5JQV

Crystal structure of Cytochrome P450 BM3 heme domain T269V/L272W/L322I/A406S (WIVS) variant with iron(III) deuteroporphyrin IX bound

PDB DOI: https://doi.org/10.2210/pdb5JQV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Priestia megaterium NBRC 15308 = ATCC 14581
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2016-05-05 Released: 2016-09-28
Deposition Author(s): Reynolds, E.W., McHenry, M.W., Cannac, F., Gober, J.G., Snow, C.D., Brustad, E.M.
Funding Organization(s): Defense Advanced Research Projects Agency, National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.284 (Depositor), 0.280 (DCC)
R-Value Work:
0.215 (Depositor), 0.210 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

An Evolved Orthogonal Enzyme/Cofactor Pair.

Reynolds, E.W., McHenry, M.W., Cannac, F., Gober, J.G., Snow, C.D., Brustad, E.M.

(2016) J Am Chem Soc 138: 12451-12458

PubMed: 27575374 Search on PubMed
DOI: https://doi.org/10.1021/jacs.6b05847
Primary Citation of Related Structures:
5JQU, 5JQV

PubMed Abstract:
We introduce a strategy that expands the functionality of hemoproteins through orthogonal enzyme/heme pairs. By exploiting the ability of a natural heme transport protein, ChuA, to promiscuously import heme derivatives, we have evolved a cytochrome P450 (P450BM3) that selectively incorporates a nonproteinogenic cofactor, iron deuteroporphyrin IX (Fe-DPIX), even in the presence of endogenous heme. Crystal structures show that selectivity gains are due to mutations that introduce steric clash with the heme vinyl groups while providing a complementary binding surface for the smaller Fe-DPIX cofactor. Furthermore, the evolved orthogonal enzyme/cofactor pair is active in non-natural carbenoid-mediated olefin cyclopropanation. This methodology for the generation of orthogonal enzyme/cofactor pairs promises to expand cofactor diversity in artificial metalloenzymes.

Organizational Affiliation

Department of Chemistry, University of North Carolina-Chapel Hill , 125 South Road, CB 3290, Chapel Hill, North Carolina 27599, United States.

Macromolecule Content

Total Structure Weight: 436.71 kDa
Atom Count: 30,012
Modelled Residue Count: 3,619
Deposited Residue Count: 3,768
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B, C, D, E A, B, C, D, E, F, G, H	471	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 4 Gene Names: cyp102A1, cyp102, BG04_163 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779 Go to UniProtKB: P14779
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14779
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FDE Query on FDE Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth G] SDF format, chain P [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth G] MOL2 format, chain P [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth G] mmCIF format, chain P [auth H]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	FE(III) DEUTEROPORPHYRIN IX C₃₀ H₂₈ Fe N₄ O₄ QQYZTXBVPVYDJC-RWRCOHKGSA-L		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.284 (Depositor), 0.280 (DCC)
R-Value Work: 0.215 (Depositor), 0.210 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.708	α = 90
b = 167.405	β = 90
c = 228.471	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Defense Advanced Research Projects Agency	United States	D13AP00024
National Science Foundation (NSF, United States)	United States	DGE1144081

Revision History (Full details and data files)

Version 1.0: 2016-09-28
Type: Initial release
Version 1.1: 2016-10-05
Changes: Database references
Version 1.2: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2019-11-27
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description