Talk:SARS-CoV-2 Papain-Like protease (PLpro)
From Proteopedia
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PLpro active site is represented by C111S and contains the canonical protease catalytic triad composed by Cys111, His272, and Asp286. Differing from the dyad of Mpro, composed of Cys145 and His41. For PLpro Cys111 acts as a nucleophile and Asp286 promotes deprotonation of His272 (OSIPIUK et al., 2021). The residue C11 is 3.6 Å from H272 and the hydrogen bond donated by H272 to D286 has a 3.0 Å distance. (GAO et al., 2021) | PLpro active site is represented by C111S and contains the canonical protease catalytic triad composed by Cys111, His272, and Asp286. Differing from the dyad of Mpro, composed of Cys145 and His41. For PLpro Cys111 acts as a nucleophile and Asp286 promotes deprotonation of His272 (OSIPIUK et al., 2021). The residue C11 is 3.6 Å from H272 and the hydrogen bond donated by H272 to D286 has a 3.0 Å distance. (GAO et al., 2021) | ||
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| + | The structure of SARS-CoV-2 PLpro is a "Thumb-palm-fingers" catalytic architecture plus a ubiquitin-like domain. It has an N-terminal ubiquitin-like (Ubl, β1-3) domain composed of five β-stands, one α-helices, and one 310-helix formed by 1 to 60 residues. The catalytic domain is comprised of three characteristic domains. The first subdomain is the thumb composed of six α-helices (α2-7) and a small β-hairpin. The second subdomain is the palm (β8-13), composed of six β-strands and the catalytic residues Cys111, His272, and Asp286 located between the thumb and palm subdomains. The third and last subdomain is the fingers (or β-stranded finger), the most complex one, it has six β-strands and two α-helices and includes a zinc-binding site ("zinc ribbon" fold group) coordinated by cysteines 189, 192, 224, and 266 located on two loops of 2 β-hairpins essential for protease activity (β4-7) (OSIPIUK et al., 2021, GAO et al., 2021) | ||
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| + | The structure and conformational change of the BL2 loop located between β11-12 plays an interesting role in the substrate binding, it recognizes P2-P4 and when the ligand is not present it presents a relatively close conformation, but when it is present the loop moves to provide space to the tetrapeptide, an interesting property for a drug target. This plasticity suggests an induced-fit mechanism, making it possible for PLpro to recognize different substrates. But the BL2 loop is sensitive for the size, big substrates promote a more close configuration physically blocking the active site, a characteristic that restricts the possibilities of drugs that can be used against COVID-19 that objective contains PLpro activity (GAO et al., 2021). | ||
Revision as of 21:57, 12 December 2021
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Introduction
Papain-like protease (PLpro) from SARS-CoV-2 is a 315 amino acids long cysteine protease is found in the large multi-domain membrane-bound non-structural protein 3 (nsp3)(1945 residues) between the SARS domain (SUD/HVR) and a nucleic acid-binding domain (NAD) (Frick et al, 2020, OSIPIUK et al., 2021). It has a high percentage of cysteine residues (3.5%) (OSIPIUK et al., 2021).
SARS-CoV-2 polyprotein
The first SARS-CoV-2 open reading frame (ORF) codes for one large polyprotein, 1ab (7096 aminoacids) or 1a (4405 amino acids) built by fifteen non-coding proteins including the two proteases responsible to cleave the polyprotein: Main protease (Mpro or 3Cl-pro) and Papain-Like protease (OSIPIUK et al., 2021).
Structure
PLpro active site is represented by C111S and contains the canonical protease catalytic triad composed by Cys111, His272, and Asp286. Differing from the dyad of Mpro, composed of Cys145 and His41. For PLpro Cys111 acts as a nucleophile and Asp286 promotes deprotonation of His272 (OSIPIUK et al., 2021). The residue C11 is 3.6 Å from H272 and the hydrogen bond donated by H272 to D286 has a 3.0 Å distance. (GAO et al., 2021)
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The structure of SARS-CoV-2 PLpro is a "Thumb-palm-fingers" catalytic architecture plus a ubiquitin-like domain. It has an N-terminal ubiquitin-like (Ubl, β1-3) domain composed of five β-stands, one α-helices, and one 310-helix formed by 1 to 60 residues. The catalytic domain is comprised of three characteristic domains. The first subdomain is the thumb composed of six α-helices (α2-7) and a small β-hairpin. The second subdomain is the palm (β8-13), composed of six β-strands and the catalytic residues Cys111, His272, and Asp286 located between the thumb and palm subdomains. The third and last subdomain is the fingers (or β-stranded finger), the most complex one, it has six β-strands and two α-helices and includes a zinc-binding site ("zinc ribbon" fold group) coordinated by cysteines 189, 192, 224, and 266 located on two loops of 2 β-hairpins essential for protease activity (β4-7) (OSIPIUK et al., 2021, GAO et al., 2021)
The structure and conformational change of the BL2 loop located between β11-12 plays an interesting role in the substrate binding, it recognizes P2-P4 and when the ligand is not present it presents a relatively close conformation, but when it is present the loop moves to provide space to the tetrapeptide, an interesting property for a drug target. This plasticity suggests an induced-fit mechanism, making it possible for PLpro to recognize different substrates. But the BL2 loop is sensitive for the size, big substrates promote a more close configuration physically blocking the active site, a characteristic that restricts the possibilities of drugs that can be used against COVID-19 that objective contains PLpro activity (GAO et al., 2021).
