5XA3

Crystal Structure of P450BM3 with Benzyloxycarbonyl-L-prolyl-L-phenylalanine

• PDB DOI: https://doi.org/10.2210/pdb5XA3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium NBRC 15308 = ATCC 14581
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-10 Released: 2018-02-21 
• Deposition Author(s): Shoji, O., Yanagisawa, S., Stanfield, J.K., Suzuki, K., Kasai, C., Cong, Z., Sugimoto, H., Shiro, Y., Watanabe, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.253 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

Direct Hydroxylation of Benzene to Phenol by Cytochrome P450BM3 Triggered by Amino Acid Derivatives.

Shoji, O., Yanagisawa, S., Stanfield, J.K., Suzuki, K., Cong, Z., Sugimoto, H., Shiro, Y., Watanabe, Y.

(2017) Angew Chem Int Ed Engl 56: 10324-10329

• PubMed: 28544674 
• DOI: https://doi.org/10.1002/anie.201703461
• Primary Citation of Related Structures:  
  5XA3


• PubMed Abstract: 
  

  The selective hydroxylation of benzene to phenol, without the formation of side products resulting from overoxidation, is catalyzed by cytochrome P450BM3 with the assistance of amino acid derivatives as decoy molecules. The catalytic turnover rate and the total turnover number reached 259 min ^-1  P450BM3 ^-1 and 40 200 P450BM3 ^-1 when N-heptyl-l-proline modified with l-phenylalanine (C7-l-Pro-l-Phe) was used as the decoy molecule. This work shows that amino acid derivatives with a totally different structure from fatty acids can be used as decoy molecules for aromatic hydroxylation by wild-type P450BM3. This method for non-native substrate hydroxylation by wild-type P450BM3 has the potential to expand the utility of P450BM3 for biotransformations.

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Organizational Affiliation: 

Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 213.78 kDa 
• Atom Count: 15,645 
• Modelled Residue Count: 1,812 
• Deposited Residue Count: 1,824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH-P450 reductase	A, B, C, D	456	Priestia megaterium NBRC 15308 = ATCC 14581	Mutation(s): 0  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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], J [auth B], O [auth C], T [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PHQ	I [auth A], N [auth B], S [auth C], X [auth D]	benzyl chlorocarbonate C8 H7 Cl O2 HSDAJNMJOMSNEV-UHFFFAOYSA-N
PHE	H [auth A], M [auth B], R [auth C], W [auth D]	PHENYLALANINE C9 H11 N O2 COLNVLDHVKWLRT-QMMMGPOBSA-N
PRO	G [auth A], L [auth B], Q [auth C], V [auth D]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
DMS	F [auth A], K [auth B], P [auth C], U [auth D]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.253 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.234	α = 90
b = 58.522	β = 90.02
c = 145.952	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Shoji, O., Yanagisawa, S., Stanfield, J.K., Suzuki, K., Kasai, C., Cong, Z., Sugimoto, H., Shiro, Y., Watanabe, Y.

Revision History  

• Version 1.0: 2018-02-21
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description