Structural basis for the erythro-stereospecificity of the L-arginine oxygenase VioC in viomycin biosynthesis.

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  • Author(s): Helmetag V;Helmetag V; Samel SA; Thomas MG; Marahiel MA; Essen LO
  • Source:
    The FEBS journal [FEBS J] 2009 Jul; Vol. 276 (13), pp. 3669-82. Date of Electronic Publication: 2009 May 26.
  • Publication Type:
    Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Published by Blackwell Pub. on behalf of the Federation of European Biochemical Societies Country of Publication: England NLM ID: 101229646 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1742-4658 (Electronic) Linking ISSN: 1742464X NLM ISO Abbreviation: FEBS J Subsets: MEDLINE
    • Publication Information:
      Original Publication: Oxford, UK : Published by Blackwell Pub. on behalf of the Federation of European Biochemical Societies, c2005-
    • Subject Terms:
      Protein Structure, Tertiary*; Anti-Bacterial Agents/*biosynthesis ; Arginine/*metabolism ; Bacterial Proteins/*chemistry ; Bacterial Proteins/*metabolism ; Nonheme Iron Proteins/*chemistry ; Nonheme Iron Proteins/*metabolism ; Oxygenases/*chemistry ; Oxygenases/*metabolism ; Streptomyces/*enzymology ; Viomycin/*biosynthesis; Arginine/chemistry ; Bacterial Proteins/genetics ; Catalytic Domain ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Nonheme Iron Proteins/genetics ; Oxygenases/genetics ; Protein Structure, Secondary ; Stereoisomerism ; Substrate Specificity
    • Abstract:
      The nonheme iron oxygenase VioC from Streptomyces vinaceus catalyzes Fe(II)-dependent and alpha-ketoglutarate-dependent Cbeta-hydroxylation of L-arginine during the biosynthesis of the tuberactinomycin antibiotic viomycin. Crystal structures of VioC were determined in complexes with the cofactor Fe(II), the substrate L-arginine, the product (2S,3S)-hydroxyarginine and the coproduct succinate at 1.1-1.3 A resolution. The overall structure reveals a beta-helix core fold with two additional helical subdomains that are common to nonheme iron oxygenases of the clavaminic acid synthase-like superfamily. In contrast to other clavaminic acid synthase-like oxygenases, which catalyze the formation of threo diastereomers, VioC produces the erythro diastereomer of Cbeta-hydroxylated L-arginine. This unexpected stereospecificity is caused by conformational control of the bound substrate, which enforces a gauche(-) conformer for chi(1) instead of the trans conformers observed for the asparagine oxygenase AsnO and other members of the clavaminic acid synthase-like superfamily. Additionally, the substrate specificity of VioC was investigated. The side chain of the L-arginine substrate projects outwards from the active site by undergoing interactions mainly with the C-terminal helical subdomain. Accordingly, VioC exerts broadened substrate specificity by accepting the analogs L-homoarginine and L-canavanine for Cbeta-hydroxylation.
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    • Grant Information:
      R01 AI065850 United States AI NIAID NIH HHS; R01 AI065850-04 United States AI NIAID NIH HHS; AI065850 United States AI NIAID NIH HHS
    • Molecular Sequence:
      PDB 2WBO; 2WBP; 2WBQ
    • Accession Number:
      0 (Anti-Bacterial Agents)
      0 (Bacterial Proteins)
      0 (Nonheme Iron Proteins)
      94ZLA3W45F (Arginine)
      EC 1.13.- (Oxygenases)
      EC 1.13.- (vioC protein, Chromobacterium violaceum)
      YVU35998K5 (Viomycin)
    • Publication Date:
      Date Created: 20090604 Date Completed: 20090925 Latest Revision: 20211020
    • Publication Date:
      20221213
    • Accession Number:
      PMC2771579
    • Accession Number:
      10.1111/j.1742-4658.2009.07085.x
    • Accession Number:
      19490124