7CU2

CRYSTAL STRUCTURE OF STREPTOMYCES ALBOGRISEOLUS FLAVIN-DEPENDENT TRYPTOPHAN 6-HALOGENASE THAL IN COMPLEX WITH REDUCED FAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Dissecting the low catalytic capability of flavin-dependent halogenases.

Phintha, A.Prakinee, K.Jaruwat, A.Lawan, N.Visitsatthawong, S.Kantiwiriyawanitch, C.Songsungthong, W.Trisrivirat, D.Chenprakhon, P.Mulholland, A.van Pee, K.H.Chitnumsub, P.Chaiyen, P.

(2020) J Biol Chem 296: 100068-100068

  • DOI: https://doi.org/10.1074/jbc.RA120.016004
  • Primary Citation of Related Structures:  
    7CU0, 7CU1, 7CU2

  • PubMed Abstract: 

    Although flavin-dependent halogenases (FDHs) are attractive biocatalysts, their practical applications are limited because of their low catalytic efficiency. Here, we investigated the reaction mechanisms and structures of tryptophan 6-halogenase (Thal) from Streptomyces albogriseolus using stopped-flow, rapid-quench flow, quantum/mechanics molecular mechanics calculations, crystallography, and detection of intermediate (hypohalous acid [HOX]) liberation. We found that the key flavin intermediate, C4a-hydroperoxyflavin (C4aOOH-FAD), formed by Thal and other FDHs (tryptophan 7-halogenase [PrnA] and tryptophan 5-halogenase [PyrH]), can react with I - , Br - , and Cl - but not F - to form C4a-hydroxyflavin and HOX. Our experiments revealed that I - reacts with C4aOOH-FAD the fastest with the lowest energy barrier and have shown for the first time that a significant amount of the HOX formed leaks out as free HOX. This leakage is probably a major cause of low product coupling ratios in all FDHs. Site-saturation mutagenesis of Lys79 showed that changing Lys79 to any other amino acid resulted in an inactive enzyme. However, the levels of liberated HOX of these variants are all similar, implying that Lys79 probably does not form a chloramine or bromamine intermediate as previously proposed. Computational calculations revealed that Lys79 has an abnormally lower pKa compared with other Lys residues, implying that the catalytic Lys may act as a proton donor in catalysis. Analysis of new X-ray structures of Thal also explains why premixing of FDHs with reduced flavin adenine dinucleotide generally results in abolishment of C4aOOH-FAD formation. These findings reveal the hidden factors restricting FDHs capability which should be useful for future development of FDHs applications.


  • Organizational Affiliation

    Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan 6-halogenase
A, B
551Streptomyces albogriseolusMutation(s): 0 
Gene Names: thalthdH
EC: 1.14.19.59
UniProt
Find proteins for A1E280 (Streptomyces albogriseolus)
Explore A1E280 
Go to UniProtKB:  A1E280
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1E280
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.454α = 90
b = 119.311β = 104.37
c = 86.627γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction
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: 2020-11-25
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description