1GK9

Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism

• PDB DOI:  https://doi.org/10.2210/pdb1GK9/pdb

• Classification: ANTIBIOTIC RESISTANCE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-08-10 Released: 2002-01-04 
• Deposition Author(s): McVey, C.E., Walsh, M.A., Dodson, G.G., Wilson, K.S., Brannigan, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.169 
• R-Value Work: 0.148 

Literature

Crystal Structures of Penicillin Acylase Enzyme-Substrate Complexes: Structural Insights Into the Catalytic Mechanism

Mcvey, C.E., Walsh, M.A., Dodson, G.G., S, K., Brannigan, J.A.

(2001) J Mol Biol 313: 139

• PubMed: 11601852 
• DOI: https://doi.org/10.1006/jmbi.2001.5043
• Primary Citation of Related Structures:  
  1GK9, 1GKF, 1GM7, 1GM8, 1GM9


• PubMed Abstract: 
  

The crystal structure of penicillin G acylase from Escherichia coli has been determined to a resolution of 1.3 A from a crystal form grown in the presence of ethylene glycol. To study aspects of the substrate specificity and catalytic mechanism of this key biotechnological enzyme, mutants were made to generate inactive protein useful for producing enzyme-substrate complexes. Owing to the intimate association of enzyme activity and precursor processing in this protein family (the Ntn hydrolases), most attempts to alter active-site residues lead to processing defects. Mutation of the invariant residue Arg B263 results in the accumulation of a protein precursor form. However, the mutation of Asn B241, a residue implicated in stabilisation of the tetrahedral intermediate during catalysis, inactivates the enzyme but does not prevent autocatalytic processing or the ability to bind substrates. The crystal structure of the Asn B241 Ala oxyanion hole mutant enzyme has been determined in its native form and in complex with penicillin G and penicillin G sulphoxide. We show that Asn B241 has an important role in maintaining the active site geometry and in productive substrate binding, hence the structure of the mutant protein is a poor model for the Michaelis complex. For this reason, we subsequently solved the structure of the wild-type protein in complex with the slowly processed substrate penicillin G sulphoxide. Analysis of this structure suggests that the reaction mechanism proceeds via direct nucleophilic attack of Ser B1 on the scissile amide and not as previously proposed via a tightly H-bonded water molecule acting as a "virtual" base.

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Related Citations: 

• Expression, Purification and Crystallisation of Penicillin G Acylase from Escherichia Coli Atcc 11105
  Hunt, P.D., Tolley, S.P., Ward, R.J., Hill, C.P., Dodson, G.G.
  (1990) Protein Eng 3: 635

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Organizational Affiliation: 

Structural Biology Laboratory Chemistry Department, University of York, York YO10 5DD, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 92.92 kDa 
• Atom Count: 7,533 
• Modelled Residue Count: 765 
• Deposited Residue Count: 817 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PENICILLIN G ACYLASE ALPHA SUBUNIT	A	260	Escherichia coli	Mutation(s): 0  Gene Names: pac EC: 3.5.1.11
UniProt
Find proteins for P06875 (Escherichia coli) Explore P06875  Go to UniProtKB:  P06875

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PENICILLIN G ACYLASE BETA SUBUNIT	B	557	Escherichia coli	Mutation(s): 0  Gene Names: pac EC: 3.5.1.11
UniProt
Find proteins for P06875 (Escherichia coli) Explore P06875  Go to UniProtKB:  P06875

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	AA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.169 
• R-Value Work: 0.148 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.3	α = 90
b = 131.6	β = 105.9
c = 63.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-04 
Deposition Author(s): McVey, C.E., Walsh, M.A., Dodson, G.G., Wilson, K.S., Brannigan, J.A.

Revision History  

• Version 1.0: 2002-01-04
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance