6LY4

The crystal structure of the BM3 mutant LG-23 in complex with testosterone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Regio- and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants.

Li, A.Acevedo-Rocha, C.G.D'Amore, L.Chen, J.Peng, Y.Garcia-Borras, M.Gao, C.Zhu, J.Rickerby, H.Osuna, S.Zhou, J.Reetz, M.T.

(2020) Angew Chem Int Ed Engl 59: 12499-12505

  • DOI: https://doi.org/10.1002/anie.202003139
  • Primary Citation of Related Structures:  
    6LY4

  • PubMed Abstract: 

    Steroidal C7β alcohols and their respective esters have shown significant promise as neuroprotective and anti-inflammatory agents to treat chronic neuronal damage like stroke, brain trauma, and cerebral ischemia. Since C7 is spatially far away from any functional groups that could direct C-H activation, these transformations are not readily accessible using modern synthetic organic techniques. Reported here are P450-BM3 mutants that catalyze the oxidative hydroxylation of six different steroids with pronounced C7 regioselectivities and β stereoselectivities, as well as high activities. These challenging transformations were achieved by a focused mutagenesis strategy and application of a novel technology for protein library construction based on DNA assembly and USER (Uracil-Specific Excision Reagent) cloning. Upscaling reactions enabled the purification of the respective steroidal alcohols in moderate to excellent yields. The high-resolution X-ray structure and molecular dynamics simulations of the best mutant unveil the origin of regio- and stereoselectivity.


  • Organizational Affiliation

    School of life science, Hubei University, State Key Laboratory of Biocatalysis and Enzyme Engineering, #368 Youyi Road, Wuhan, 430062, P.R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional cytochrome P450/NADPH--P450 reductase481Priestia megaterium NBRC 15308 = ATCC 14581Mutation(s): 14 
Gene Names: cyp102A1cyp102BG04_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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14779
Sequence Annotations
Expand
  • 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 
K [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
TES (Subject of Investigation/LOI)
Query on TES

Download Ideal Coordinates CCD File 
B [auth A]TESTOSTERONE
C19 H28 O2
MUMGGOZAMZWBJJ-DYKIIFRCSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
C [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.543α = 90
b = 55.738β = 94.336
c = 94.396γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2020-11-25
    Changes: Database references
  • Version 2.0: 2021-06-02
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Structure summary
  • Version 2.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description