PDBsum entry 4wl2

Hydrolase

PDB id: 4wl2

Contents

Protein chains

(+ 2 more) 347 a.a.

Waters ×46

PDB id:

4wl2

Name:

Hydrolase

Title:

Structure of penicillin v acylase from pectobacterium atrosepticum

Structure:

Putative exported choloylglycine hydrolase. Chain: a, b, c, d, e, f, g, h. Fragment: unp residues 30-376. Synonym: papva. Engineered: yes

Source:

Pectobacterium atrosepticum scri1043. Organism_taxid: 218491. Gene: eca3205. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.220 R-free: 0.248

Authors:

S.Ramasamy,V.S.Avinash,A.V.Pundle,C.G.Suresh

Key ref:

V.S.Avinash et al. (2016). Structural analysis of a penicillin V acylase from Pectobacterium atrosepticum confirms the importance of two Trp residues for activity and specificity. J Struct Biol, 193, 85-94. PubMed id: 26707624 DOI: 10.1016/j.jsb.2015.12.008

Date:

06-Oct-14 Release date: 07-Oct-15

Protein chains

Q6D291  (Q6D291_PECAS) -  Penicillin V acylase from Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)

Seq: 376 a.a.

Struc: 347 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.1.11 - penicillin amidase.
• Pathway: Penicillin Biosynthesis and Metabolism
• Reaction: a penicillin + H2O = 6-aminopenicillanate + a carboxylate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jsb.2015.12.008

J Struct Biol 193:85-94 (2016)

PubMed id: 26707624

Structural analysis of a penicillin V acylase from Pectobacterium atrosepticum confirms the importance of two Trp residues for activity and specificity.

V.S.Avinash, P.Panigrahi, D.Chand, A.Pundle, C.G.Suresh, S.Ramasamy.

ABSTRACT

Penicillin V acylases (PVA) catalyze the deacylation of the beta-lactam antibiotic phenoxymethylpenicillin (Pen V). They are members of the Ntn hydrolase family and possess an N-terminal cysteine as the main catalytic nucleophile residue. They form the evolutionarily related cholylglycine hydrolase (CGH) group which includes bile salt hydrolases (BSH) responsible for bile deconjugation. Even though a few PVA and BSH structures have been reported, no structure of a functional PVA from Gram-negative bacteria is available. Here, we report the crystal structure of a highly active PVA from Gram-negative Pectobacterium atrosepticum (PaPVA) at 2.5Å resolution. Structural comparison with PVAs from Gram-positive bacteria revealed that PaPVA had a distinctive tetrameric structure and active site organization. In addition, mutagenesis of key active site residues and biochemical characterization of the resultant variants elucidated the role of these residues in substrate binding and catalysis. The importance of residue Trp23 and Trp87 side chains in binding and correct positioning of Pen V by PVAs was confirmed using mutagenesis and substrate docking with a 15ns molecular dynamics simulation. These results establish the unique nature of Gram-negative CGHs and necessitate further research about their substrate spectrum.