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Q9ZFE7

- MTND_KLEOX

UniProt

Q9ZFE7 - MTND_KLEOX

Protein

Acireductone dioxygenase

Gene

mtnD

Organism
Klebsiella oxytoca
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 66 (01 Oct 2014)
      Sequence version 2 (20 Jan 2009)
      Previous versions | rss
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    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

    Binds 1 iron ion per monomer. Can be replaced by magnesium ion, but with lower activity.
    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

    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

    1. acireductone dioxygenase (Ni2+-requiring) activity Source: UniProtKB-HAMAP
    2. acireductone dioxygenase [iron(II)-requiring] activity Source: UniProtKB-HAMAP
    3. iron ion binding Source: UniProtKB-HAMAP
    4. nickel cation binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. L-methionine biosynthetic process from methylthioadenosine Source: UniProtKB-UniPathway
    2. L-methionine biosynthetic process from S-adenosylmethionine Source: UniProtKB-HAMAP

    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.
    BRENDAi1.13.11.54. 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

    Structurei

    Secondary structure

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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

    MSALTIFSVK DPQNSLWHST NAEEIQQQLN AKGVRFERWQ ADRDLGAAPT    50
    AETVIAAYQH AIDKLVAEKG YQSWDVISLR ADNPQKEALR EKFLNEHTHG 100
    EDEVRFFVEG AGLFCLHIGD EVFQVLCEKN DLISVPAHTP HWFDMGSEPN 150
    FTAIRIFDNP EGWIAQFTGD DIASAYPRLA 180
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00148 Genomic DNA. Translation: AAC43184.1.
    AF102514 Genomic DNA. Translation: AAD11793.1.
    PIRiA59159.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00148 Genomic DNA. Translation: AAC43184.1 .
    AF102514 Genomic DNA. Translation: AAD11793.1 .
    PIRi A59159.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1ZRR NMR - A 2-180 [» ]
    2HJI NMR - A 2-180 [» ]
    ProteinModelPortali Q9ZFE7.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00904 ; UER00878 .
    BioCyci MetaCyc:MONOMER-1323.
    BRENDAi 1.13.11.54. 2811.

    Miscellaneous databases

    EvolutionaryTracei Q9ZFE7.

    Family and domain databases

    Gene3Di 2.60.120.10. 1 hit.
    HAMAPi MF_01682. Salvage_MtnD.
    InterProi IPR023956. Acireductn_d0ase.
    IPR004313. Acireductn_dOase_family.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view ]
    PANTHERi PTHR23418. PTHR23418. 1 hit.
    Pfami PF03079. ARD. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51182. SSF51182. 1 hit.
    ProtoNeti Search...

    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: October 1, 2014
    This is version 66 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