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Catalytic Site Atlas

CSA LITERATURE entry for 1pxv

E.C. nameCYSTEINE PROTEASE
SpeciesStaphylococcus aureus (Bacteria)
E.C. Number (IntEnz) 3.4.22.-
CSA Homologues of 1pxv1x9y,1y4h,
CSA Entries With UniProtID
CSA Entries With EC Number 3.4.22.-
PDBe Entry 1pxv
PDBSum Entry 1pxv
MACiE Entry 1pxv

Literature Report

IntroductionStaphopain B is a possible virulence factor from Staphylococcus aureus, and is a member of the papain superfamily of cysteine proteases. Staphostatin B is a specific inhibitor of staphopain B encoded in the same operon. Inhibition of staphopains is a target for treatment of antibiotic-resistant S. aureus infections.
1PXV uses the C243A mutant to deactivate the enzyme in order to obtain the crystal structure.
MechansimCys 243 and His 340 are held as a thiolate-imidazolium ion pair. The thiolate is nucleophilic and attacks the electrophilic scissile amide bond of the substrate to form a tetrahedral intermediate. This intermediate collapses, with His 340 acting as a general acid to the leaving group, and results in acylation of Cys 243.
Deacylation is by hydrolysis, with His 340 acting as a general base to activate the water molecule. Water is a nucleophile and attacks the electrophilic thioester group of the Cys 243-substrate bond, forming a tetrahedral intermediate. This intermediate collapses, with the cationic His 340 stabilising the Cys 243 thiolate leaving group, and the formation of the product.
Asn 360 is hydrogen bonded to His 340; Asn stabilises the cationic form of His and increases the basicity of the neutral form of His.
Gln 237 acts as an oxyanion hole and acts by stabilising the negative charge of the transition states and tetrahedral intermediates via its side chain amide. By homology with other papain-type enzymes, the main chain amide of Cys 243 is assumed to also form part of the oxyanion hole.

Catalytic Sites for 1pxv

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA340340macie:sideChain Increases the nucleophilicity of Cys 243 by ionising it and holding it in an ion pair. Acts as a general acid to the amine product leaving group. Activates water by acting as a general base.
AlaA243243macie:sideChain Cys 243 is held as a thiolate and is the nucleophile that attacks the scissile amide electrophile, forming a tetrahedral intermediate. Collapse of this intermediate results in acylation of Cys 243. After hydrolysis of the acyl-enzyme, Cys 243 is the leaving group. In papain-type enzymes, the backbone amide of the nucleophilic Cys is part of the oxyanion hole, stabilising transition states and intermediates.
AlaA243243macie:mainChainAmide Cys 243 is held as a thiolate and is the nucleophile that attacks the scissile amide electrophile, forming a tetrahedral intermediate. Collapse of this intermediate results in acylation of Cys 243. After hydrolysis of the acyl-enzyme, Cys 243 is the leaving group. In papain-type enzymes, the backbone amide of the nucleophilic Cys is part of the oxyanion hole, stabilising transition states and intermediates.
GlnA237237macie:mainChainAmideThe backbone NH acts as an oxyanion hole to stabilise transition states and intermediates by hydrogen bonding.
AsnA360360macie:sideChainStabilises the cationic form of His 340 and increases the basicity of the neutral form of His 340, by hydrogen bonding via the O of its side chain.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisB340340macie:sideChain Increases the nucleophilicity of Cys 243 by ionising it and holding it in an ion pair. Acts as a general acid to the amine product leaving group. Activates water by acting as a general base.
AlaB243243macie:sideChain Cys 243 is held as a thiolate and is the nucleophile that attacks the scissile amide electrophile, forming a tetrahedral intermediate. Collapse of this intermediate results in acylation of Cys 243. After hydrolysis of the acyl-enzyme, Cys 243 is the leaving group. In papain-type enzymes, the backbone amide of the nucleophilic Cys is part of the oxyanion hole, stabilising transition states and intermediates.
AlaB243243macie:mainChainAmide Cys 243 is held as a thiolate and is the nucleophile that attacks the scissile amide electrophile, forming a tetrahedral intermediate. Collapse of this intermediate results in acylation of Cys 243. After hydrolysis of the acyl-enzyme, Cys 243 is the leaving group. In papain-type enzymes, the backbone amide of the nucleophilic Cys is part of the oxyanion hole, stabilising transition states and intermediates.
GlnB237237macie:mainChainAmideThe backbone NH acts as an oxyanion hole to stabilise transition states and intermediates by hydrogen bonding.
AsnB360360macie:sideChainStabilises the cationic form of His 340 and increases the basicity of the neutral form of His 340, by hydrogen bonding via the O of its side chain.

Literature References

Notes:The crystal structure of mature staphopain B has not yet been crystallised. Staphopain B is a papain-type cysteine protease. As for all papain-type enzymes, the exact mechanism is debatable and may proceed either via tetrahedral oxyanion intermediates, or as a concerted mechanism with simultaneous making and breaking of bonds - there is some computer modelling evidence to suggest the latter.
Filipek R
Prostaphopain B structure: a comparison of proregion-mediated and staphostatin-mediated protease inhibition.
Biochemistry 2004 43 14306-14315
PubMed: 15518582
Filipek R
The Staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease.
J Biol Chem 2003 278 40959-40966
PubMed: 12874290
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