5XNT

Structure of CYP106A2 from Bacillus sp. PAMC 23377


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

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Literature

Crystal Structure and Functional Characterization of a Cytochrome P450 (BaCYP106A2) fromBacillussp. PAMC 23377.

Kim, K.H.Lee, C.W.Dangi, B.Park, S.H.Park, H.Oh, T.J.Lee, J.H.

(2017) J Microbiol Biotechnol 27: 1472-1482

  • DOI: https://doi.org/10.4014/jmb.1706.06013
  • Primary Citation of Related Structures:  
    5XNT

  • PubMed Abstract: 

    Bacterial cytochrome P450 (CYP) steroid hydroxylases are effectively useful in the pharmaceutical industry for introducing hydroxyl groups to a wide range of steroids. We found a putative CYP steroid hydroxylase ( Ba CYP106A2) from the bacterium Bacillus sp. PAMC 23377 isolated from Kara Sea of the Arctic Ocean, showing 94% sequence similarity with Bm CYP106A2 ( Bacillus megaterium ATCC 13368). In this study, soluble Ba CYP106A2 was overexpressed to evaluate its substrate-binding activity. The substrate affinity ( K d value) to 4-androstenedione was 387 ± 37 µM. Moreover, the crystal structure of Ba CYP106A2 was determined at 2.7 Å resolution. Structural analysis suggested that the α8-α9 loop region of Ba CYP106A2 is intrinsically mobile and might be important for initial ligand binding. The hydroxyl activity of Ba CYP106A2 was identified using in vitro enzyme assays. Its activity was confirmed with two kinds of steroid substrates, 4-androstenedione and nandrolone, using chromatography and mass spectrometry methods. The main products were monohydroxylated compounds with high conversion yields. This is the second study on the structure of CYP106A steroid hydroxylases, and should contribute new insight into the interactions of bacterial CYP106A with steroid substrates, providing baseline data for studying the CYP106A steroid hydroxylase from the structural and enzymatic perspectives.


  • Organizational Affiliation

    Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 31460, Republic of Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 CYP106411Peribacillus butanolivoransMutation(s): 0 
UniProt
Find proteins for Q06069 (Priestia megaterium)
Explore Q06069 
Go to UniProtKB:  Q06069
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06069
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.658α = 90
b = 77.658β = 90
c = 282.216γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data processing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release