2Y5N

Structure of the mixed-function P450 MycG in complex with mycinamicin V in P21 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.118 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

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

  • DOI: https://doi.org/10.1074/jbc.M112.410340
  • Primary Citation of Related Structures:  
    2Y46, 2Y5N, 2Y5Z, 2Y98, 2YCA, 2YGX, 3ZSN, 4AW3

  • PubMed Abstract: 

    The majority of characterized cytochrome P450 enzymes in actinomycete secondary metabolic pathways are strictly substrate-, regio-, and stereo-specific. Examples of multifunctional biosynthetic cytochromes P450 with broader substrate and regio-specificity are growing in number and are of particular interest for biosynthetic and chemoenzymatic applications. MycG is among the first P450 monooxygenases characterized that catalyzes both hydroxylation and epoxidation reactions in the final biosynthetic steps, leading to oxidative tailoring of the 16-membered ring macrolide antibiotic mycinamicin II in the actinomycete Micromonospora griseorubida. The ordering of steps to complete the biosynthetic process involves a complex substrate recognition pattern by the enzyme and interplay between three tailoring modifications as follows: glycosylation, methylation, and oxidation. To understand the catalytic properties of MycG, we structurally characterized the ligand-free enzyme and its complexes with three native metabolites. These include substrates mycinamicin IV and V and their biosynthetic precursor mycinamicin III, which carries the monomethoxy sugar javose instead of the dimethoxylated sugar mycinose. The two methoxy groups of mycinose serve as sensors that mediate initial recognition to discriminate between closely related substrates in the post-polyketide oxidative tailoring of mycinamicin metabolites. Because x-ray structures alone did not explain the mechanisms of macrolide hydroxylation and epoxidation, paramagnetic NMR relaxation measurements were conducted. Molecular modeling based on these data indicates that in solution substrate may penetrate the active site sufficiently to place the abstracted hydrogen atom of mycinamicin IV within 6 Å of the heme iron and ~4 Å of the oxygen of iron-ligated water.


  • Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P-450-LIKE PROTEIN
A, B
417Micromonospora griseorubidaMutation(s): 0 
EC: 1.14
UniProt
Find proteins for Q59523 (Micromonospora griseorubida)
Explore Q59523 
Go to UniProtKB:  Q59523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59523
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYV
Query on MYV

Download Ideal Coordinates CCD File 
D [auth A],
O [auth B]
MYCINAMICIN V
C37 H61 N O12
YZYNKVRRUWKKRX-JGPZLTFNSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
M [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.118 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.752α = 90
b = 57.428β = 113.47
c = 101.929γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2012-09-05
    Changes: Derived calculations
  • Version 1.2: 2012-09-19
    Changes: Database references
  • Version 1.3: 2012-11-14
    Changes: Database references
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description