6J0Z | pdb_00006j0z

Crystal structure of AlpK

• PDB DOI: https://doi.org/10.2210/pdb6J0Z/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces ambofaciens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-12-27 Released: 2019-03-06 
• Deposition Author(s): Wang, W., Liu, Y., Liang, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.301 (Depositor), 0.305 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.258 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of AlpK: An essential monooxygenase involved in the biosynthesis of kinamycin

Wang, W., Li, J., Li, H., Fan, K., Liu, Y.

(2019) Biochem Biophys Res Commun 510: 601-605

• PubMed: 30739782 
• DOI: https://doi.org/10.1016/j.bbrc.2019.01.077
• Primary Citation Related Structures: 
  6J0Z


• PubMed Abstract: 
  

  AlpK is an essential monooxygenase involved in the biosynthesis of kinamycin. It catalyzes the C5-hyfroxylattion of the crucial benzo[b]-fluorence intermediate in kinamycin synthesis. However, the structure and mechanism of AlpK is unclear. Here, we report the first structure of AlpK in complex with FAD. Our structure sheds light on the catalytic mechanism of AlpK.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
School of Medicine, Sun Yat-Sen University, Shenzhen, 510080, China.
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, China. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology, gel filtration

Macromolecule Content 

• Total Structure Weight: 53.11 kDa 
• Atom Count: 3,727 
• Modeled Residue Count: 488 
• Deposited Residue Count: 491 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative angucycline-like polyketide oxygenase	A [auth C]	491	Streptomyces ambofaciens	Mutation(s): 0  Gene Names: alpK
UniProt
Find proteins for Q6VMI4 (Streptomyces ambofaciens) Explore Q6VMI4  Go to UniProtKB:  Q6VMI4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.301 (Depositor), 0.305 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.258 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.882	α = 90
b = 89.882	β = 90
c = 260.737	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-06 
Deposition Author(s): Wang, W., Liu, Y., Liang, H.

Revision History  

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