5UAO

Crystal structure of MibH, a lathipeptide tryptophan 5-halogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Two Flavoenzymes Catalyze the Post-Translational Generation of 5-Chlorotryptophan and 2-Aminovinyl-Cysteine during NAI-107 Biosynthesis.

Ortega, M.A.Cogan, D.P.Mukherjee, S.Garg, N.Li, B.Thibodeaux, G.N.Maffioli, S.I.Donadio, S.Sosio, M.Escano, J.Smith, L.Nair, S.K.van der Donk, W.A.

(2017) ACS Chem Biol 12: 548-557

  • DOI: https://doi.org/10.1021/acschembio.6b01031
  • Primary Citation of Related Structures:  
    5UAO

  • PubMed Abstract: 

    Lantibiotics are ribosomally synthesized and post-translationally modified antimicrobial peptides containing thioether rings. In addition to these cross-links, the clinical candidate lantibiotic NAI-107 also possesses a C-terminal S-[(Z)-2-aminovinyl]-d-cysteine (AviCys) and a unique 5-chloro-l-tryptophan (ClTrp) moiety linked to its potent bioactivity. Bioinformatic and genetic analyses on the NAI-107 biosynthetic gene cluster identified mibH and mibD as genes encoding flavoenzymes responsible for the formation of ClTrp and AviCys, respectively. The biochemical basis for the installation of these modifications on NAI-107 and the substrate specificity of either enzyme is currently unknown. Using a combination of mass spectrometry, liquid chromatography, and bioinformatic analyses, we demonstrate that MibD is an FAD-dependent Cys decarboxylase and that MibH is an FADH 2 -dependent Trp halogenase. Most FADH 2 -dependent Trp halogenases halogenate free Trp, but MibH was only active when Trp was embedded within its cognate peptide substrate deschloro NAI-107. Structural comparison of the 1.88-Å resolution crystal structure of MibH with other flavin-dependent Trp halogenases revealed that subtle amino acid differences within the MibH substrate binding site generates a solvent exposed crevice presumably involved in determining the substrate specificity of this unusual peptide halogenase.


  • Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Roger Adams Laboratory , 600 S. Mathews Ave., Urbana, Illinois 61801, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophane-5-halogenase
A, B, C, D
541Microbispora sp. ATCC PTA-5024Mutation(s): 0 
Gene Names: mlbHMPTA5024_21495
UniProt
Find proteins for W2EQU4 (Microbispora sp. ATCC PTA-5024)
Explore W2EQU4 
Go to UniProtKB:  W2EQU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW2EQU4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.436α = 64.58
b = 87.887β = 69.9
c = 100.632γ = 76.26
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata 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: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description