: 2010/5/16
Updated in MMDB: 2010/07
Experimental Method:
x-ray diffraction
Resolution: 2.23  Å
Source Organism:
Similar Structures:
Biological Unit for 3N1N: monomeric; determined by author and by software (PISA)
Molecular Components in 3N1N
Label Count Molecule
Protein (1 molecule)
Ribosome Inactivating Protein
Molecule annotation
Chemicals (3 molecules)
* Click molecule labels to explore molecular sequence information.

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