Overview for MACiE Entry M0241

Version history

General Information

EC Number: (A member of the Hydrolases, Acting on carbon-nitrogen bonds, other than peptide bonds, In linear amides)

Enzyme Name: penicillin amidase

Biological Species: Bacillus sphaericus (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 3pva - PENICILLIN V ACYLASE FROM B. SPHAERICUS (Resolution = 2.80 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of Penicillin V

Image of water

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Image of Phenoxyacetate

Image of 6-Aminopenicillanate

Penicillin V

Overall Comment: This enzyme undergoes post-translational autocatalytic cleavage to produce the mature enzyme. A tripeptide of Met-Leu-Gly is removed to expose the catalytic N-terminal residue.

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Stepwise Description of the Reaction

Step 1The alpha-amine of Cys1 deprotonates the thiol group. The resulting thiolate is the nucleophile for attack on the carbonyl carbon. The tetrahedral intermediate is stabilised by the oxyanion hole.
Step 2The tetrahedral intermediate collapses and eliminates 6-aminopenicillanate, with proton transfer from the alpha amine to the leaving group.
Step 3The alpha amine deprotonates water, which then acts as the nucleophile for attack on the carbonyl carbon. The tetrahedral intermediate is stabilised by the oxyanion hole.
Step 4The tetrahedral intermediate collapses and eliminates Cys1 phenoxyacetate. The Cys1 thiolate is protonated by the alpha amine.

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Catalytic Residues Involved

Type Number Chain Location of Function
Cys 1 A Main Chain N Terminus
Side Chain
Asn 175 A Side Chain
Tyr 82 A Main Chain Amide
Arg 228 A Side Chain


  1. M. Morillas et al. (1999), Biochem. J., 338, 235-239. The kinetics of acylation and deacylation of penicillin acylase from Escherichia coli ATCC 11105: evidence for lowered pKa values of groups near the catalytic centre.
    Medline: 9931321
  2. C. E. McVey et al. (2001), J. Mol. Biol., 313, 139-150. Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic mechanism.
    Medline: 11601852
  3. H. J. Duggleby et al. (1955), Nature, 373, 264-268. Penicillin acylase has a single-amino-acid catalytic centre.
    Medline: 7816145
  4. J. A. Brannigan et al. (1995), Nature, 378, 416-419. A protein catalytic framework with an N-terminal nucleophile is capable of self-activation.
    Medline: 7477383
  5. P. Rathinaswamy et al. (2005), Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 680-683. Cloning, purification, crystallization and preliminary structural studies of penicillin V acylase from Bacillus subtilis.
    Medline: 16511127
  6. C. G. Suresh et al. (1999), Nat. Struct. Biol., 6, 414-416. Penicillin V acylase crystal structure reveals new Ntn-hydrolase family members.
    Medline: 10331865

Homologue information for M0241 (3pva)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)

Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
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Link to EzCatDB

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penicillin amidase activity (molecular function)
hydrolase activity (molecular function)
response to antibiotic (biological process)