5F9P

Crystal structure study of anthrone oxidase-like protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.078 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1021/acschembio.6b00621

  • 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 struct ...

    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

    Institute of Molecular and Clinical Medicine, Kunming Medical University , Kunming 650500, China.,iHuman Institute, ShanghaiTech University , Shanghai 201210, People's Republic of China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing 100101, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anthrone oxidase-like protein
A, B
241Streptomyces ambofaciensMutation(s): 0 
Gene Names: alpJ
Find proteins for Q6VMI5 (Streptomyces ambofaciens)
Go to UniProtKB:  Q6VMI5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.078 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.155 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 90.273α = 90.00
b = 90.273β = 90.00
c = 94.745γ = 120.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXphasing
HKL-2000data processing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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