6MCW

Crystal structure of the P450 domain of the CYP51-ferredoxin fusion protein from Methylococcus capsulatus, complex with the detergent Anapoe-X-114


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Concerning P450 evolution: Structural Analyses Support Bacterial Origin of Sterol 14 alpha-Demethylases.

Lamb, D.C.Hargrove, T.Y.Zhao, B.Wawrzak, Z.Goldstone, J.V.Nes, W.D.Kelly, S.L.Waterman, M.R.Stegeman, J.J.Lepesheva, G.I.

(2020) Mol Biol Evol 

  • DOI: 10.1093/molbev/msaa260
  • Primary Citation of Related Structures:  
    6MCW, 6MI0

  • PubMed Abstract: 
  • Sterol biosynthesis, primarily associated with eukaryotic kingdoms of life, occurs as an abbreviated pathway in the bacterium Methylococcus capsulatus. Sterol 14α-demethylation is an essential step in this pathway and is catalyzed by cytochrome P450 51 (CYP51) ...

    Sterol biosynthesis, primarily associated with eukaryotic kingdoms of life, occurs as an abbreviated pathway in the bacterium Methylococcus capsulatus. Sterol 14α-demethylation is an essential step in this pathway and is catalyzed by cytochrome P450 51 (CYP51). In M. capsulatus, the enzyme consists of the P450 domain naturally fused to a ferredoxin domain at the C-terminus (CYP51fx). The structure of M. capsulatus CYP51fx was solved to 2.7 Å resolution and is the first structure of a bacterial sterol biosynthetic enzyme. The structure contained one P450 molecule per asymmetric unit with no electron density seen for ferredoxin. We connect this with the requirement of P450 substrate binding in order to activate productive ferredoxin binding. Further, the structure of the P450 domain with bound detergent (which replaced the substrate upon crystallization) was solved to 2.4 Å resolution. Comparison of these two structures to the CYP51s from human, fungi, and protozoa reveals strict conservation of the overall protein architecture. However, the structure of an "orphan" P450 from nonsterol-producing Mycobacterium tuberculosis that also has CYP51 activity reveals marked differences, suggesting that loss of function in vivo might have led to alterations in the structural constraints. Our results are consistent with the idea that eukaryotic and bacterial CYP51s evolved from a common cenancestor and that early eukaryotes may have recruited CYP51 from a bacterial source. The idea is supported by bioinformatic analysis, revealing the presence of CYP51 genes in >1,000 bacteria from nine different phyla, >50 of them being natural CYP51fx fusion proteins.


    Organizational Affiliation

    Center for Structural Biology, Vanderbilt University, Nashville, TN.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 51A551Methylococcus capsulatus str. BathMutation(s): 0 
Gene Names: cyp51MCA2711
EC: 1.14.13.70
UniProt
Find proteins for Q603T8 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath))
Explore Q603T8 
Go to UniProtKB:  Q603T8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ603T8
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]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
JDJ
Query on JDJ

Download Ideal Coordinates CCD File 
B [auth A]23-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]-3,6,9,12,15,18,21-heptaoxatricosan-1-ol
C30 H54 O9
OJLRAIOADFIRJN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.685α = 90
b = 150.685β = 90
c = 66.321γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01067871

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2021-01-20
    Changes: Database references