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Catalytic Site Atlas

CSA LITERATURE entry for 1cmx

E.C. nameubiquitinyl hydrolase 1
SpeciesSaccharomyces cerevisiae (Baker's yeast)
E.C. Number (IntEnz) 3.4.19.12
CSA Homologues of 1cmx1uch,1xd3,2etl,2wdt,2we6,3a7s,3ihr,
CSA Entries With UniProtID P35127
CSA Entries With EC Number 3.4.19.12
PDBe Entry 1cmx
PDBSum Entry 1cmx
MACiE Entry 1cmx

Literature Report

IntroductionUbiquitin C-terminal hydrolases catalyse the hydrolysis of the peptide bond between the C-terminus of ubiquitin and either the epsilon amino group of a lysine residue or the alpha amino group of a protein. This reaction is important for several reasons. Firstly, ubiquitin genes encode fusion proteins of either alpha-linked polyubiquitin or ubiquitin followed by a C-terminal peptide extension; in both cases proteolytic processing is required to generate ubiquitin monomers. Secondly, proteins are targeted for degradation by attachment of polyubiquitin chains: one ubiquitin molecule is linked to a lysine epsilon amino group of the protein to be targeted, a second ubiquitin is attached to a lysine residue of the first, and so on. Proteolytic processing is therefore required for release of polyubiquitin from the remnants of 26S proteasome substrates and for disassembly of polyubiquitin in order to recycle monomeric ubiquitin.
Ubiquitin C-terminal hydrolases (UCHs) constitute one of two main classes of de-ubiquitinating enzymes, the other being the UBPs (ubiquitin-specific proteases). In yeast UCH and UBP substrate specificities probably overlap, although the physiological substrates of UCH are unclear. Higher organisms can contain several different UCH enzymes, some of which are tissue specific and likely to target distinct substrates.
MechansimUCH is though to use the same catalytic mechanism as that established for the well-studied papain family of cysteine proteases. Cys 90 acts as a nucleophile to attack the peptide bond carbonyl and form an acyl-enzyme intermediate which is subsequently attacked and hydrolysed by a water molecule. His 166 functions to deprotonate Cys 90 and so generate the nucleophilic thiolate. It also protonates the departing amine leaving group during formation of the acyl-enzyme intermediate, and deprotonates the hydrolytic water molecule. Its pKa is modified by Asp 181. The backbone NH of Cys 90 and the sidechain amide of Gln 84 form an 'oxyanion-hole' that stabilises accumulation of negative charge on the carbonyl oxygen during nucleophilic attack on the peptide group.
Reaction

Catalytic Sites for 1cmx

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AspA181181macie:sideChainModifies the pKa of His 166.
CysA9090macie:sideChainActs as a nucleophile to attack the substrate carbonyl and form an acyl enzyme intermediate. Backbone NH forms part of the 'oxyanion hole' that stabilises negative charge accumulation on the carbonyl oxygen during nucleophilic attack.
CysA9090macie:mainChainAmideActs as a nucleophile to attack the substrate carbonyl and form an acyl enzyme intermediate. Backbone NH forms part of the 'oxyanion hole' that stabilises negative charge accumulation on the carbonyl oxygen during nucleophilic attack.
HisA166166macie:sideChainDeprotonates Cys 90 to generate the attacking thiolate nucleophile. Protonates the departing amine leaving group during formation of the acyl-enzyme intermediate. Deprotonates the nucleophilic water molecule that hydrolyses the acyl-enzyme.
GlnA8484macie:sideChainForms part of the 'oxyanion hole' that stabilises negative charge accumulation on the carbonyl oxygen during nucleophilic attack.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisC566166macie:sideChainDeprotonates Cys 90 to generate the attacking thiolate nucleophile. Protonates the departing amine leaving group during formation of the acyl-enzyme intermediate. Deprotonates the nucleophilic water molecule that hydrolyses the acyl-enzyme.
CysC49090macie:sideChainActs as a nucleophile to attack the substrate carbonyl and form an acyl enzyme intermediate. Backbone NH forms part of the 'oxyanion hole' that stabilises negative charge accumulation on the carbonyl oxygen during nucleophilic attack.
CysC49090macie:mainChainAmideActs as a nucleophile to attack the substrate carbonyl and form an acyl enzyme intermediate. Backbone NH forms part of the 'oxyanion hole' that stabilises negative charge accumulation on the carbonyl oxygen during nucleophilic attack.
GlnC48484macie:sideChainForms part of the 'oxyanion hole' that stabilises negative charge accumulation on the carbonyl oxygen during nucleophilic attack.
AspC581181macie:sideChainModifies the pKa of His 166.

Literature References

Notes:
Johnston SC
Structural basis for the specificity of ubiquitin C-terminal hydrolases.
EMBO J 1999 18 3877-3887
PubMed: 10406793
Larsen CN
Substrate binding and catalysis by ubiquitin C-terminal hydrolases: identification of two active site residues.
Biochemistry 1996 35 6735-6744
PubMed: 8639624
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