8DSG | pdb_00008dsg

P411-PFA carbene transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.218 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Chemodivergent C(sp 3 )-H and C(sp 2 )-H Cyanomethylation Using Engineered Carbene Transferases.

Zhang, J.Maggiolo, A.O.Alfonzo, E.Mao, R.Porter, N.J.Abney, N.Arnold, F.H.

(2023) Nat Catal 6: 152-160

  • DOI: https://doi.org/10.1038/s41929-022-00908-x
  • Primary Citation Related Structures: 
    8DSG

  • PubMed Abstract: 

    The ubiquity of C-H bonds presents an attractive opportunity to elaborate and build complexity in organic molecules. Methods for selective functionalization, however, often must differentiate among multiple chemically similar and, in some cases indistinguishable, C-H bonds. An advantage of enzymes is that they can be finely tuned using directed evolution to achieve control over divergent C-H functionalization pathways. Here, we demonstrate engineered enzymes that effect a new-to-nature C-H alkylation with unparalleled selectivity: two complementary carbene C-H transferases derived from a cytochrome P450 from Bacillus megaterium deliver an α -cyanocarbene into the α -amino C(sp 3 )-H bonds or the ortho -arene C(sp 2 )-H bonds of N -substituted arenes. These two transformations proceed via different mechanisms, yet only minimal changes to the protein scaffold (nine mutations, less than 2% of the sequence) were needed to adjust the enzyme's control over the site-selectivity of cyanomethylation. The X-ray crystal structure of the selective C(sp 3 )-H alkylase, P411-PFA, reveals an unprecedented helical disruption which alters the shape and electrostatics in the enzyme active site. Overall, this work demonstrates the advantages of enzymes as C-H functionalization catalysts for divergent molecular derivatization.


  • Organizational Affiliation
    • Division of Chemistry and Chemical Engineering, California Institute of Technology; Pasadena, California, United States.

Macromolecule Content 

  • Total Structure Weight: 219.84 kDa 
  • Atom Count: 15,955 
  • Modeled Residue Count: 1,795 
  • Deposited Residue Count: 1,888 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome P450-BM3 variant P411-PFA
A, B, C, D
472Priestia megateriumMutation(s): 26 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14779
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B],
R [auth C],
U [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BTB

Query on BTB



Download:Ideal Coordinates CCD File
J [auth A],
O [auth B]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
P [auth B]
Q [auth C]
X [auth D]
H [auth A],
I [auth A],
P [auth B],
Q [auth C],
X [auth D],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
L [auth B]
M [auth B]
N [auth B]
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
S [auth C],
T [auth C],
V [auth D],
W [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.218 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.254α = 90
b = 172.462β = 90
c = 225.623γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM138740

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-05-01
    Changes: Database references