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 

Starting Model: experimental
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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
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  • 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

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J [auth AAA],
L [auth AAA]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PGE
Query on PGE

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D [auth AAA]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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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

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P [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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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

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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