Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 95.55 kDa 
• Atom Count: 7239 
• Residue Count: 855 
• Unique protein chains: 1

1MLY

Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the cis isomer of amiclenomycin

• DOI: 10.2210/pdb1MLY/pdb

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


• Deposited: 2002-09-02 Released: 2002-12-04 
• Deposition Author(s): Sandmark, J., Mann, S., Marquet, A., Schneider, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.220 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin

Sandmark, J., Mann, S., Marquet, A., Schneider, G.

(2002) J Biol Chem 277: 43352-43358

• PubMed: 12218056 
• DOI: 10.1074/jbc.M207239200
• Primary Citation of Related Structures:  
  1MLZ, 1MLY


• PubMed Abstract: 
  

The antibiotic amiclenomycin blocks the biosynthesis of biotin by inhibiting the pyridoxal-phosphate-dependent enzyme diaminopelargonic acid synthase. Inactivation of the enzyme is stereoselective, i.e. the cis isomer of amiclenomycin is a potent inhibitor, whereas the trans isomer is much less reactive. The crystal structure of the complex of the holoenzyme and amiclenomycin at 1.8 A resolution reveals that the internal aldimine linkage between the cofactor and the side chain of the catalytic residue Lys-274 is broken. Instead, a covalent bond is formed between the 4-amino nitrogen of amiclenomycin and the C4' carbon atom of pyridoxal-phosphate. The electron density for the bound inhibitor suggests that aromatization of the cyclohexadiene ring has occurred upon formation of the covalent adduct. This process could be initiated by proton abstraction at the C4 carbon atom of the cyclohexadiene ring, possibly by the proximal side chain of Lys-274, leading to the tautomer Schiff base followed by the removal of the second allylic hydrogen. The carboxyl tail of the amiclenomycin moiety forms a salt link to the conserved residue Arg-391 in the substrate-binding site. Modeling suggests steric hindrance at the active site as the determinant of the weak inhibiting potency of the trans isomer.

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Organizational Affiliation: 

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-diamino-pelargonic acid aminotransferase	A, B	429	Escherichia coli	Mutation(s): 0  Gene Names: bioA EC: 2.6.1.62
Find proteins for P12995 (Escherichia coli (strain K12)) Explore P12995  Go to UniProtKB:  P12995

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	A, B	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
ACZ	A, B	CIS-AMICLENOMYCIN C10 H16 N2 O2 LAJWZJCOWPUSOA-SMOXQLQSSA-N
NA	A, B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.220 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.655	α = 90
b = 56.073	β = 109.86
c = 116.174	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-02 
• Released Date: 2002-12-04 
Deposition Author(s): Sandmark, J., Mann, S., Marquet, A., Schneider, G.

Revision History 

• Version 1.0: 2002-12-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2018-03-07
  Changes: Advisory, Data collection