Crystal structure study of anthrone oxidase-like protein

Experimental Data Snapshot

  • Resolution: 2.08 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 

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This is version 1.2 of the entry. See complete history


Structure and Function of a C-C Bond Cleaving Oxygenase in Atypical Angucycline Biosynthesis

Pan, G.Gao, X.Fan, K.Liu, J.Meng, B.Gao, J.Wang, B.Zhang, C.Han, H.Ai, G.Chen, Y.Wu, D.Liu, Z.J.Yang, K.

(2017) ACS Chem Biol 12: 142-152

  • DOI: https://doi.org/10.1021/acschembio.6b00621
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    C-C bond ring cleaving oxygenases represent a unique family of enzymes involved in the B ring cleavage reaction only observed in atypical angucycline biosynthesis. B ring cleavage is the key reaction leading to dramatic divergence in the final structures of atypical angucyclines. Here, we present the crystal structure of AlpJ, the first structure of this family of enzymes. AlpJ has been verified as the enzyme catalyzing C-C bond cleavage in kinamycin biosynthesis. The crystal structure of the AlpJ monomer resembles the dimeric structure of ferredoxin-like proteins. The N- and C-terminal halves of AlpJ are homologous, and both contain a putative hydrophobic substrate binding pocket in the "closed" and "open" conformations, respectively. Structural comparison of AlpJ with ActVA-Orf6 and protein-ligand docking analysis suggest that the residues including Asn60, Trp64, and Trp181 are possibly involved in substrate recognition. Site-directed mutagenesis results supported our hypothesis, as mutation of these residues led to nearly a complete loss of the activity of AlpJ. Structural analysis also revealed that AlpJ possesses an intramolecular domain-domain interface, where the residues His50 and Tyr178 form a hydrogen bond that probably stabilizes the three-dimensional structure of AlpJ. Site-directed mutagenesis showed that the two residues, His50 and Tyr178, were vital for the activity of AlpJ. Our findings shed light on the structure and catalytic mechanism of the AlpJ family of oxygenases, which presumably involves two active sites that might function in a cooperative manner.

  • Organizational Affiliation

    State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anthrone oxidase-like protein
A, B
241Streptomyces ambofaciensMutation(s): 0 
Gene Names: alpJDSMT0187
Find proteins for Q6VMI5 (Streptomyces ambofaciens)
Explore Q6VMI5 
Go to UniProtKB:  Q6VMI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6VMI5
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.08 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.273α = 90
b = 90.273β = 90
c = 94.745γ = 120
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection, Database references