5YY3 | pdb_00005yy3

Crystal structure of AsqI

• PDB DOI: https://doi.org/10.2210/pdb5YY3/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Aspergillus nidulans FGSC A4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-07 Released: 2018-08-01 
• Deposition Author(s): Hara, K., Hashimoto, H., Kishimoto, S., Watanabe, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.220 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Enzymatic one-step ring contraction for quinolone biosynthesis.

Kishimoto, S., Hara, K., Hashimoto, H., Hirayama, Y., Champagne, P.A., Houk, K.N., Tang, Y., Watanabe, K.

(2018) Nat Commun 9: 2826-2826

• PubMed: 30026518 
• DOI: https://doi.org/10.1038/s41467-018-05221-5
• Primary Citation Related Structures: 
  5YY2, 5YY3


• PubMed Abstract: 
  

  The 6,6-quinolone scaffolds on which viridicatin-type fungal alkaloids are built are frequently found in metabolites that display useful biological activities. Here we report in vitro and computational analyses leading to the discovery of a hemocyanin-like protein AsqI from the Aspergillus nidulans aspoquinolone biosynthetic pathway that forms viridicatins via a conversion of the cyclopenin-type 6,7-bicyclic system into the viridicatin-type 6,6-bicyclic core through elimination of carbon dioxide and methylamine through methyl isocyanate.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, USA.
Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California, 90095, USA.
Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 85.64 kDa 
• Atom Count: 4,943 
• Modeled Residue Count: 577 
• Deposited Residue Count: 749 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein AsqI	A	749	Aspergillus nidulans FGSC A4	Mutation(s): 0  Gene Names: ANIA_11193 EC: 4.1.99.27
UniProt
Find proteins for C8VJQ3 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139)) Explore C8VJQ3  Go to UniProtKB:  C8VJQ3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.220 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.082	α = 90
b = 117.435	β = 90
c = 159	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-01 
Deposition Author(s): Hara, K., Hashimoto, H., Kishimoto, S., Watanabe, K.

Revision History  

• Version 1.0: 2018-08-01
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references