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Protein

3-methylitaconate isomerase

Gene

mii

Organism
Eubacterium barkeri (Clostridium barkeri)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible isomerization of (R)-3-methylitaconate to 2,3-dimethylmaleate. Has very low isomerase activity with itaconate.1 Publication

Catalytic activityi

Methylitaconate = 2,3-dimethylmaleate.3 Publications

Enzyme regulationi

Inhibited by oxidized glutathione, p-chloromercuriphenylsulfonic acid and iodoacetic acid. Not inhibited by the chelating agent alpha,alpha-dipyridyl. Activity is slightly increased by EDTA. Not activated by Fe2+, Mg2+, Mn2+ or Ca2+. Unaffected by K+, Na+, NH4+, Rb+ or Li+.1 Publication

Kineticsi

  1. KM=7 mM for (R,S)-3-methylitaconate2 Publications
  2. KM=60 mM for itaconate2 Publications

    pH dependencei

    Optimum pH is 6.8-8.2.2 Publications

    Pathwayi: nicotinate degradation

    This protein is involved in step 6 of the subpathway that synthesizes propanoate and pyruvate from 6-hydroxynicotinate.1 Publication
    Proteins known to be involved in the 8 steps of the subpathway in this organism are:
    1. 6-hydroxynicotinate reductase (Hnr)
    2. Enamidase (Ena)
    3. 2-(hydroxymethyl)glutarate dehydrogenase (Hgd)
    4. no protein annotated in this organism
    5. 2-methyleneglutarate mutase (mgm)
    6. 3-methylitaconate isomerase (mii)
    7. 2,3-dimethylmalate dehydratase small subunit (DmdB), 2,3-dimethylmalate dehydratase large subunit (dmdA)
    8. 2,3-dimethylmalate lyase (Dml)
    This subpathway is part of the pathway nicotinate degradation, which is itself part of Cofactor degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes propanoate and pyruvate from 6-hydroxynicotinate, the pathway nicotinate degradation and in Cofactor degradation.

    GO - Molecular functioni

    • methylitaconate delta-isomerase activity Source: UniProtKB

    GO - Biological processi

    • cofactor catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-11717.
    BRENDAi5.3.3.6. 1459.
    UniPathwayiUPA01010; UER01017.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    3-methylitaconate isomerase (EC:5.3.3.6)
    Alternative name(s):
    (R)-3-methylitaconate isomerase1 Publication
    3-methylitaconate delta-isomerase
    Gene namesi
    Name:mii
    OrganismiEubacterium barkeri (Clostridium barkeri)
    Taxonomic identifieri1528 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesEubacteriaceaeEubacterium

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 3803803-methylitaconate isomerasePRO_0000404092Add
    BLAST

    Proteomic databases

    PRIDEiQ0QLE6.

    Expressioni

    Inductioni

    By nicotinate.1 Publication

    Interactioni

    Subunit structurei

    Homotetramer.2 Publications

    Structurei

    Secondary structure

    1
    380
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 1411Combined sources
    Beta strandi17 – 237Combined sources
    Helixi24 – 263Combined sources
    Helixi31 – 4212Combined sources
    Beta strandi52 – 543Combined sources
    Helixi58 – 603Combined sources
    Beta strandi61 – 688Combined sources
    Beta strandi75 – 839Combined sources
    Beta strandi85 – 884Combined sources
    Helixi97 – 10913Combined sources
    Beta strandi117 – 12610Combined sources
    Turni127 – 1293Combined sources
    Beta strandi132 – 1409Combined sources
    Beta strandi155 – 1573Combined sources
    Beta strandi162 – 1654Combined sources
    Helixi167 – 1693Combined sources
    Turni171 – 1744Combined sources
    Beta strandi175 – 1784Combined sources
    Beta strandi185 – 1873Combined sources
    Beta strandi194 – 21017Combined sources
    Helixi211 – 2133Combined sources
    Helixi221 – 2255Combined sources
    Helixi228 – 24417Combined sources
    Helixi251 – 2577Combined sources
    Beta strandi259 – 26911Combined sources
    Turni276 – 2783Combined sources
    Beta strandi288 – 2947Combined sources
    Beta strandi296 – 2994Combined sources
    Helixi305 – 31612Combined sources
    Helixi321 – 3255Combined sources
    Beta strandi334 – 3396Combined sources
    Beta strandi342 – 35110Combined sources
    Beta strandi354 – 3629Combined sources
    Beta strandi364 – 37512Combined sources
    Helixi376 – 3783Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3G7KX-ray2.70A/B/C/D1-380[»]
    ProteinModelPortaliQ0QLE6.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ0QLE6.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the PrpF family.Curated

    Family and domain databases

    InterProiIPR007400. PrpF_protein.
    [Graphical view]
    PfamiPF04303. PrpF. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q0QLE6-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSDQMRIPCV IMRAGTSKGI FLKGNDLPAD QELRDKVILR IFGSPDVRQI
    60 70 80 90 100
    DGLAGADPLT SKLAIIGPST HPDADVDYTF AQVSITDAVV DYNGNCGNIS
    110 120 130 140 150
    AGVGPFAIDE SFVKAVEPMT RVCIHNTNTG KLLYAEVEVE DGKAKVSGDC
    160 170 180 190 200
    KIDGVPGTNA PELMDFSDTA GAATGKVLPT GNVVDVLSTS KGDIDVSIVD
    210 220 230 240 250
    VANPCIFVHA KDVNMTGTET PDVINGNADL LAYLEEIRAK CCVKIGMAAT
    260 270 280 290 300
    EKEASEKSPA FPMIAFVTKP EDYVDFSTGN TISGDDVDLV SRLMFMQVLH
    310 320 330 340 350
    KTYAGTATAC TGSAARIPGT IVNQVLRDTG DEDTVRIGHP AGVIPVVSIV
    360 370 380
    KDGKVEKAAL IRTARRIMEG YVYVEKAKLV
    Length:380
    Mass (Da):40,273
    Last modified:September 5, 2006 - v1
    Checksum:i6D37CCBC1CD128D9
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    DQ310789 Genomic DNA. Translation: ABC88404.1.

    Genome annotation databases

    KEGGiag:ABC88404.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    DQ310789 Genomic DNA. Translation: ABC88404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3G7KX-ray2.70A/B/C/D1-380[»]
    ProteinModelPortaliQ0QLE6.
    ModBaseiSearch...
    MobiDBiSearch...

    Proteomic databases

    PRIDEiQ0QLE6.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:ABC88404.

    Enzyme and pathway databases

    UniPathwayiUPA01010; UER01017.
    BioCyciMetaCyc:MONOMER-11717.
    BRENDAi5.3.3.6. 1459.

    Miscellaneous databases

    EvolutionaryTraceiQ0QLE6.

    Family and domain databases

    InterProiIPR007400. PrpF_protein.
    [Graphical view]
    PfamiPF04303. PrpF. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    1. "Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri."
      Alhapel A., Darley D.J., Wagener N., Eckel E., Elsner N., Pierik A.J.
      Proc. Natl. Acad. Sci. U.S.A. 103:12341-12346(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PATHWAY.
      Strain: ATCC 25849 / DSM 1223 / JCM 1389 / NCIB 10623Imported.
    2. "Nicotinic acid metabolism. VI. Purification and properties of alpha-methyleneglutarate mutase (B 12-dependent) and methylitaconate isomerase."
      Kung H.F., Stadtman T.C.
      J. Biol. Chem. 246:3378-3388(1971) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, ENZYME REGULATION, INDUCTION, BIOPHYSICOCHEMICAL PROPERTIES.
    3. "Assay and purification of the adenosylcobalamin-dependent 2-methyleneglutarate mutase from Clostridium barkeri."
      Michel C., Hartrampf G., Buckel W.
      Eur. J. Biochem. 184:103-107(1989) [PubMed] [Europe PMC] [Abstract]
      Cited for: CATALYTIC ACTIVITY, SUBUNIT.
      Strain: ATCC 25849 / DSM 1223 / JCM 1389 / NCIB 106231 Publication.
    4. "Crystal structure and putative mechanism of 3-methylitaconate-delta-isomerase from Eubacterium barkeri."
      Velarde M., Macieira S., Hilberg M., Broker G., Tu S.M., Golding B.T., Pierik A.J., Buckel W., Messerschmidt A.
      J. Mol. Biol. 391:609-620(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.

    Entry informationi

    Entry nameiMII_EUBBA
    AccessioniPrimary (citable) accession number: Q0QLE6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 8, 2011
    Last sequence update: September 5, 2006
    Last modified: December 9, 2015
    This is version 33 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure

    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.