3EJE

Crystal Structure of P450BioI in complex with octadec-9Z-enoic acid ligated Acyl Carrier Protein

PDB DOI: https://doi.org/10.2210/pdb3EJE/pdb

Classification: OXIDOREDUCTASE/LIPID TRANSPORT
Organism(s): Escherichia coli K-12, Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-18 Released: 2008-10-07
Deposition Author(s): Cryle, M.J., Schlichting, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.274
R-Value Work: 0.240
R-Value Observed: 0.242

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex.

Cryle, M.J., Schlichting, I.

(2008) Proc Natl Acad Sci U S A 105: 15696-15701

PubMed: 18838690 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.0805983105
Primary Citation of Related Structures:
3EJB, 3EJD, 3EJE

PubMed Abstract:
Cytochrome P450(BioI) (CYP107H1) from the biotin operon of Bacillus subtilis forms a seven-carbon diacid through a multistep oxidative cleavage of a fatty acid linked to acyl carrier protein (ACP). Crystal structures of P450(BioI) in complex with three different length fatty acyl-ACP (Escherichia coli) ligands show that P450(BioI) binds the fatty acid such as to force the carbon chain into a U-shape above the active site heme. This positions the C7 and C8 carbons for oxidation, with a large additional cavity extending beyond the heme to accommodate the methyl termini of fatty acids beyond the site of cleavage. The structures explain the experimentally observed lack of stereo- and regiospecificity in the hydroxylation and cleavage of free fatty acids. The P450(BioI)-ACP complexes represent the only structurally characterized P450-carrier protein complexes to date, which has allowed the generation of a model of the interaction of the vancomycin biosynthetic P450 OxyB with its proposed carrier protein bound substrate.

Organizational Affiliation

Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany. [email protected]

Macromolecule Content

Total Structure Weight: 233.71 kDa
Atom Count: 15,827
Modelled Residue Count: 1,833
Deposited Residue Count: 2,004
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl carrier protein	A, C, E, G	97	Escherichia coli K-12	Mutation(s): 0 Gene Names: acpP, b1094, JW1080
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12)) Explore P0A6A8 Go to UniProtKB: P0A6A8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6A8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin biosynthesis cytochrome P450-like enzyme	B, D, F, H	404	Bacillus subtilis	Mutation(s): 0 Gene Names: bioI, CYP107H, BSU30190 EC: 1.14 (PDB Primary Data), 1.14.14.46 (UniProt)
UniProt
Find proteins for P53554 (Bacillus subtilis (strain 168)) Explore P53554 Go to UniProtKB: P53554
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53554
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZMO Query on ZMO Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain Q [auth E] SDF format, chain T [auth G] SDF format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth G] MOL2 format, chain I [auth A] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth E] mmCIF format, chain T [auth G] mmCIF format, chain I [auth A]	I [auth A], M [auth C], Q [auth E], T [auth G]	S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-octadec-9-enethioate C₂₉ H₅₅ N₂ O₈ P S AINKKKUPSQZPIP-FRSJXWKWSA-N		Interactions Focus chain I [auth A] Focus chain M [auth C] Focus chain Q [auth E] Focus chain T [auth G] Interactions & Density Focus chain I [auth A] Focus chain M [auth C] Focus chain Q [auth E] Focus chain T [auth G]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain O [auth D] SDF format, chain S [auth F] SDF format, chain V [auth H] MOL2 format, chain K [auth B] MOL2 format, chain O [auth D] MOL2 format, chain S [auth F] MOL2 format, chain V [auth H] mmCIF format, chain K [auth B] mmCIF format, chain O [auth D] mmCIF format, chain S [auth F] mmCIF format, chain V [auth H]	K [auth B], O [auth D], S [auth F], V [auth H]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain K [auth B] Focus chain O [auth D] Focus chain S [auth F] Focus chain V [auth H] Interactions & Density Focus chain K [auth B] Focus chain O [auth D] Focus chain S [auth F] Focus chain V [auth H]
HTG Query on HTG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain U [auth G] SDF format, chain R [auth E] SDF format, chain W [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain U [auth G] MOL2 format, chain R [auth E] MOL2 format, chain W [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain U [auth G] mmCIF format, chain R [auth E] mmCIF format, chain W [auth H]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], U [auth G], W [auth H]	heptyl 1-thio-beta-D-glucopyranoside C₁₃ H₂₆ O₅ S HPEGNLMTTNTJSP-LBELIVKGSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain U [auth G] Focus chain W [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.274
R-Value Work: 0.240
R-Value Observed: 0.242
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.2	α = 109.3
b = 92	β = 90.8
c = 108	γ = 90.1

Software Package:

Software Name	Purpose
XDS	data scaling
Coot	model building
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-10-07

Deposition Author(s):

Cryle, M.J.

Schlichting, I.

Revision History (Full details and data files)

Version 1.0: 2008-10-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-03-08
Changes: Non-polymer description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Structure summary