2WBP
Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydroxyarginine, and succinate
Summary for 2WBP
| Entry DOI | 10.2210/pdb2wbp/pdb |
| Related | 2WBO 2WBQ |
| Descriptor | L-ARGININE BETA-HYDROXYLASE, ARGININE, FE (II) ION, ... (7 entities in total) |
| Functional Keywords | oxidoreductase, non-heme fe(ii) hydroxylase, cbeta-hydroxylation, nrps, viomycin, alpha-ketoglutarate |
| Biological source | STREPTOMYCES VINACEUS |
| Total number of polymer chains | 1 |
| Total formula weight | 40112.64 |
| Authors | Helmetag, V.,Samel, S.A.,Thomas, M.G.,Marahiel, M.A.,Essen, L.-O. (deposition date: 2009-03-02, release date: 2009-06-23, Last modification date: 2023-12-13) |
| Primary citation | Helmetag, V.,Samel, S.A.,Thomas, M.G.,Marahiel, M.A.,Essen, L.-O. Structural Basis for the Erythro-Stereospecificity of the L-Arginine Oxygenase Vioc in Viomycin Biosynthesis. FEBS J., 276:3669-, 2009 Cited by PubMed 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. PubMed: 19490124DOI: 10.1111/J.1742-4658.2009.07085.X PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.16 Å) |
Structure validation
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