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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 Fe2+ 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

    Pathwayi: 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. Methylthioribose-1-phosphate isomerase (mtnA), Methylthioribose-1-phosphate isomerase (mtnA), Methylthioribose-1-phosphate isomerase (mtnA), Methylthioribose-1-phosphate isomerase (mtnA), Methylthioribose-1-phosphate isomerase (mtnA), Methylthioribose-1-phosphate isomerase (mtnA), Methylthioribose-1-phosphate isomerase (mtnA), Methylthioribose-1-phosphate isomerase (mtnA), Methylthioribose-1-phosphate isomerase (mtnA)
    2. Methylthioribulose-1-phosphate dehydratase (mtnB), Methylthioribulose-1-phosphate dehydratase (mtnB), Methylthioribulose-1-phosphate dehydratase (mtnB), Methylthioribulose-1-phosphate dehydratase (mtnB), Methylthioribulose-1-phosphate dehydratase (mtnB), Methylthioribulose-1-phosphate dehydratase (mtnB), Methylthioribulose-1-phosphate dehydratase (mtnB), Methylthioribulose-1-phosphate dehydratase (mtnB)
    3. Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC)
    4. Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC), Enolase-phosphatase E1 (mtnC)
    5. Acireductone dioxygenase (mtnD), Acireductone dioxygenase (mtnD), Acireductone dioxygenase (mtnD), Acireductone dioxygenase (mtnD), Acireductone dioxygenase (mtnD), Acireductone dioxygenase (mtnD), Acireductone dioxygenase (mtnD), Acireductone dioxygenase (mtnD), Acireductone dioxygenase (mtnD), 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)DescriptionActionsGraphical viewLength
    Sitei96May play a role in metal incorporation in vivo1
    Metal bindingi97Iron; alternate1
    Metal bindingi97Nickel; alternate1
    Metal bindingi99Iron; alternate1
    Metal bindingi99Nickel; alternate1
    Sitei102May play a role in transmitting local conformational changes1
    Metal bindingi103Iron; alternate1
    Metal bindingi103Nickel; alternate1
    Sitei105Important to generate the dianion1
    Metal bindingi141Iron; alternate1
    Metal bindingi141Nickel; alternate1

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeKlebsiella

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi96E → A: Loss of dioxygenase activity and decrease in expression of soluble protein. 1 Publication1
    Mutagenesisi97H → A: Loss of dioxygenase activity and strong decrease in expression of soluble protein. 1 Publication1
    Mutagenesisi99H → A: Loss of dioxygenase activity and decrease in expression of soluble protein. 1 Publication1
    Mutagenesisi99H → S: Loss of dioxygenase activity, and little affinity for either Ni(2+) or Fe(3+) ions. 1 Publication1
    Mutagenesisi101E → 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 Publication1
    Mutagenesisi102D → A: Shows a slight decrease in dioxygenase activity and high affinity for both Ni(2+) and Fe(3+) ions. 1 Publication1
    Mutagenesisi103E → A: Loss of dioxygenase activity and strong decrease in expression of soluble protein. 1 Publication1
    Mutagenesisi141H → A: No expression of soluble protein. 1 Publication1
    Mutagenesisi141H → F: Strong decrease in expression of soluble protein. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00003592001 – 180Acireductone dioxygenaseAdd BLAST180

    Interactioni

    Subunit structurei

    Monomer.3 Publications

    Protein-protein interaction databases

    STRINGi1006551.KOX_14110.

    Structurei

    Secondary structure

    1180
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 7Combined sources5
    Beta strandi12 – 14Combined sources3
    Beta strandi15 – 19Combined sources5
    Helixi23 – 31Combined sources9
    Beta strandi35 – 37Combined sources3
    Helixi51 – 69Combined sources19
    Beta strandi72 – 77Combined sources6
    Helixi85 – 94Combined sources10
    Beta strandi97 – 101Combined sources5
    Beta strandi103 – 110Combined sources8
    Beta strandi122 – 126Combined sources5
    Beta strandi132 – 135Combined sources4
    Beta strandi141 – 144Combined sources4
    Beta strandi152 – 157Combined sources6
    Helixi160 – 162Combined sources3
    Beta strandi163 – 165Combined sources3
    Helixi173 – 175Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1ZRRNMR-A2-180[»]
    2HJINMR-A2-180[»]
    ProteinModelPortaliQ9ZFE7.
    SMRiQ9ZFE7.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9ZFE7.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4108CAF. Bacteria.
    COG1791. LUCA.
    KOiK08967.

    Family and domain databases

    Gene3Di2.60.120.10. 1 hit.
    HAMAPiMF_01682. Salvage_MtnD. 1 hit.
    InterProiIPR004313. ARD.
    IPR023956. ARD_bac.
    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.
    RefSeqiWP_004135399.1. NZ_JWBI01000217.1.

    Genome annotation databases

    KEGGiag:AAD11793.

    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.
    RefSeqiWP_004135399.1. NZ_JWBI01000217.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1ZRRNMR-A2-180[»]
    2HJINMR-A2-180[»]
    ProteinModelPortaliQ9ZFE7.
    SMRiQ9ZFE7.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi1006551.KOX_14110.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:AAD11793.

    Phylogenomic databases

    eggNOGiENOG4108CAF. Bacteria.
    COG1791. LUCA.
    KOiK08967.

    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. 1 hit.
    InterProiIPR004313. ARD.
    IPR023956. ARD_bac.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view]
    PANTHERiPTHR23418. PTHR23418. 1 hit.
    PfamiPF03079. ARD. 1 hit.
    [Graphical view]
    SUPFAMiSSF51182. SSF51182. 1 hit.
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 73 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

    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 one 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.