About: Crystal Structures Reveal an Induced-fit Binding of a Substrate-like Aza-peptide Epoxide to SARS Coronavirus Main Peptidase

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About: Crystal Structures Reveal an Induced-fit Binding of a Substrate-like Aza-peptide Epoxide to SARS Coronavirus Main Peptidase Goto Sponge NotDistinct Permalink

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Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Crystal Structures Reveal an Induced-fit Binding of a Substrate-like Aza-peptide Epoxide to SARS Coronavirus Main Peptidase
Creator	Liu, Jie Lee, Ting-Wai Cherney, Maia Eltis, Lindsay James, Karen James, Michael Powers, James
Source	Elsevier; Medline; PMC
abstract	Abstract The SARS coronavirus main peptidase (SARS-CoV Mpro) plays an essential role in the life-cycle of the virus and is a primary target for the development of anti-SARS agents. Here, we report the crystal structure of Mpro at a resolution of 1.82 Å, in space group P21 at pH 6.0. In contrast to the previously reported structure of Mpro in the same space group at the same pH, the active sites and the S1 specificity pockets of both protomers in the structure of Mpro reported here are in the catalytically competent conformation, suggesting their conformational flexibility. We report two crystal structures of Mpro having an additional Ala at the N terminus of each protomer (M+A(-1) pro), both at a resolution of 2.00 Å, in space group P43212: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). In the unbound form, the active sites and the S1 specificity pockets of both protomers of M+A(-1) pro are observed in a collapsed (catalytically incompetent) conformation; whereas they are in an open (catalytically competent) conformation in the APE-bound form. The observed conformational flexibility of the active sites and the S1 specificity pockets suggests that these parts of Mpro exist in dynamic equilibrium. The structural data further suggest that the binding of APE to Mpro follows an induced-fit model. The substrate likely also binds in an induced-fit manner in a process that may help drive the catalytic cycle.
has issue date	2007-02-23(xsd:dateTime)
bibo:doi	10.1016/j.jmb.2006.11.078
bibo:pmid	17196984
has license	els-covid
sha1sum (hex)	0f351d5be0c24d0b2e5dc0b8d941ce63bcbda449
schema:url	https://doi.org/10.1016/j.jmb.2006.11.078
resource representing a document's title	Crystal Structures Reveal an Induced-fit Binding of a Substrate-like Aza-peptide Epoxide to SARS Coronavirus Main Peptidase
has PubMed Central identifier	PMC7094323
has PubMed identifier	17196984
schema:publication	Journal of Molecular Biology
resource representing a document's body	covid:0f351d5be0c24d0b2e5dc0b8d941ce63bcbda449#body_text
is schema:about of	named entity 'essential' named entity 'pro' named entity 'active sites' named entity 'space group' named entity 'incompetent' named entity 'conformational' named entity 'conformation' named entity 'space group' named entity 'Structures' covid:arg/0f351d5be0c24d0b2e5dc0b8d941ce63bcbda449 named entity 'collapsed' named entity 'contrast' named entity 'pro' named entity 'catalytic cycle' named entity 'process' named entity 'observed' named entity 'active sites' named entity 'APE' named entity 'space group' named entity 'pro' named entity 'SARS Coronavirus' named entity 'dynamic equilibrium' named entity 'conformational flexibility' named entity 'catalytic cycle' named entity 'crystal structures' named entity 'virus' named entity 'SARS-CoV' named entity 'SARS' named entity 'Coronavirus' named entity 'atom' named entity 'protomer' named entity 'protomer' named entity 'conjugation' named entity 'protomers' named entity 'space group' named entity 'atom' named entity 'Gln' named entity 'space group' named entity 'deprotonation' named entity 'π-stacking' named entity 'Gln' named entity 'conformational flexibility' named entity 'replicase' named entity 'reversible inhibitor' named entity 'wild-type' named entity 'active sites' named entity 'protomers' named entity 'protomers' named entity 'SARS-CoV' named entity 'discovery 20' named entity 'significant difference' named entity 'imidazole ring' named entity 'cysteine peptidase' named entity 'pH 8' named entity 'peptidomimetic' named entity 'crystal structures' named entity 'SARS' named entity 'atom' named entity 'porcine transmissible gastroenteritis coronavirus' named entity 'atom' named entity 'protomer' named entity 'pH 8' named entity 'phenyl ring' named entity 'protomer' named entity 'atom' named entity 'imidazole ring' named entity 'side-chain' named entity 'SARS-CoV' named entity 'atom' named entity 'Cys' named entity 'water molecule' named entity 'conformationally' named entity 'protomer' named entity 'inhibitory activity' named entity 'conformations'

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