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Protein

D-lysine 5,6-aminomutase alpha subunit

Gene

kamD

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 the 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
    Binding sitei238 – 2381Pyridoxal phosphate1 Publication
    Binding sitei263 – 2631Pyridoxal phosphate1 Publication
    Binding sitei268 – 2681Pyridoxal phosphate1 Publication
    Binding sitei299 – 2991Pyridoxal phosphate1 Publication

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Ligandi

    Cobalamin, Cobalt, Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciCSTI499177:GJE9-1428-MONOMER.
    UniPathwayiUPA00225.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-lysine 5,6-aminomutase alpha subunitImported (EC:5.4.3.41 Publication)
    Short name:
    5,6-LAM1 Publication
    Gene namesi
    Name:kamD
    Ordered Locus Names:CLOST_1379
    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 – 519519D-lysine 5,6-aminomutase alpha subunitPRO_0000416982Add
    BLAST

    Interactioni

    Subunit structurei

    Heterotetramer of 2 alpha and 2 beta subunits.1 Publication

    Protein-protein interaction databases

    IntActiE3PRJ5. 1 interaction.
    STRINGi499177.CLOST_1379.

    Structurei

    Secondary structure

    1
    519
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi12 – 3423Combined sources
    Beta strandi36 – 383Combined sources
    Helixi39 – 4810Combined sources
    Helixi61 – 7111Combined sources
    Turni75 – 773Combined sources
    Helixi79 – 8810Combined sources
    Helixi94 – 10310Combined sources
    Turni108 – 1103Combined sources
    Helixi116 – 14833Combined sources
    Beta strandi155 – 1606Combined sources
    Helixi165 – 17713Combined sources
    Beta strandi181 – 1855Combined sources
    Helixi191 – 1933Combined sources
    Helixi213 – 23018Combined sources
    Beta strandi235 – 2395Combined sources
    Helixi245 – 25511Combined sources
    Beta strandi258 – 2614Combined sources
    Helixi266 – 2716Combined sources
    Helixi275 – 29117Combined sources
    Beta strandi295 – 2973Combined sources
    Helixi301 – 3044Combined sources
    Beta strandi305 – 3073Combined sources
    Turni309 – 3113Combined sources
    Helixi313 – 32917Combined sources
    Helixi334 – 3363Combined sources
    Beta strandi340 – 3423Combined sources
    Helixi352 – 36615Combined sources
    Beta strandi373 – 3753Combined sources
    Helixi385 – 40218Combined sources
    Beta strandi405 – 4084Combined sources
    Turni412 – 4165Combined sources
    Helixi421 – 43717Combined sources
    Turni438 – 4403Combined sources
    Helixi441 – 4444Combined sources
    Helixi452 – 48130Combined sources
    Turni482 – 4876Combined sources
    Helixi498 – 5003Combined sources
    Beta strandi501 – 5033Combined sources
    Helixi511 – 5166Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1XRSX-ray2.80A5-519[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni54 – 563Adenosylcobalamin binding1 Publication
    Regioni184 – 1896Pyridoxal phosphate binding1 Publication

    Sequence similaritiesi

    Belongs to the KamD family.Sequence Analysis

    Phylogenomic databases

    HOGENOMiHOG000223893.
    KOiK01844.
    OMAiSGLCMPE.

    Family and domain databases

    Gene3Di3.20.20.440. 1 hit.
    InterProiIPR016176. Cbl-dep_enz_cat.
    IPR015130. Lys-AminoMut_A.
    [Graphical view]
    PfamiPF09043. Lys-AminoMut_A. 1 hit.
    [Graphical view]
    SUPFAMiSSF51703. SSF51703. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    E3PRJ5-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MISVESKLNL DFNLVEKARA KAKAIAIDTQ EFIEKHTTVT VERAVCRLLG
    60 70 80 90 100
    IDGVDTDEVP LPNIVVDHIK ENNGLNLGAA MYIANAVLNT GKTPQEIAQA
    110 120 130 140 150
    ISAGELDLTK LPMKDLFEVK TKALSMAKET VEKIKNNRSI RESRFEEYGD
    160 170 180 190 200
    KSGPLLYVIV ATGNIYEDIT QAVAAAKQGA DVIAVIRTTG QSLLDYVPYG
    210 220 230 240 250
    ATTEGFGGTY ATQENFRLMR EALDKVGAEV GKYIRLCNYC SGLCMPEIAA
    260 270 280 290 300
    MGAIERLDVM LNDALYGILF RDINMQRTMI DQNFSRIING FAGVIINTGE
    310 320 330 340 350
    DNYLTTADAF EEAHTVLASQ FINEQFALLA GLPEEQMGLG HAFEMDPELK
    360 370 380 390 400
    NGFLYELSQA QMAREIFPKA PLKYMPPTKF MTGNIFKGHI QDALFNMVTI
    410 420 430 440 450
    MTNQRIHLLG MLTEALHTPF MSDRALSIEN AQYIFNNMES ISEEIQFKED
    460 470 480 490 500
    GLIQKRAGFV LEKANELLEE IEQLGLFDTL EKGIFGGVKR PKDGGKGLNG
    510
    VVSKDENYYN PFVELMLNK
    Length:519
    Mass (Da):57,626
    Last modified:January 11, 2011 - v1
    Checksum:i6FE0DEB4EC481DB1
    GO

    Sequence cautioni

    The sequence CBH21499.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti4 – 41V → M in AAC79717 (PubMed:10617592).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF104259 Genomic DNA. Translation: AAC79717.1.
    FP565809 Genomic DNA. Translation: CBH21499.1. Different initiation.

    Genome annotation databases

    EnsemblBacteriaiCBH21499; CBH21499; CLOST_1379.
    KEGGicst:CLOST_1379.
    PATRICi42273393. VBICloSti32817_1368.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF104259 Genomic DNA. Translation: AAC79717.1.
    FP565809 Genomic DNA. Translation: CBH21499.1. Different initiation.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1XRSX-ray2.80A5-519[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiE3PRJ5. 1 interaction.
    STRINGi499177.CLOST_1379.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCBH21499; CBH21499; CLOST_1379.
    KEGGicst:CLOST_1379.
    PATRICi42273393. VBICloSti32817_1368.

    Phylogenomic databases

    HOGENOMiHOG000223893.
    KOiK01844.
    OMAiSGLCMPE.

    Enzyme and pathway databases

    UniPathwayiUPA00225.
    BioCyciCSTI499177:GJE9-1428-MONOMER.

    Family and domain databases

    Gene3Di3.20.20.440. 1 hit.
    InterProiIPR016176. Cbl-dep_enz_cat.
    IPR015130. Lys-AminoMut_A.
    [Graphical view]
    PfamiPF09043. Lys-AminoMut_A. 1 hit.
    [Graphical view]
    SUPFAMiSSF51703. SSF51703. 1 hit.
    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 nameiKAMDD_CLOSD
    AccessioniPrimary (citable) accession number: E3PRJ5
    Secondary accession number(s): Q9ZFE6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 18, 2012
    Last sequence update: January 11, 2011
    Last modified: July 22, 2015
    This is version 25 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.