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Protein

Acireductone dioxygenase

Gene

mtnD

Organism
Klebsiella oxytoca
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes 2 different reactions between oxygene and the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene) depending upon the metal bound in the active site. Fe-containing acireductone dioxygenase (Fe-ARD) produces formate and 2-keto-4-methylthiobutyrate (KMTB), the alpha-ketoacid precursor of methionine in the methionine recycle pathway. Ni-containing acireductone dioxygenase (Ni-ARD) produces methylthiopropionate, carbon monoxide and formate, and does not lie on the methionine recycle pathway.1 Publication

Catalytic activityi

1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 3-(methylthio)propanoate + formate + CO.1 Publication
1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + O2 = 4-(methylthio)-2-oxobutanoate + formate.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • Fe2+, Mg2+Note: Binds 1 Fe(2+) ion per monomer. Can be replaced by Mg2+, but with lower activity.
  • Ni2+, Mn2+, Co2+Note: Binds 1 nickel ion per monomer. Can be replaced by manganese or cobalt ions.

Kineticsi

  1. KM=50 µM for 1,2-dihydroxy-3-keto-1-hexene (with Ni-ARD)1 Publication
  2. KM=52 µM for 1,2-dihydroxy-3-keto-1-hexene (with Fe-ARD)1 Publication
  3. KM=47 µM for oxygene (with Fe-ARD)1 Publication
  4. KM=110 µM for oxygene (with Ni-ARD)1 Publication

    Pathway: L-methionine biosynthesis via salvage pathway

    This protein is involved in step 5 of the subpathway that synthesizes L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate.
    Proteins known to be involved in the 6 steps of the subpathway in this organism are:
    1. no protein annotated in this organism
    2. no protein annotated in this organism
    3. Enolase-phosphatase E1 (mtnC)
    4. Enolase-phosphatase E1 (mtnC)
    5. Acireductone dioxygenase (mtnD)
    6. no protein annotated in this organism
    This subpathway is part of the pathway L-methionine biosynthesis via salvage pathway, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-methionine from S-methyl-5-thio-alpha-D-ribose 1-phosphate, the pathway L-methionine biosynthesis via salvage pathway and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei96 – 961May play a role in metal incorporation in vivo
    Metal bindingi97 – 971Iron; alternate
    Metal bindingi97 – 971Nickel; alternate
    Metal bindingi99 – 991Iron; alternate
    Metal bindingi99 – 991Nickel; alternate
    Sitei102 – 1021May play a role in transmitting local conformational changes
    Metal bindingi103 – 1031Iron; alternate
    Metal bindingi103 – 1031Nickel; alternate
    Sitei105 – 1051Important to generate the dianion
    Metal bindingi141 – 1411Iron; alternate
    Metal bindingi141 – 1411Nickel; alternate

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Dioxygenase, Oxidoreductase

    Keywords - Biological processi

    Amino-acid biosynthesis, Methionine biosynthesis

    Keywords - Ligandi

    Iron, Metal-binding, Nickel

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-1323.
    BRENDAi1.13.11.53. 2811.
    1.13.11.54. 2811.
    UniPathwayiUPA00904; UER00878.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Acireductone dioxygenase
    Alternative name(s):
    1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
    Short name:
    DHK-MTPene dioxygenase
    Acireductone dioxygenase (Fe(2+)-requiring) (EC:1.13.11.54)
    Short name:
    ARD'
    Short name:
    Fe-ARD
    Acireductone dioxygenase (Ni(2+)-requiring) (EC:1.13.11.53)
    Short name:
    ARD
    Short name:
    Ni-ARD
    Gene namesi
    Name:mtnD
    Synonyms:masB
    OrganismiKlebsiella oxytoca
    Taxonomic identifieri571 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeKlebsiella

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi96 – 961E → A: Loss of dioxygenase activity and decrease in expression of soluble protein. 1 Publication
    Mutagenesisi97 – 971H → A: Loss of dioxygenase activity and strong decrease in expression of soluble protein. 1 Publication
    Mutagenesisi99 – 991H → A: Loss of dioxygenase activity and decrease in expression of soluble protein. 1 Publication
    Mutagenesisi99 – 991H → S: Loss of dioxygenase activity, and little affinity for either Ni(2+) or Fe(3+) ions. 1 Publication
    Mutagenesisi101 – 1011E → A: Strong decrease in dioxygenase activity. Exhibits high affinity for both Ni(2+) and Fe(3+) ions, but the activities of both Ni(2+)- and Fe(3+)-reconstituted mutant are considerably lower than wild-type enzymes. 1 Publication
    Mutagenesisi102 – 1021D → A: Shows a slight decrease in dioxygenase activity and high affinity for both Ni(2+) and Fe(3+) ions. 1 Publication
    Mutagenesisi103 – 1031E → A: Loss of dioxygenase activity and strong decrease in expression of soluble protein. 1 Publication
    Mutagenesisi141 – 1411H → A: No expression of soluble protein. 1 Publication
    Mutagenesisi141 – 1411H → F: Strong decrease in expression of soluble protein. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 180180Acireductone dioxygenasePRO_0000359200Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.3 Publications

    Protein-protein interaction databases

    STRINGi1006551.KOX_14110.

    Structurei

    Secondary structure

    1
    180
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 75Combined sources
    Beta strandi12 – 143Combined sources
    Beta strandi15 – 195Combined sources
    Helixi23 – 319Combined sources
    Beta strandi35 – 373Combined sources
    Helixi51 – 6919Combined sources
    Beta strandi72 – 776Combined sources
    Helixi85 – 9410Combined sources
    Beta strandi97 – 1015Combined sources
    Beta strandi103 – 1108Combined sources
    Beta strandi122 – 1265Combined sources
    Beta strandi132 – 1354Combined sources
    Beta strandi141 – 1444Combined sources
    Beta strandi152 – 1576Combined sources
    Helixi160 – 1623Combined sources
    Beta strandi163 – 1653Combined sources
    Helixi173 – 1753Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1ZRRNMR-A2-180[»]
    2HJINMR-A2-180[»]
    ProteinModelPortaliQ9ZFE7.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9ZFE7.

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di2.60.120.10. 1 hit.
    HAMAPiMF_01682. Salvage_MtnD.
    InterProiIPR023956. Acireductn_d0ase.
    IPR004313. Acireductn_dOase_family.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view]
    PANTHERiPTHR23418. PTHR23418. 1 hit.
    PfamiPF03079. ARD. 1 hit.
    [Graphical view]
    SUPFAMiSSF51182. SSF51182. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q9ZFE7-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSALTIFSVK DPQNSLWHST NAEEIQQQLN AKGVRFERWQ ADRDLGAAPT
    60 70 80 90 100
    AETVIAAYQH AIDKLVAEKG YQSWDVISLR ADNPQKEALR EKFLNEHTHG
    110 120 130 140 150
    EDEVRFFVEG AGLFCLHIGD EVFQVLCEKN DLISVPAHTP HWFDMGSEPN
    160 170 180
    FTAIRIFDNP EGWIAQFTGD DIASAYPRLA
    Length:180
    Mass (Da):20,329
    Last modified:January 20, 2009 - v2
    Checksum:i7EC4B7E668C91F14
    GO

    Mass spectrometryi

    Molecular mass is 20252 Da from positions 2 - 180. Determined by ESI. Ni-ARD.2 Publications
    Molecular mass is 20238 Da from positions 2 - 180. Determined by ESI. Fe-ARD.1 Publication
    Molecular mass is 20236 Da from positions 2 - 180. Determined by ESI. Fe-ARD.1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00148 Genomic DNA. Translation: AAC43184.1.
    AF102514 Genomic DNA. Translation: AAD11793.1.
    PIRiA59159.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00148 Genomic DNA. Translation: AAC43184.1.
    AF102514 Genomic DNA. Translation: AAD11793.1.
    PIRiA59159.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1ZRRNMR-A2-180[»]
    2HJINMR-A2-180[»]
    ProteinModelPortaliQ9ZFE7.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi1006551.KOX_14110.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayiUPA00904; UER00878.
    BioCyciMetaCyc:MONOMER-1323.
    BRENDAi1.13.11.53. 2811.
    1.13.11.54. 2811.

    Miscellaneous databases

    EvolutionaryTraceiQ9ZFE7.

    Family and domain databases

    Gene3Di2.60.120.10. 1 hit.
    HAMAPiMF_01682. Salvage_MtnD.
    InterProiIPR023956. Acireductn_d0ase.
    IPR004313. Acireductn_dOase_family.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view]
    PANTHERiPTHR23418. PTHR23418. 1 hit.
    PfamiPF03079. ARD. 1 hit.
    [Graphical view]
    SUPFAMiSSF51182. SSF51182. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Appendix. Cloning and sequence of the gene encoding enzyme E-1 from the methionine salvage pathway of Klebsiella oxytoca."
      Balakrishnan R., Frohlich M., Rahaim P.T., Backman K., Yocum R.R.
      J. Biol. Chem. 268:24792-24795(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-82.
      Strain: M5a1.
    2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 2-180, PROTEIN SEQUENCE OF N-TERMINUS, MASS SPECTROMETRY, COFACTOR.
      Strain: UNF932.
    3. "A bacterial enzyme that catalyzes formation of carbon monoxide."
      Wray J.W., Abeles R.H.
      J. Biol. Chem. 268:21466-21469(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
    4. "Mechanistic studies of two dioxygenases in the methionine salvage pathway of Klebsiella pneumoniae."
      Dai Y., Pochapsky T.C., Abeles R.H.
      Biochemistry 40:6379-6387(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: MASS SPECTROMETRY, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
    5. "Characterization of metal binding in the active sites of acireductone dioxygenase isoforms from Klebsiella ATCC 8724."
      Chai S.C., Ju T., Dang M., Goldsmith R.B., Maroney M.J., Pochapsky T.C.
      Biochemistry 47:2428-2438(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF GLU-96; HIS-97; HIS-99; GLU-101; ASP-102; GLU-103 AND HIS-141, COFACTOR.
    6. "Modeling and experiment yields the structure of acireductone dioxygenase from Klebsiella pneumoniae."
      Pochapsky T.C., Pochapsky S.S., Ju T., Mo H., Al-Mjeni F., Maroney M.J.
      Nat. Struct. Biol. 9:966-972(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR, SUBUNIT, COFACTOR.
    7. "A refined model for the structure of acireductone dioxygenase from Klebsiella ATCC 8724 incorporating residual dipolar couplings."
      Pochapsky T.C., Pochapsky S.S., Ju T., Hoefler C., Liang J.
      J. Biomol. NMR 34:117-127(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR.
    8. "One protein, two enzymes revisited: a structural entropy switch interconverts the two isoforms of acireductone dioxygenase."
      Ju T., Goldsmith R.B., Chai S.C., Maroney M.J., Pochapsky S.S., Pochapsky T.C.
      J. Mol. Biol. 363:823-834(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR, SUBUNIT.

    Entry informationi

    Entry nameiMTND_KLEOX
    AccessioniPrimary (citable) accession number: Q9ZFE7
    Secondary accession number(s): Q48390
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 20, 2009
    Last sequence update: January 20, 2009
    Last modified: June 24, 2015
    This is version 70 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.