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Catalytic Site Atlas

CSA LITERATURE entry for 1nbf

E.C. nameubiquitinyl hydrolase 1
SpeciesHomo sapiens (Human)
E.C. Number (IntEnz) 3.4.19.12
CSA Homologues of 1nbf1nb8,2ayn,2ayo,2f1z,2gfo,2hd5,
CSA Entries With UniProtID Q93009
CSA Entries With EC Number 3.4.19.12
PDBe Entry 1nbf
PDBSum Entry 1nbf
MACiE Entry 1nbf

Literature Report

IntroductionDeubiquinylation is a vital process in eukaryotic cells because it protects proteins from degradation. It involves the hydrolysis of the peptide bond that joins the C terminal residue of ubiquitin to the lysine residue in the protein, and is catalysed by DUPs (Deubiquinylating proteins) such as HAUSP, described here. This family of enzymes is one of the largest in the human genome, reflecting their importance in the cell. For example, the tumour suppressing protein p53 relies on HAUSP action in order to prevent it from being degraded; thus malfunctions in the expression or activity of HAUSP can lead to cancer. HAUSP, along with the rest of the homologous family, is a cysteine protease, and displays structural and sequence homology to other cysteine proteases with different roles in the cell.
MechansimThe scissile peptide bond targeted by HAUSP is between a Lysine residue's epsilon amino group and the glycine residue that makes up the C terminal of ubiquitin. Cys 223 acts as the nucleophile, with deprotonation by His 464, with Asp 481 acting as a primer. This leads to a tetrahedral intermediate which is stabilised by the amide portion of Cys 223 and the side chain of Asn 281. Protonation of the leaving group by His 464 results in the release of the protein and forms a thioacyl intermediate where the ubiquitin remains bound to the enzyme. Hydrolysis of this intermediate by a water molecule activated by His 464 results in the release of the ubiquitin and the completion of the reaction cycle.
Reaction

Catalytic Sites for 1nbf

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnA218218macie:sideChainActs to stabilise the tetrahedral intermediate through hydrogen bonding between its side chain and the oxyanion that forms in the reaction. Subsequent collapse of the tetrahedral intermediate results in product release.
CysA223223macie:sideChainActs as a nucleophile, attacking the scissile peptide bond to form a tetrahedral intermediate which subsequently collapses and is hydrolysed to the products. Also stabilises the tetrahedral intermediate through its NH group's hydrogen bonding capacity.
CysA223223macie:mainChainAmideActs as a nucleophile, attacking the scissile peptide bond to form a tetrahedral intermediate which subsequently collapses and is hydrolysed to the products. Also stabilises the tetrahedral intermediate through its NH group's hydrogen bonding capacity.
AspA481481macie:sideChainActs to modify the pKa of His 464 to increase its ability to act as an acid base during the reaction.
HisA464464macie:sideChainActs as acid base to deprotonate Cys 223 so it can act as a nucleophile. Subsequently protonates the leaving group to allow the thioacyl enzyme intermediate to form. Finally deprotonates the attacking water molecule to allow hydrolysis of the thioacyl enzyme intermediate to release ubiquitin.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnB218218macie:sideChainActs to stabilise the tetrahedral intermediate through hydrogen bonding between its side chain and the oxyanion that forms in the reaction. Subsequent collapse of the tetrahedral intermediate results in product release.
CysB223223macie:sideChainActs as a nucleophile, attacking the scissile peptide bond to form a tetrahedral intermediate which subsequently collapses and is hydrolysed to the products. Also stabilises the tetrahedral intermediate through its NH group's hydrogen bonding capacity.
CysB223223macie:mainChainAmideActs as a nucleophile, attacking the scissile peptide bond to form a tetrahedral intermediate which subsequently collapses and is hydrolysed to the products. Also stabilises the tetrahedral intermediate through its NH group's hydrogen bonding capacity.
AspB481481macie:sideChainActs to modify the pKa of His 464 to increase its ability to act as an acid base during the reaction.
HisB464464macie:sideChainActs as acid base to deprotonate Cys 223 so it can act as a nucleophile. Subsequently protonates the leaving group to allow the thioacyl enzyme intermediate to form. Finally deprotonates the attacking water molecule to allow hydrolysis of the thioacyl enzyme intermediate to release ubiquitin.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnE218218macie:sideChainActs to stabilise the tetrahedral intermediate through hydrogen bonding between its side chain and the oxyanion that forms in the reaction. Subsequent collapse of the tetrahedral intermediate results in product release.
CysE223223macie:sideChainActs as a nucleophile, attacking the scissile peptide bond to form a tetrahedral intermediate which subsequently collapses and is hydrolysed to the products. Also stabilises the tetrahedral intermediate through its NH group's hydrogen bonding capacity.
CysE223223macie:mainChainAmideActs as a nucleophile, attacking the scissile peptide bond to form a tetrahedral intermediate which subsequently collapses and is hydrolysed to the products. Also stabilises the tetrahedral intermediate through its NH group's hydrogen bonding capacity.
AspE481481macie:sideChainActs to modify the pKa of His 464 to increase its ability to act as an acid base during the reaction.
HisE464464macie:sideChainActs as acid base to deprotonate Cys 223 so it can act as a nucleophile. Subsequently protonates the leaving group to allow the thioacyl enzyme intermediate to form. Finally deprotonates the attacking water molecule to allow hydrolysis of the thioacyl enzyme intermediate to release ubiquitin.

Literature References

Notes:
Hu M
Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde.
Cell 2002 111 1041-1054
PubMed: 12507430
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