1JVZ | pdb_00001jvz

Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid

• PDB DOI: https://doi.org/10.2210/pdb1JVZ/pdb

• Classification: HYDROLASE
• Organism(s): Brevundimonas diminuta
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-09-01 Released: 2002-09-01 
• Deposition Author(s): Kim, Y., Hol, W.G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.214 (Depositor) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid and glutarate: insight into the basis of its substrate specificity

Kim, Y., Hol, W.G.

(2001) Chem Biol 8: 1253-1264

• PubMed: 11755403 
• DOI: https://doi.org/10.1016/s1074-5521(01)00092-8
• Primary Citation Related Structures: 
  1JVZ, 1JW0


• PubMed Abstract: 
  

  Semisynthetic cephalosporins are primarily synthesized from 7-aminocephalosporanic acid (7-ACA), which is obtained by environmentally toxic chemical deacylation of cephalosporin C (CPC). Thus, the enzymatic conversion of CPC to 7-ACA by cephalosporin acylase (CA) would be of great interest. However, CAs use glutaryl-7-ACA (GL-7-ACA) as a primary substrate and the enzyme has low turnover rates for CPC. The binary complex structures of CA with GL-7-ACA and glutarate (the side-chain of GL-7-ACA) show extensive interactions between the glutaryl moiety of GL-7-ACA and the seven residues that form the side-chain pocket. These interactions explain why the D-alpha-aminoadipyl side-chain of CPC yields a poorer substrate than GL-7-ACA. This understanding of the nature of substrate specificity may be useful in the design of an enzyme with an improved performance for the conversion of CPC to 7-ACA. Additionally, the catalytic mechanism of the deacylation reaction was revealed by the ligand bound structures.

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Organizational Affiliation: 
• School of Chemical Engineering, Yeungnam University, South Korea. [e-mail]

Biological Assembly 1  

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: 76.54 kDa 
• Atom Count: 5,741 
• Modeled Residue Count: 672 
• Deposited Residue Count: 678 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cephalosporin acylase alpha chain	A	158	Brevundimonas diminuta	Mutation(s): 1  EC: 3.5.1.93
UniProt
Find proteins for Q9L5D6 (Brevundimonas diminuta) Explore Q9L5D6  Go to UniProtKB:  Q9L5D6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cephalosporin acylase beta chain	B	520	Brevundimonas diminuta	Mutation(s): 12  EC: 3.5.1.93
UniProt
Find proteins for Q9L5D6 (Brevundimonas diminuta) Explore Q9L5D6  Go to UniProtKB:  Q9L5D6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CEN	C [auth B]	7BETA-(4CARBOXYBUTANAMIDO) CEPHALOSPORANIC ACID C15 H18 N2 O8 S IXUSDMGLUJZNFO-BXUZGUMPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.214 (Depositor) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.14	α = 90
b = 74.14	β = 90
c = 379.82	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-09-01 
Deposition Author(s): Kim, Y., Hol, W.G.J.

Revision History  

• Version 1.0: 2002-09-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary