3K3W

Thermostable Penicillin G acylase from Alcaligenes faecalis in orthorhombic form


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 

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This is version 1.3 of the entry. See complete history


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

  • 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 ...

    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.


    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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin G acylaseA196Alcaligenes faecalisMutation(s): 0 
Gene Names: pac
EC: 3.5.1.11
UniProt
Find proteins for O34142 (Alcaligenes faecalis)
Explore O34142 
Go to UniProtKB:  O34142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34142
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin G acylaseB551Alcaligenes faecalisMutation(s): 0 
Gene Names: pac
EC: 3.5.1.11
UniProt
Find proteins for O34142 (Alcaligenes faecalis)
Explore O34142 
Go to UniProtKB:  O34142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34142
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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 = 72.929α = 90
b = 86.016β = 90
c = 260.181γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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