6J84 | pdb_00006j84

Crystal structure of TleB with hydroxyl analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.226 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.181 (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

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: https://doi.org/10.1038/s41589-019-0380-9
  • Primary Citation Related Structures: 
    6J82, 6J83, 6J84, 6J85, 6J86, 6J87, 6J88

  • 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. 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
    • Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 47.93 kDa 
  • Atom Count: 3,433 
  • Modeled Residue Count: 392 
  • Deposited Residue Count: 418 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome P-450418Streptomyces blastmyceticusMutation(s): 0 
Gene Names: tleB
UniProt
Find proteins for A0A077KEB8 (Streptomyces blastmyceticus)
Explore A0A077KEB8 
Go to UniProtKB:  A0A077KEB8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A077KEB8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
B9U

Query on B9U



Download:Ideal Coordinates CCD File
C [auth A](2S)-2-hydroxy-N-[(2S)-1-hydroxy-3-(1H-indol-3-yl)propan-2-yl]-3-methylbutanamide
C16 H22 N2 O3
DXJFYGFPQOYURY-WFASDCNBSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.808α = 90
b = 84.241β = 90
c = 112.901γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description