5UHU

Solution conformation of cytochrome P450 MycG with mycinamicin IV bound


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1200 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Solution Conformations and Dynamics of Substrate-Bound Cytochrome P450 MycG.

Tietz, D.R.Podust, L.M.Sherman, D.H.Pochapsky, T.C.

(2017) Biochemistry 56: 2701-2714

  • DOI: 10.1021/acs.biochem.7b00291

  • PubMed Abstract: 
  • MycG is a P450 monooxygenase that catalyzes the sequential hydroxylation and epoxidation of mycinamicin IV (M-IV), the last two steps in the biosynthesis of mycinamicin II, a macrolide antibiotic isolated from Micromonospora griseorubida. The crystal ...

    MycG is a P450 monooxygenase that catalyzes the sequential hydroxylation and epoxidation of mycinamicin IV (M-IV), the last two steps in the biosynthesis of mycinamicin II, a macrolide antibiotic isolated from Micromonospora griseorubida. The crystal structure of MycG with M-IV bound was previously determined but showed the bound substrate in an orientation that did not rationalize the observed regiochemistry of M-IV hydroxylation. Nuclear magnetic resonance paramagnetic relaxation enhancements provided evidence of an orientation of M-IV in the MycG active site more compatible with the observed chemistry, but substrate-induced changes in the enzyme structure were not characterized. We now describe the use of amide 1 H- 15 N residual dipolar couplings as experimental restraints in solvated "soft annealing" molecular dynamics simulations to generate solution structural ensembles of M-IV-bound MycG. Chemical shift perturbations, hydrogen-deuterium exchange, and 15 N relaxation behavior provide insight into the dynamic and electronic perturbations in the MycG structure in response to M-IV binding. The solution and crystallographic structures are compared, and the possibility that the crystallographic orientation of bound M-IV represents an inhibitory mode is discussed.


    Related Citations: 
    • Substrate recognition by the multifunctional cytochrome P450 MycG in mycinamicin hydroxylation and epoxidation reactions.
      Li, S.,Tietz, D.R.,Rutaganira, F.U.,Kells, P.M.,Anzai, Y.,Kato, F.,Pochapsky, T.C.,Sherman, D.H.,Podust, L.M.
      (2012) J. Biol. Chem. 287: 37880


    Organizational Affiliation

    Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109-2216, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California , San Diego, California 92093, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mycinamicin IV hydroxylase/epoxidase
A
397Micromonospora griseorubidaMutation(s): 0 
Gene Names: mycG
EC: 1.14.-.-
Find proteins for Q59523 (Micromonospora griseorubida)
Go to UniProtKB:  Q59523
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MIV
Query on MIV

Download SDF File 
Download CCD File 
A
MYCINAMICIN IV
C37 H61 N O11
DBTIHDIIXPQOFR-JMHKOBKLSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1200 
  • Conformers Submitted: 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM44191

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence