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Protein

D-lysine 5,6-aminomutase beta subunit

Gene

kamE

Organism
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.1 Publication

Catalytic activityi

D-lysine = 2,5-diaminohexanoate.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • adenosylcob(III)alamin1 Publication
  • pyridoxal 5'-phosphate1 Publication

Enzyme regulationi

Rapidly inactivated in the presence of D-lysine and to a lesser extent in the absence of adenosylcobalamin (Adocbl). Activity is stable in the presence of Adocbl when D-lysine is absent. Adocbl imparts thermal stability at 37 degrees Celsius.1 Publication

Kineticsi

  1. KM=6.6 µM for adenosylcobalamin (for recombinant alpha and beta subunits expressed together in E.coli to overcome presence of corrinoids in native system)1 Publication

    Pathway:ilysine degradation

    This protein is involved in the pathway lysine degradation, which is part of Amino-acid metabolism.1 Publication
    View all proteins of this organism that are known to be involved in the pathway lysine degradation and in Amino-acid metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi133 – 1331Cobalt (adenosylcobalamin axial ligand); via tele nitrogenImported

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Ligandi

    Cobalamin, Cobalt, Metal-binding, Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciCSTI499177:GJE9-1427-MONOMER.
    UniPathwayiUPA00225.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-lysine 5,6-aminomutase beta subunitImported (EC:5.4.3.41 Publication)
    Short name:
    5,6-LAM1 Publication
    Gene namesi
    Name:kamE
    Ordered Locus Names:CLOST_1378
    OrganismiClostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
    Taxonomic identifieri499177 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaePeptoclostridium
    ProteomesiUP000007041 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 262262D-lysine 5,6-aminomutase beta subunitPRO_0000416984Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei144 – 1441N6-(pyridoxal phosphate)lysine1 Publication

    Interactioni

    Subunit structurei

    Heterotetramer of 2 alpha and 2 beta subunits.1 Publication

    Protein-protein interaction databases

    IntActiE3PRJ4. 1 interaction.
    STRINGi499177.CLOST_1378.

    Structurei

    Secondary structure

    1
    262
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi34 – 429Combined sources
    Helixi46 – 5712Combined sources
    Beta strandi65 – 739Combined sources
    Beta strandi76 – 838Combined sources
    Helixi106 – 11611Combined sources
    Beta strandi121 – 1288Combined sources
    Helixi135 – 1417Combined sources
    Helixi152 – 1543Combined sources
    Beta strandi158 – 1625Combined sources
    Beta strandi165 – 1673Combined sources
    Helixi169 – 17810Combined sources
    Beta strandi182 – 1876Combined sources
    Helixi195 – 20915Combined sources
    Helixi213 – 2153Combined sources
    Beta strandi216 – 2216Combined sources
    Helixi227 – 2315Combined sources
    Turni232 – 2343Combined sources
    Beta strandi236 – 2394Combined sources
    Helixi245 – 26016Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1XRSX-ray2.80B1-262[»]
    ProteinModelPortaliE3PRJ4.
    SMRiE3PRJ4. Positions 33-261.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiE3PRJ4.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini120 – 262143B12-bindingPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni130 – 1367Adenosylcobalamin binding1 Publication
    Regioni185 – 1928Adenosylcobalamin binding1 Publication
    Regioni219 – 2235Adenosylcobalamin binding1 Publication
    Regioni239 – 2446Adenosylcobalamin binding1 Publication

    Sequence similaritiesi

    Belongs to the KamE family.Sequence Analysis
    Contains 1 B12-binding domain.PROSITE-ProRule annotation

    Phylogenomic databases

    HOGENOMiHOG000223896.
    KOiK18011.
    OMAiAIMNMKG.

    Family and domain databases

    Gene3Di3.30.30.60. 1 hit.
    3.40.50.280. 1 hit.
    InterProiIPR006158. Cobalamin-bd.
    IPR028991. KamE_N.
    [Graphical view]
    PfamiPF02310. B12-binding. 1 hit.
    [Graphical view]
    SUPFAMiSSF117778. SSF117778. 1 hit.
    SSF52242. SSF52242. 1 hit.
    PROSITEiPS51332. B12_BINDING. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    E3PRJ4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSSGLYSMEK KEFDKVLDLE RVKPYGDTMN DGKVQLSFTL PLKNNERSAE
    60 70 80 90 100
    AAKQIALKMG LEEPSVVMQQ SLDEEFTFFV VYGNFVQSVN YNEIHVEAVN
    110 120 130 140 150
    SEILSMEETD EYIKENIGRK IVVVGASTGT DAHTVGIDAI MNMKGYAGHY
    160 170 180 190 200
    GLERYEMIDA YNLGSQVANE DFIKKAVELE ADVLLVSQTV TQKNVHIQNM
    210 220 230 240 250
    THLIELLEAE GLRDRFVLLC GGPRINNEIA KELGYDAGFG PGRFADDVAT
    260
    FAVKTLNDRM NS
    Length:262
    Mass (Da):29,224
    Last modified:March 8, 2011 - v1
    Checksum:i248765160F6EF46F
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF104259 Genomic DNA. Translation: AAC79718.1.
    FP565809 Genomic DNA. Translation: CBH21498.1.

    Genome annotation databases

    EnsemblBacteriaiCBH21498; CBH21498; CLOST_1378.
    KEGGicst:CLOST_1378.
    PATRICi42273391. VBICloSti32817_1367.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF104259 Genomic DNA. Translation: AAC79718.1.
    FP565809 Genomic DNA. Translation: CBH21498.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1XRSX-ray2.80B1-262[»]
    ProteinModelPortaliE3PRJ4.
    SMRiE3PRJ4. Positions 33-261.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiE3PRJ4. 1 interaction.
    STRINGi499177.CLOST_1378.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCBH21498; CBH21498; CLOST_1378.
    KEGGicst:CLOST_1378.
    PATRICi42273391. VBICloSti32817_1367.

    Phylogenomic databases

    HOGENOMiHOG000223896.
    KOiK18011.
    OMAiAIMNMKG.

    Enzyme and pathway databases

    UniPathwayiUPA00225.
    BioCyciCSTI499177:GJE9-1427-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiE3PRJ4.

    Family and domain databases

    Gene3Di3.30.30.60. 1 hit.
    3.40.50.280. 1 hit.
    InterProiIPR006158. Cobalamin-bd.
    IPR028991. KamE_N.
    [Graphical view]
    PfamiPF02310. B12-binding. 1 hit.
    [Graphical view]
    SUPFAMiSSF117778. SSF117778. 1 hit.
    SSF52242. SSF52242. 1 hit.
    PROSITEiPS51332. B12_BINDING. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-lysine 5, 6-aminomutase from Clostridium sticklandii."
      Chang C.H., Frey P.A.
      J. Biol. Chem. 275:106-114(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF N-TERMINUS, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, EPR SPECTROSCOPY, PATHWAY.
    2. "Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence."
      Fonknechten N., Chaussonnerie S., Tricot S., Lajus A., Andreesen J.R., Perchat N., Pelletier E., Gouyvenoux M., Barbe V., Salanoubat M., Le Paslier D., Weissenbach J., Cohen G.N., Kreimeyer A.
      BMC Genomics 11:555-555(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654.
    3. "A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase."
      Berkovitch F., Behshad E., Tang K.H., Enns E.A., Frey P.A., Drennan C.L.
      Proc. Natl. Acad. Sci. U.S.A. 101:15870-15875(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH B12 AND PYRIDOXAL PHOSPHATE, COFACTOR, SUBUNIT.

    Entry informationi

    Entry nameiKAMED_CLOSD
    AccessioniPrimary (citable) accession number: E3PRJ4
    Secondary accession number(s): Q9ZFE5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 18, 2012
    Last sequence update: March 8, 2011
    Last modified: July 22, 2015
    This is version 29 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, Complete proteome, Direct protein sequencing, Reference proteome

    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.