3K9Y

Crystal structure of rat mitochondrial P450 24A1 S57D in complex with CYMAL-5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of CYP24A1, a mitochondrial cytochrome P450 involved in vitamin D metabolism.

Annalora, A.J.Goodin, D.B.Hong, W.X.Zhang, Q.Johnson, E.F.Stout, C.D.

(2010) J.Mol.Biol. 396: 441-451

  • DOI: 10.1016/j.jmb.2009.11.057
  • Primary Citation of Related Structures:  3K9V

  • PubMed Abstract: 
  • Cytochrome P450 (CYP) 24A1 catalyzes the side-chain oxidation of the hormonal form of vitamin D. Expression of CYP24A1 is up-regulated to attenuate vitamin D signaling associated with calcium homeostasis and cellular growth processes. The development ...

    Cytochrome P450 (CYP) 24A1 catalyzes the side-chain oxidation of the hormonal form of vitamin D. Expression of CYP24A1 is up-regulated to attenuate vitamin D signaling associated with calcium homeostasis and cellular growth processes. The development of therapeutics for disorders linked to vitamin D insufficiency would be greatly facilitated by structural knowledge of CYP24A1. Here, we report the crystal structure of rat CYP24A1 at 2.5 A resolution. The structure exhibits an open cleft leading to the active-site heme prosthetic group on the distal surface that is likely to define the path of substrate access into the active site. The entrance to the cleft is flanked by conserved hydrophobic residues on helices A' and G', suggesting a mode of insertion into the inner mitochondrial membrane. A docking model for 1alpha,25-dihydroxyvitamin D(3) binding in the open form of CYP24A1 that clarifies the structural determinants of secosteroid recognition and validates the predictive power of existing homology models of CYP24A1 is proposed. Analysis of CYP24A1's proximal surface identifies the determinants of adrenodoxin recognition as a constellation of conserved residues from helices K, K'', and L that converge with an adjacent lysine-rich loop for binding the redox protein. Overall, the CYP24A1 structure provides the first template for understanding membrane insertion, substrate binding, and redox partner interaction in mitochondrial P450s.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. annalora@scripps.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial
A, B
482Rattus norvegicusGene Names: Cyp24a1 (Cyp24)
EC: 1.14.15.16
Find proteins for Q09128 (Rattus norvegicus)
Go to UniProtKB:  Q09128
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CM5
Query on CM5

Download SDF File 
Download CCD File 
A
5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE
5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE; CYMAL-5
C23 H42 O11
RVTGFZGNOSKUDA-ZNGNCRBCSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.251 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 182.297α = 90.00
b = 81.303β = 122.44
c = 108.707γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance