6J87

Crystal structure of HinD with NMFT and NO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Molecular basis for the P450-catalyzed C-N bond formation in indolactam biosynthesis.

He, F.Mori, T.Morita, I.Nakamura, H.Alblova, M.Hoshino, S.Awakawa, T.Abe, I.

(2019) Nat Chem Biol 15: 1206-1213

  • DOI: 10.1038/s41589-019-0380-9
  • Primary Citation of Related Structures:  
    6J85, 6J84, 6J87, 6J86, 6J88, 6J83, 6J82

  • PubMed Abstract: 
  • The catalytic versatility of cytochrome P450 monooxygenases is remarkable. Here, we present mechanistic and structural characterizations of TleB from Streptomyces blastmyceticus and its homolog HinD from Streptoalloteichus hindustanus, which catalyze unusual intramolecular C-N bond formation to generate indolactam V from the dipeptide N-methylvalyl-tryptophanol ...

    The catalytic versatility of cytochrome P450 monooxygenases is remarkable. Here, we present mechanistic and structural characterizations of TleB from Streptomyces blastmyceticus and its homolog HinD from Streptoalloteichus hindustanus, which catalyze unusual intramolecular C-N bond formation to generate indolactam V from the dipeptide N-methylvalyl-tryptophanol. In vitro analyses demonstrated that both P450s exhibit promiscuous substrate specificity, and modification of the N13-methyl group resulted in the formation of indole-fused 6/5/6 tricyclic products. Furthermore, X-ray crystal structures in complex with substrates and structure-based mutagenesis revealed the intimate structural details of the enzyme reactions. We propose that the generation of a diradical species is critical for the indolactam formation, and that the intramolecular C(sp 2 )-H amination is initiated by the abstraction of the N1 indole hydrogen. After indole radical repositioning and subsequent removal of the N13 hydrogen, the coupling of the properly-folded diradical leads to the formation of the C4-N13 bond of indolactam.


    Organizational Affiliation

    Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan. abei@mol.f.u-tokyo.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nocardicin N-oxygenaseA, B435Streptoalloteichus hindustanusMutation(s): 0 
Gene Names: SAMN05444320_102263
UniProt
Find proteins for A0A1M4Y7D5 (Streptoalloteichus hindustanus)
Explore A0A1M4Y7D5 
Go to UniProtKB:  A0A1M4Y7D5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
B9L (Subject of Investigation/LOI)
Query on B9L

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]N-[(2S)-1-hydroxy-3-(1H-indol-3-yl)propan-2-yl]-Nalpha-methyl-L-phenylalaninamide
C21 H25 N3 O2
KYNKFSNOGATNQP-PXNSSMCTSA-N
 Ligand Interaction
NO
Query on NO

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.212α = 90
b = 155.029β = 115.54
c = 56.556γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references