4R21

Zebra fish cytochrome P450 17A2 with Progesterone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and Kinetic Basis of Steroid 17 alpha, 20-Lyase Activity in Teleost Fish Cytochrome P450 17A1 and Its Absence in Cytochrome P450 17A2.

Pallan, P.S.Nagy, L.D.Lei, L.Gonzalez, E.Kramlinger, V.M.Azumaya, C.M.Wawrzak, Z.Waterman, M.R.Guengerich, F.P.Egli, M.

(2015) J Biol Chem 290: 3248-3268

  • DOI: 10.1074/jbc.M114.627265
  • Primary Citation of Related Structures:  
    4R1Z, 4R20, 4R21

  • PubMed Abstract: 
  • Cytochrome P450 (P450) 17A enzymes play a critical role in the oxidation of the steroids progesterone (Prog) and pregnenolone (Preg) to glucocorticoids and androgens. In mammals, a single enzyme, P450 17A1, catalyzes both 17α-hydroxylation and a subsequent 17α,20-lyase reaction with both Prog and Preg ...

    Cytochrome P450 (P450) 17A enzymes play a critical role in the oxidation of the steroids progesterone (Prog) and pregnenolone (Preg) to glucocorticoids and androgens. In mammals, a single enzyme, P450 17A1, catalyzes both 17α-hydroxylation and a subsequent 17α,20-lyase reaction with both Prog and Preg. Teleost fish contain two 17A P450s; zebrafish P450 17A1 catalyzes both 17α-hydroxylation and lyase reactions with Prog and Preg, and P450 17A2 is more efficient in pregnenolone 17α-hydroxylation but does not catalyze the lyase reaction, even in the presence of cytochrome b5. P450 17A2 binds all substrates and products, although more loosely than P450 17A1. Pulse-chase and kinetic spectral experiments and modeling established that the two-step P450 17A1 Prog oxidation is more distributive than the Preg reaction, i.e. 17α-OH product dissociates more prior to the lyase step. The drug orteronel selectively blocked the lyase reaction of P450 17A1 but only in the case of Prog. X-ray crystal structures of zebrafish P450 17A1 and 17A2 were obtained with the ligand abiraterone and with Prog for P450 17A2. Comparison of the two fish P450 17A-abiraterone structures with human P450 17A1 (DeVore, N. M., and Scott, E. E. (2013) Nature 482, 116-119) showed only a few differences near the active site, despite only ∼50% identity among the three proteins. The P450 17A2 structure differed in four residues near the heme periphery. These residues may allow the proposed alternative ferric peroxide mechanism for the lyase reaction, or residues removed from the active site may allow conformations that lead to the lyase activity.


    Organizational Affiliation

    From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 and martin.egli@vanderbilt.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 family 17 polypeptide 2A, B486Danio rerioMutation(s): 0 
Gene Names: cyp17a2
Membrane Entity: Yes 
UniProt
Find proteins for A7U483 (Danio rerio)
Explore A7U483 
Go to UniProtKB:  A7U483
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7U483
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
STR
Query on STR

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
PROGESTERONE
C21 H30 O2
RJKFOVLPORLFTN-LEKSSAKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.94α = 90
b = 78.63β = 92.03
c = 95.41γ = 90
Software Package:
Software NamePurpose
MD2data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2014-08-08 
  • Released Date: 2014-12-31 
  • Deposition Author(s): Pallan, P.S., Egli, M.

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references