7QAN

Cytochrome P450 Enzyme AbyV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Role of Cytochrome P450 AbyV in the Final Stages of Abyssomicin C Biosynthesis.

Devine, A.J.Parnell, A.E.Back, C.R.Lees, N.R.Johns, S.T.Zulkepli, A.Z.Barringer, R.Zorn, K.Stach, J.E.M.Crump, M.P.Hayes, M.A.van der Kamp, M.W.Race, P.R.Willis, C.L.

(2023) Angew Chem Int Ed Engl 62: e202213053-e202213053

  • DOI: https://doi.org/10.1002/anie.202213053
  • Primary Citation of Related Structures:  
    7QAN

  • PubMed Abstract: 

    Abyssomicin C and its atropisomer are potent inhibitors of bacterial folate metabolism. They possess complex polycyclic structures, and their biosynthesis has been shown to involve several unusual enzymatic transformations. Using a combination of synthesis and in vitro assays we reveal that AbyV, a cytochrome P450 enzyme from the aby gene cluster, catalyses a key late-stage epoxidation required for the installation of the characteristic ether-bridged core of abyssomicin C. The X-ray crystal structure of AbyV has been determined, which in combination with molecular dynamics simulations provides a structural framework for our functional data. This work demonstrates the power of combining selective carbon-13 labelling with NMR spectroscopy as a sensitive tool to interrogate enzyme-catalysed reactions in vitro with no need for purification.


  • Organizational Affiliation

    School of Chemistry, University of Bristol, BS81TS, Bristol, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450A [auth AAA],
B [auth BBB]
414Micromonospora maris AB-18-032Mutation(s): 0 
Gene Names: abyVVAB18032_16385
UniProt
Find proteins for F4F6Q5 (Micromonospora maris (strain DSM 45365 / JCM 31040 / NBRC 109089 / NRRL B-24793 / AB-18-032))
Explore F4F6Q5 
Go to UniProtKB:  F4F6Q5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4F6Q5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth AAA],
T [auth BBB]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
P33
Query on P33

Download Ideal Coordinates CCD File 
M [auth AAA]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
P6G
Query on P6G

Download Ideal Coordinates CCD File 
J [auth AAA],
L [auth AAA]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
D [auth AAA]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth AAA],
H [auth AAA],
I [auth AAA],
K [auth AAA],
O [auth AAA]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth AAA],
G [auth AAA],
N [auth AAA],
U [auth BBB]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
P [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
Q [auth AAA],
R [auth AAA],
S [auth AAA],
V [auth BBB],
W [auth BBB]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.77α = 90
b = 91.83β = 92.36
c = 82.55γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L01386X/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M025624/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M012107/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T001968/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-30
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references
  • Version 1.2: 2023-01-18
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description