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Catalytic Site Atlas

CSA LITERATURE entry for 3s8r

E.C. nameglutaryl-7-aminocephalosporanic-acid acylase
SpeciesPseudomonas sp. sy-77 ()
E.C. Number (IntEnz) 3.5.1.93
CSA Homologues of 3s8rThere are 16 Homologs
CSA Entries With UniProtID
CSA Entries With EC Number 3.5.1.93
PDBe Entry 3s8r
PDBSum Entry 3s8r
MACiE Entry M0288

Literature Report

IntroductionGlutaryl 7-aminocephalosporanic acid (7-ACA) acylase catalyses the hydrolysis of Glutaryl 7-ACA to Glutaric acid and 7-ACA. It belongs to the family of N-terminal hydrolase.
7-ACA is the starting compound for the synthesis of cephalosporin antibiotics and it is usually obtained industrially by chemical deacylation of cephalosporin C(CPC). Since the chemical production of 7-ACA is expensive and produce toxic chemical wastes, the enzymatic conversion of CPC to 7-ACA by 7-ACA acylase is of great interest.
MechansimSer170 alpha-amino group acts as a base to deprotonate its own hydroxyl group, which nucleophilically attacks the carbonyl group of the substrate. This results in the formation of a covalent enzyme-substrate transition state, stabilised by the oxyanion hole formed by the mainchain nitrogen atom of Val239 and the side chain of Asn413. Alpha-amino group of Ser170 then protonates the leaving group and deprotonates a water molecule to allow it to restore the enzyme by a nucleophilic attack to the acylenzyme.
Reaction

Catalytic Sites for 3s8r

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
SerA1700macie:sideChainIts alpha-amino group acts as a base to deprotonate its own hydroxyl group, which nucleophilically attacks the carbonyl group of the substrate. Alpha-amino group of Ser 170 then protonates the leaving group and deprotonates a water molecule to allow it to restore the enzyme by a nucleophilic attack to the acylenzyme.
AsnA4130macie:sideChainIt forms the oxyanion hole to stabilise the transition state.
ValA2390macie:mainChainAmideIts mainchain nitrogen atom forms an oxyanion hole to stabilise the transition state.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
SerB1700macie:sideChainIts alpha-amino group acts as a base to deprotonate its own hydroxyl group, which nucleophilically attacks the carbonyl group of the substrate. Alpha-amino group of Ser 170 then protonates the leaving group and deprotonates a water molecule to allow it to restore the enzyme by a nucleophilic attack to the acylenzyme.
AsnB4130macie:sideChainIt forms the oxyanion hole to stabilise the transition state.
ValB2390macie:mainChainAmideIts mainchain nitrogen atom forms an oxyanion hole to stabilise the transition state.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisA1920macie:sideChainIts side chain activate a water molecule to promote its nucleophilic attack on the ester bond formed between Ser 170 and Gly 169. Its backbone nitrogen forms a oxyanion hole to stabilise the transition states.
HisA1920macie:mainChainAmideIts side chain activate a water molecule to promote its nucleophilic attack on the ester bond formed between Ser 170 and Gly 169. Its backbone nitrogen forms a oxyanion hole to stabilise the transition states.
SerA1700macie:sideChainIt acts as a nucleophile to attack the carbonyl carbon of Gly 169 upon deprotonation by a water molecule to form a hydroxazolidine ring intermediate.
GluA6240macie:sideChainIt hydrogen bonds to His 192, altering the pKa of His 192 to enhance its activity as a base.
AsnA4130macie:sideChainIt stabilises the transition state of a hydroxazolidine ring.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
HisB1920macie:sideChainIts side chain activate a water molecule to promote its nucleophilic attack on the ester bond formed between Ser 170 and Gly 169. Its backbone nitrogen forms a oxyanion hole to stabilise the transition states.
HisB1920macie:mainChainAmideIts side chain activate a water molecule to promote its nucleophilic attack on the ester bond formed between Ser 170 and Gly 169. Its backbone nitrogen forms a oxyanion hole to stabilise the transition states.
SerB1700macie:sideChainIt acts as a nucleophile to attack the carbonyl carbon of Gly 169 upon deprotonation by a water molecule to form a hydroxazolidine ring intermediate.
GluB6240macie:sideChainIt hydrogen bonds to His 192, altering the pKa of His 192 to enhance its activity as a base.
AsnB4130macie:sideChainIt stabilises the transition state of a hydroxazolidine ring.

Literature References

Notes:Apart from its catalytic activity, 7-ACA acylase also contains an autoproteolytic activity which results in catalytic activation. The mechanism and catalytic residues involved in the first step of autoproteolysis are described in another entry under 1oqz.
Kim Y
The 2.0 A crystal structure of cephalosporin acylase.
Structure 2000 8 1059-1068
PubMed: 11080627
Kim Y
Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid and glutarate: insight into the basis of its substrate specificity.
Chem Biol 2001 8 1253-1264
PubMed: 11755403
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