7QAN | pdb_00007qan

Cytochrome P450 Enzyme AbyV

PDB DOI: https://doi.org/10.2210/pdb7QAN/pdb

Classification: OXIDOREDUCTASE
Organism(s): Micromonospora maris AB-18-032
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-17 Released: 2022-11-30
Deposition Author(s): Parnell, A.E., Back, C.R., Race, P.R.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)

Starting Model: experimental
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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

PubMed: 36314667 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/anie.202213053
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 92.11 kDa
Atom Count: 5,776
Modeled Residue Count: 724
Deposited Residue Count: 828
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A [auth AAA], B [auth BBB]	414	Micromonospora maris AB-18-032	Mutation(s): 0 Gene Names: abyV, VAB18032_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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F4F6Q5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain T [auth BBB] SDF format, chain C [auth AAA] MOL2 format, chain T [auth BBB] MOL2 format, chain C [auth AAA] mmCIF format, chain T [auth BBB] mmCIF format, chain C [auth AAA]	C [auth AAA], T [auth BBB]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth AAA] Focus chain T [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain T [auth BBB]
P33 Query on P33 Download:Ideal Coordinates CCD File SDF format, chain M [auth AAA] MOL2 format, chain M [auth AAA] mmCIF format, chain M [auth AAA]	M [auth AAA]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain M [auth AAA] Interactions & Density Focus chain M [auth AAA]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain L [auth AAA] SDF format, chain J [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain J [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain J [auth AAA]	J [auth AAA], L [auth AAA]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain J [auth AAA] Focus chain L [auth AAA] Interactions & Density Focus chain J [auth AAA] Focus chain L [auth AAA]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] MOL2 format, chain D [auth AAA] mmCIF format, chain D [auth AAA]	D [auth AAA]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Interactions & Density Focus chain D [auth AAA]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain O [auth AAA] SDF format, chain K [auth AAA] SDF format, chain I [auth AAA] SDF format, chain H [auth AAA] SDF format, chain F [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain K [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain K [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA], H [auth AAA], I [auth AAA], K [auth AAA], O [auth AAA]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain K [auth AAA] Focus chain O [auth AAA] Interactions & Density Focus chain F [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain K [auth AAA] Focus chain O [auth AAA]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain U [auth BBB] SDF format, chain N [auth AAA] SDF format, chain G [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain U [auth BBB] MOL2 format, chain N [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain U [auth BBB] mmCIF format, chain N [auth AAA] mmCIF format, chain G [auth AAA] mmCIF format, chain E [auth AAA]	E [auth AAA], G [auth AAA], N [auth AAA], U [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain G [auth AAA] Focus chain N [auth AAA] Focus chain U [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain G [auth AAA] Focus chain N [auth AAA] Focus chain U [auth BBB]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth AAA] MOL2 format, chain P [auth AAA] mmCIF format, chain P [auth AAA]	P [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain P [auth AAA] Interactions & Density Focus chain P [auth AAA]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain W [auth BBB] SDF format, chain V [auth BBB] SDF format, chain S [auth AAA] SDF format, chain R [auth AAA] SDF format, chain Q [auth AAA] MOL2 format, chain W [auth BBB] MOL2 format, chain V [auth BBB] MOL2 format, chain S [auth AAA] MOL2 format, chain R [auth AAA] MOL2 format, chain Q [auth AAA] mmCIF format, chain W [auth BBB] mmCIF format, chain V [auth BBB] mmCIF format, chain S [auth AAA] mmCIF format, chain R [auth AAA] mmCIF format, chain Q [auth AAA]	Q [auth AAA], R [auth AAA], S [auth AAA], V [auth BBB], W [auth BBB]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA] Focus chain V [auth BBB] Focus chain W [auth BBB] Interactions & Density Focus chain Q [auth AAA] Focus chain R [auth AAA] Focus chain S [auth AAA] Focus chain V [auth BBB] Focus chain W [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.238 (Depositor), 0.238 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.77	α = 90
b = 91.83	β = 92.36
c = 82.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-30

Deposition Author(s):

Parnell, A.E.

Back, C.R.

Race, P.R.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/L01386X/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M025624/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/M012107/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/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

7QAN | pdb_00007qan

Cytochrome P450 Enzyme AbyV

Literature

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

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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