3HIS

Crystal structure of Saporin-L1 from Saponaria officinalis

Summary for 3HIS

• Entry DOI: 10.2210/pdb3his/pdb
• Related: 3HIO 3HIQ 3HIT 3HIV 3HIW
• Descriptor: Vacuolar saporin (2 entities in total)
• Functional Keywords: transition state analogue, ribosome inactivating proteins, rips, hydrolase, plant defense, protein synthesis inhibitor, toxin
• Biological source: Saponaria officinalis (Common soapwort)
• Total number of polymer chains: 2
• Total formula weight: 57535.55

Authors

Ho, M.,Sturm, M.B.,Almo, S.C.,Schramm, V.L. (deposition date: 2009-05-20, release date: 2009-12-08, Last modification date: 2024-02-21)

Primary citation

Ho, M.C.,Sturm, M.B.,Almo, S.C.,Schramm, V.L.
Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins.
Proc.Natl.Acad.Sci.USA, 106:20276-20281, 2009

PubMed Abstract: Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple pi-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the pi-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common features of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H(2)O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.

PubMed: 19920175
DOI: 10.1073/pnas.0911606106

Experimental method

X-RAY DIFFRACTION (1.49 Å)