6AKD

Crystal structure of IdnL7

• PDB DOI: https://doi.org/10.2210/pdb6AKD/pdb

• Classification: LIGASE
• Organism(s): Streptomyces sp. ML694-90F3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-31 Released: 2019-03-06 
• Deposition Author(s): Cieslak, J., Miyanaga, A., Kudo, F., Eguchi, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.220 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesis.

Cieslak, J., Miyanaga, A., Takaishi, M., Kudo, F., Eguchi, T.

(2019) Acta Crystallogr F Struct Biol Commun 75: 299-306

• PubMed: 30950831 
• DOI: https://doi.org/10.1107/S2053230X19002863
• Primary Citation of Related Structures:  
  6AKD


• PubMed Abstract: 
  

  Adenylation enzymes play an important role in the selective incorporation of the cognate carboxylate substrates in natural product biosynthesis. Here, the biochemical and structural characterization of the adenylation enzyme IdnL7, which is involved in the biosynthesis of the macrolactam polyketide antibiotic incednine, is reported. Biochemical analysis showed that IdnL7 selects and activates several small amino acids. The structure of IdnL7 in complex with an L-alanyl-adenylate intermediate mimic, 5'-O-[N-(L-alanyl)sulfamoyl]adenosine, was determined at 2.1 Å resolution. The structure of IdnL7 explains the broad substrate specificity of IdnL7 towards small L-amino acids.

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Organizational Affiliation: 

Department of Chemistry and Materials Science, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8551, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 58.12 kDa 
• Atom Count: 3,877 
• Modelled Residue Count: 488 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMP-dependent synthetase and ligase	A	538	Streptomyces sp. ML694-90F3	Mutation(s): 0  Gene Names: idnL7
UniProt
Find proteins for A0A077KUW8 (Streptomyces sp. ML694-90F3) Explore A0A077KUW8  Go to UniProtKB:  A0A077KUW8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A5A	B [auth A]	'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE C13 H19 N7 O7 S CWWYMWDIYBJVLP-YTMOPEAISA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.220 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.526	α = 90
b = 68.526	β = 90
c = 225.169	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-06 
Deposition Author(s): Cieslak, J., Miyanaga, A., Kudo, F., Eguchi, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	25850050

Revision History  

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description