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Catalytic Site Atlas

CSA LITERATURE entry for 2bx4

E.C. nameubiquitinyl hydrolase 1
SpeciesHuman sars coronavirus (Virus)
E.C. Number (IntEnz) 3.4.19.12
CSA Homologues of 2bx4There are 73 Homologs
CSA Entries With UniProtID P0C6X7
CSA Entries With EC Number 3.4.19.12
PDBe Entry 2bx4
PDBSum Entry 2bx4
MACiE Entry 2bx4

Literature Report

IntroductionThe SARS coronavirus main protease dimer (Mpro) is the key enzyme in the processing of the viral polyproteins and thus an attractive target for the discovery of drugs against SARS.
The SARS CoV main protease is a cysteine proteinase with a chymostrypsin-like fold. The enzyme cleaves the two overlapping translation products of the SARS coronavirus replicase gene. Hence, inhibition of Mpro leads to prevention of the proteolytic processing of coronavirus replicase polyproteins, stopping the production of of infectious virus particles.
The dimer is the enzymatically active species and the conformational state of Mpro is highly pH-sensitive due to the pH-dependence of the protonation state of two histidine residues in the substrate binding site.
MechansimThe Mpro active site is situated in a cleft between domains I (residues 8-101) and II (residues 102-184) and comprises a catalytic dyad consiting of conserved residues Cys 145 and His 41. A buried water molecule is hydrogen bonded to His 41 and is considered the third component of a catalytic triad. The fold of the Mpro enzyme at the catalytic site resembles that of the serine proteinase, chymotrypsin, but with an active-site serine-to-cysteine substitution.
The catalytic site contains a hydrogen bonded thiol....imidazole ion pair , with the uncharged thiol acting as the nucleophile, and the His 41 as a general base. The buried water molecule is found at the position normally occupied by the side chain of a third residue, and forms three hydrogen bonds to His 41, His 164 and Asp 187.
1. Deprotonation of the Cys 145 sulfhydryl by an adjacent residue with a basic side chain. The thiolate ion is stabilised through the formation of an ion pair with the neighbouring imidazolium group of His 41. A buried water molecule completes the catalytic triad by forming a hydrogen bond to the N(e2)H of His 41. This effect of this is to both stabilise the ion pair and also keep the imidazole ring of the His residue in favourable orientation. The oxyanion is stabilised by an oxyanion hole.
2. Nucleophilic attack of the anionic cysteine S (thiolate ion) on the peptide carbonyl carbon. In this step, a fragment of the substrate is released with an amine terminus, the histidine residue in the protease is restored to its deprotonated form, and a thioester intermediate linking the new carboxy-terminus of the substrate to the cysteine thiol is formed.
3. The thioester bond is subsequently hydrolysed to generate a carboxylic acid moiety on the remaining substrate fragment, whilst regenerating the free enzyme
Reaction

Catalytic Sites for 2bx4

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
CysA1453385macie:sideChainDeprotonation of Cys 145 activates it towrads nucleophilic attack of the peptide bond in the substrate. The thiolate ion is stabilised by the formation of an active site ion pair with the His 41 imidazole ring. The main chain NH of Cys 145 forms part of the oxyanion hole, which stabilises the transition state.
CysA1453385macie:mainChainAmideDeprotonation of Cys 145 activates it towrads nucleophilic attack of the peptide bond in the substrate. The thiolate ion is stabilised by the formation of an active site ion pair with the His 41 imidazole ring. The main chain NH of Cys 145 forms part of the oxyanion hole, which stabilises the transition state.
HisA413281macie:sideChainThe basic side chain of the His residue deprotonates the Cys thiol, activating it towards nucleophilic attack, The His imidazole ring forms an active site ion pair with the Cys thiol. His 41 also forms a hydrogen bond to the buried water molecule that completes that catalytic triad.

Literature References

Notes:
Tan J
pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses.
J Mol Biol 2005 354 25-40
PubMed: 16242152
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