3C89

Crystal structure of the catalytic domain of botulinum neurotoxin serotype A with inhibitory peptide RRGM

Summary for 3C89

• Entry DOI: 10.2210/pdb3c89/pdb
• Related: 3BWI 3C88 3C8A 3C8B
• Descriptor: Botulinum neurotoxin A light chain, Inhibitor peptide RRGM, ZINC ION, ... (5 entities in total)
• Functional Keywords: botulinum neurotoxin type a, catalytic domain, endopeptidase, bio-warfare agent, metalloprotease, protease, secreted, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Clostridium botulinum
• Cellular location: Botulinum neurotoxin A light chain: Secreted. Botulinum neurotoxin A heavy chain: Secreted: A5HZZ9
• Total number of polymer chains: 2
• Total formula weight: 50530.25

Authors

Kumaran, D.,Swaminathan, S. (deposition date: 2008-02-11, release date: 2008-04-22, Last modification date: 2023-08-30)

Primary citation

Kumaran, D.,Rawat, R.,Ludivico, M.L.,Ahmed, S.A.,Swaminathan, S.
Structure- and Substrate-based Inhibitor Design for Clostridium botulinum Neurotoxin Serotype A
J.Biol.Chem., 283:18883-18891, 2008

PubMed Abstract: The seven antigenically distinct serotypes of Clostridium botulinum neurotoxins cleave specific soluble N-ethylmaleimide-sensitive factor attachment protein receptor complex proteins and block the release of neurotransmitters that cause flaccid paralysis and are considered potential bioweapons. Botulinum neurotoxin type A is the most potent among the clostridial neurotoxins, and to date there is no post-exposure therapeutic intervention available. To develop inhibitors leading to drug design, it is imperative that critical interactions between the enzyme and the substrate near the active site are known. Although enzyme-substrate interactions at exosites away from the active site are mapped in detail for botulinum neurotoxin type A, information about the active site interactions is lacking. Here, we present the crystal structures of botulinum neurotoxin type A catalytic domain in complex with four inhibitory substrate analog tetrapeptides, viz. RRGC, RRGL, RRGI, and RRGM at resolutions of 1.6-1.8 A. These structures show for the first time the interactions between the substrate and enzyme at the active site and delineate residues important for substrate stabilization and catalytic activity. We show that OH of Tyr(366) and NH(2) of Arg(363) are hydrogen-bonded to carbonyl oxygens of P1 and P1' of the substrate analog and position it for catalytic activity. Most importantly, the nucleophilic water is replaced by the amino group of the N-terminal residue of the tetrapeptide. Furthermore, the S1' site is formed by Phe(194), Thr(215), Thr(220), Asp(370), and Arg(363). The K(i) of the best inhibitory tetrapeptide is 157 nm.

PubMed: 18434312
DOI: 10.1074/jbc.M801240200

Experimental method

X-RAY DIFFRACTION (1.58 Å)