5H1Z | pdb_00005h1z

CYP153D17 from Sphingomonas sp. PAMC 26605

• PDB DOI: https://doi.org/10.2210/pdb5H1Z/pdb

• Classification: HYDROLASE
• Organism(s): Sphingomonas sp. PAMC 26605
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-13 Released: 2017-01-11 
• Deposition Author(s): Lee, C.W., Lee, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.340 (Depositor), 0.348 (DCC) 
• R-Value Work: 
  0.262 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.266 (Depositor) 

Literature

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

• PubMed: 27941697 
• DOI: https://doi.org/10.3390/ijms17122067
• Primary Citation Related Structures: 
  5H1Z


• 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.

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Organizational Affiliation: 
• Unit of Polar Genomics, Korea Polar Research Institute, Incheon 406-840, Korea. [e-mail].
Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea. [e-mail].
Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asansi 336-708, Korea. [e-mail].
Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asansi 336-708, Korea. [e-mail].
Unit of Polar Genomics, Korea Polar Research Institute, Incheon 406-840, Korea. [e-mail].
Unit of Polar Genomics, Korea Polar Research Institute, Incheon 406-840, Korea. [e-mail].
Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea. [e-mail].
Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asansi 336-708, Korea. [e-mail].
Unit of Polar Genomics, Korea Polar Research Institute, Incheon 406-840, Korea. [e-mail].
Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Korea. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 47.61 kDa 
• Atom Count: 3,295 
• Modeled Residue Count: 400 
• Deposited Residue Count: 407 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative CYP alkane hydroxylase CYP153D17	A	407	Sphingomonas sp. PAMC 26605	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAR9 (Sphingomonas sp. PAMC 26605) Explore A0ACD6BAR9  Go to UniProtKB:  A0ACD6BAR9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
D12	C [auth A]	DODECANE C12 H26 SNRUBQQJIBEYMU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.340 (Depositor), 0.348 (DCC) 
• R-Value Work:  0.262 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.266 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.837	α = 90
b = 110.837	β = 90
c = 113.18	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-11 
Deposition Author(s): Lee, C.W., Lee, J.H.

Revision History  

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