CYP153D17 from Sphingomonas sp. PAMC 26605

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.266 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Crystal Structure of a Putative Cytochrome P450 Alkane Hydroxylase (CYP153D17) from Sphingomonas sp. PAMC 26605 and Its Conformational Substrate Binding

Lee, C.W.Yu, S.C.Lee, J.H.Park, S.H.Park, H.Oh, T.J.Lee, J.H.

(2016) Int J Mol Sci 17

  • DOI: https://doi.org/10.3390/ijms17122067
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Enzymatic alkane hydroxylation reactions are useful for producing pharmaceutical and agricultural chemical intermediates from hydrocarbons. Several cytochrome P450 enzymes catalyze the regio- and stereo-specific hydroxylation of alkanes. We evaluated the substrate binding of a putative CYP alkane hydroxylase (CYP153D17) from the bacterium Sphingomonas sp. PAMC 26605. Substrate affinities to C10-C12 n-alkanes and C10-C14 fatty acids with K d values varied from 0.42 to 0.59 μM. A longer alkane (C12) bound more strongly than a shorter alkane (C10), while shorter fatty acids (C10, capric acid; C12, lauric acid) bound more strongly than a longer fatty acid (C14, myristic acid). These data displayed a broad substrate specificity of CYP153D17, hence it was named as a putative CYP alkane hydroxylase. Moreover, the crystal structure of CYP153D17 was determined at 3.1 Å resolution. This is the first study to provide structural information for the CYP153D family. Structural analysis showed that a co-purified alkane-like compound bound near the active-site heme group. The alkane-like substrate is in the hydrophobic pocket containing Thr74, Met90, Ala175, Ile240, Leu241, Val244, Leu292, Met295, and Phe393. Comparison with other CYP structures suggested that conformational changes in the β1-β2, α3-α4, and α6-α7 connecting loop are important for incorporating the long hydrophobic alkane-like substrate. These results improve the understanding of the catalytic mechanism of CYP153D17 and provide valuable information for future protein engineering studies.

  • Organizational Affiliation

    Unit of Polar Genomics, Korea Polar Research Institute, Incheon 406-840, Korea. justay@kopri.re.kr.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
putative CYP alkane hydroxylase CYP153D17407Sphingomonas sp. PAMC 26605Mutation(s): 0 
Find proteins for A0A1S4NYE0 (Sphingomonas sp. PAMC 26605)
Explore A0A1S4NYE0 
Go to UniProtKB:  A0A1S4NYE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S4NYE0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C34 H32 Fe N4 O4
Query on D12

Download Ideal Coordinates CCD File 
C12 H26
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.266 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.837α = 90
b = 110.837β = 90
c = 113.18γ = 120
Software Package:
Software NamePurpose
HKL-2000data processing
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references