Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 85.16 kDa 
• Atom Count: 6011 
• Modelled Residue Count: 747 
• Deposited Residue Count: 747 
• Unique protein chains: 2

3K3W

Thermostable Penicillin G acylase from Alcaligenes faecalis in orthorhombic form

• PDB DOI: 10.2210/pdb3K3W/pdb

• Classification: HYDROLASE
• Organism(s): Alcaligenes faecalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-05 Released: 2009-11-10 
• Deposition Author(s): Varshney, N.K., Kumar, R.S., Ignatova, Z., Dodson, E., Suresh, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.315 
• R-Value Work: 0.281 
• R-Value Observed: 0.283 

Literature

Crystallization and X-ray structure analysis of a thermostable penicillin G acylase from Alcaligenes faecalis.

Varshney, N.K., Kumar, R.S., Ignatova, Z., Prabhune, A., Pundle, A., Dodson, E., Suresh, C.G.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 273-277

• PubMed: 22442220 
• DOI: 10.1107/S1744309111053930
• Primary Citation of Related Structures:  
  3K3W, 3ML0


• PubMed Abstract: 
  

The enzyme penicillin G acylase (EC 3.5.1.11) catalyzes amide-bond cleavage in benzylpenicillin (penicillin G) to yield 6-aminopenicillanic acid, an intermediate chemical used in the production of semisynthetic penicillins. A thermostable penicillin G acylase from Alcaligenes faecalis (AfPGA) has been crystallized using the hanging-drop vapour-diffusion method in two different space groups: C222(1), with unit-cell parameters a = 72.9, b = 86.0, c = 260.2 , and P4(1)2(1)2, with unit-cell parameters a = b = 85.6, c = 298.8 . Data were collected at 293 and the structure was determined using the molecular-replacement method. Like other penicillin acylases, AfPGA belongs to the N-terminal nucleophilic hydrolase superfamily, has undergone post-translational processing and has a serine as the N-terminal residue of the β-chain. A disulfide bridge has been identified in the structure that was not found in the other two known penicillin G cylase structures. The presence of the disulfide bridge is perceived to be one factor that confers higher stability to this enzyme.

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Related Citations: 

• Fragments of pro-peptide activate mature penicillin amidase of Alcaligenes faecalis
  Kasche, V., Galunsky, B., Ignatova, Z.
  (2003) Eur J Biochem 270: 4721

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Organizational Affiliation: 

Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin G acylase	A	196	Alcaligenes faecalis	Mutation(s): 0  Gene Names: pac EC: 3.5.1.11
UniProt
Find proteins for O34142 (Alcaligenes faecalis) Explore O34142  Go to UniProtKB:  O34142

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin G acylase	B	551	Alcaligenes faecalis	Mutation(s): 0  Gene Names: pac EC: 3.5.1.11
UniProt
Find proteins for O34142 (Alcaligenes faecalis) Explore O34142  Go to UniProtKB:  O34142

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.315 
• R-Value Work: 0.281 
• R-Value Observed: 0.283 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.929	α = 90
b = 86.016	β = 90
c = 260.181	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-05 
• Released Date: 2009-11-10 
Deposition Author(s): Varshney, N.K., Kumar, R.S., Ignatova, Z., Dodson, E., Suresh, C.G.

Revision History  

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-14
  Changes: Database references, Structure summary
• Version 1.3: 2020-01-01
  Changes: Advisory, Database references