3-Mercaptopropionate dioxygenase Mdo (VPARA_05600, B9U5L8; EC 1.13.11.66 / BRENDA 1.13.11.91, MetaCyc MONOMER-18546) in Variovorax paradoxus strain TBEA6 is a biochemically and genetically characterized 195-amino-acid cytosolic non-heme Fe(2+)-dependent thiol dioxygenase of the RmlC-like cupin / cysteine dioxygenase type-I family (CDD cd10548, Pfam PF05995, InterPro IPR010300, PANTHER PTHR12918:SF1) encoded on genomic contig JZWI01000003 (EMBL KLN58445.1, KEGG ag:ACB72254). Mdo coordinates a mononuclear catalytic ferrous iron (Fe(2+)) center via a conserved 3-His cupin facial triad at His90, His92 (within 89-IHNHTVW-95), and His143 (PIRSR PIRSR610300-51). In the Variovorax paradoxus TBEA6 3,3'-thiodipropionic acid (TDP) catabolic pathway, Mdo catalyzes the dioxygenation of the TDP cleavage product 3-mercaptopropionate (3MP) with molecular oxygen to yield 3-sulfinopropionate (3SP), without oxidizing L-cysteine or cysteamine, supplying 3SP for CoA activation by Act (VPARA_05450) and desulfination to propionyl-CoA and sulfite by Acd (VPARA_05440).
Definition: Catalysis of the reaction: 3-mercaptopropanoate + O2 = 3-sulfinopropanoate + H+ (EC 1.13.11.66, RHEA:53808).
Justification: Directly demonstrated for purified Variovorax paradoxus TBEA6 Mdo (B9U5L8, VPARA_05600) in PMID:19001372, which oxygenates 3-mercaptopropionate to 3-sulfinopropionate and does not accept L-cysteine (GO:0017172) or cysteamine (GO:0047800).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005506 iron ion binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: True but uninformative parent molecular function already entailed by the accepted specific child term GO:0008198 (ferrous iron binding). Reason: GO:0005506 (iron ion binding) is a general parent term already entailed by GO:0008198 (ferrous iron binding) accepted in this review. Supporting Evidence: file:VARPD/mdo/mdo-uniprot.txt FT BINDING 90 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_note="catalytic" FT /evidence="ECO:0000256|PIRSR:PIRSR610300-51" |
| GO:0008198 ferrous iron binding | IEA GO_REF:0000118 | ACCEPT | Summary: Core cofactor-binding activity; Mdo coordinates a catalytic mononuclear non-heme Fe(2+) center via its conserved cupin 3-His triad (His90, His92, His143). Reason: Mdo (CDD cd10548, Pfam PF05995, InterPro IPR010300) coordinates a catalytic mononuclear Fe(2+) cofactor via His90, His92, and His143 (PIRSR PIRSR610300-51) required for thiol dioxygenase catalysis (PMID:19001372). Supporting Evidence: file:VARPD/mdo/mdo-uniprot.txt FT BINDING 90 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_note="catalytic" FT /evidence="ECO:0000256|PIRSR:PIRSR610300-51" FT BINDING 92 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_note="catalytic" FT /evidence="ECO:0000256|PIRSR:PIRSR610300-51" FT BINDING 143 FT /ligand="Fe cation" FT /ligand_id="ChEBI:CHEBI:24875" FT /ligand_note="catalytic" FT /evidence="ECO:0000256|PIRSR:PIRSR610300-51" |
| GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | IEA GO_REF:0000120 | ACCEPT | Summary: Core catalytic activity; Mdo is a biochemically verified 3-mercaptopropionate dioxygenase (EC 1.13.11.66 / BRENDA 1.13.11.91) in Variovorax paradoxus TBEA6 that incorporates both atoms of O2 into 3-mercaptopropionate to form 3-sulfinopropionate. Reason: Purified Variovorax paradoxus TBEA6 Mdo (B9U5L8, VPARA_05600) directly catalyzes the oxygenation of 3-mercaptopropionate to 3-sulfinopropionate in vivo and in vitro without activity toward L-cysteine or cysteamine (PMID:19001372). Because GO currently lacks a specific leaf term for 3-mercaptopropionate dioxygenase activity (EC 1.13.11.66), GO:0016702 is the most specific available GO term and is accepted. Supporting Evidence: PMID:19001372 Detection of 3-sulfinopropionate in the supernatant of one of these mutants during cultivation on 3,3-thiodipropionic acid as well as in vivo and in vitro enzyme assays using purified protein demonstrated oxygenation of 3-mercaptopropionic acid to 3-sulfinopropionate by this enzyme; cysteine and cysteamine were not used as substrate. file:VARPD/mdo/mdo-uniprot.txt DR BioCyc; MetaCyc:MONOMER-18546; -. DR BRENDA; 1.13.11.91; 234. |
| GO:0005829 cytosol | IC file:VARPD/mdo/mdo-uniprot.txt | NEW | Summary: Core subcellular localization of the soluble 195-aa cytoplasmic Mdo enzyme. Reason: Inferred by curator (IC) from the 195-aa sequence in file:VARPD/mdo/mdo-uniprot.txt lacking signal peptides or transmembrane helices and its purification as a soluble cytosolic enzyme (PMID:19001372). Supporting Evidence: file:VARPD/mdo/mdo-uniprot.txt PMID:19001372 Detection of 3-sulfinopropionate in the supernatant of one of these mutants during cultivation on 3,3-thiodipropionic acid as well as in vivo and in vitro enzyme assays using purified protein demonstrated oxygenation of 3-mercaptopropionic acid to 3-sulfinopropionate by this enzyme |
| GO:0044273 sulfur compound catabolic process | IMP PMID:19001372 3-mercaptopropionate dioxygenase, a cysteine dioxygenase hom... | NEW | Summary: Core biological process; Tn5::mob disruption of mdo in Variovorax paradoxus TBEA6 abolishes catabolism of 3,3'-thiodipropionic acid and 3-mercaptopropionate. Reason: Tn5::mob mutagenesis of mdo (VPARA_05600) in Variovorax paradoxus TBEA6 impairs growth on 3,3'-thiodipropionic acid and blocks conversion of the cleavage intermediate 3-mercaptopropionate to 3-sulfinopropionate (PMID:19001372). Supporting Evidence: PMID:19001372 Tn5::mob mutagenesis of isolate Variovorax paradoxus TBEA6 yielded ten mutants fully or partially impaired in growth on 3,3-thiodipropionic acid. Genotypic characterization of two 3,3-thiodipropionic acid-negative mutants demonstrated the involvement of a bacterial cysteine dioxygenase (EC 1.13.11.22) homologue in the further catabolism of the 3,3-thiodipropionic acid cleavage product 3-mercaptopropionic acid. |
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Download this section (compressed HTML)Q: Which active-site residues in the cupin barrel of Variovorax paradoxus Mdo (B9U5L8, VPARA_05600) enforce strict specificity for 3-mercaptopropionate while excluding L-cysteine and cysteamine?
Suggested experts: Steinbuchel A, Wubbeler JH, Pierce BS
Experiment: Determine the X-ray crystal structure and EPR/Mossbauer spectra of Fe(2+)-bound Variovorax paradoxus Mdo (B9U5L8) in complex with 3-mercaptopropionate and nitric oxide.
Hypothesis: Arg/Gln residues lining the cupin pocket form a salt bridge with the 3-mercaptopropionate carboxylate while sterically or electrostatically disfavoring the alpha-amino group of L-cysteine.
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