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E3PRJ5

- KAMDD_CLOSD

UniProt

E3PRJ5 - KAMDD_CLOSD

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: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 19 (01 Oct 2014)
      Sequence version 1 (11 Jan 2011)
      Previous versions | rss
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    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

    Adenosylcobalamin.1 Publication
    Pyridoxal phosphate.1 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

    Pathwayi

    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

    1. cobalamin binding Source: UniProtKB-KW
    2. D-lysine 5,6-aminomutase activity Source: UniProtKB-EC

    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: 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.

    Structurei

    Secondary structure

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    OMAiFRDINMK.

    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

    MISVESKLNL DFNLVEKARA KAKAIAIDTQ EFIEKHTTVT VERAVCRLLG    50
    IDGVDTDEVP LPNIVVDHIK ENNGLNLGAA MYIANAVLNT GKTPQEIAQA 100
    ISAGELDLTK LPMKDLFEVK TKALSMAKET VEKIKNNRSI RESRFEEYGD 150
    KSGPLLYVIV ATGNIYEDIT QAVAAAKQGA DVIAVIRTTG QSLLDYVPYG 200
    ATTEGFGGTY ATQENFRLMR EALDKVGAEV GKYIRLCNYC SGLCMPEIAA 250
    MGAIERLDVM LNDALYGILF RDINMQRTMI DQNFSRIING FAGVIINTGE 300
    DNYLTTADAF EEAHTVLASQ FINEQFALLA GLPEEQMGLG HAFEMDPELK 350
    NGFLYELSQA QMAREIFPKA PLKYMPPTKF MTGNIFKGHI QDALFNMVTI 400
    MTNQRIHLLG MLTEALHTPF MSDRALSIEN AQYIFNNMES ISEEIQFKED 450
    GLIQKRAGFV LEKANELLEE IEQLGLFDTL EKGIFGGVKR PKDGGKGLNG 500
    VVSKDENYYN PFVELMLNK 519
    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.

    Experimental Info

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

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF104259 Genomic DNA. Translation: AAC79717.1.
    FP565809 Genomic DNA. Translation: CBH21499.1. Different initiation.
    RefSeqiYP_003936404.1. NC_014614.1.

    Genome annotation databases

    EnsemblBacteriaiCBH21499; CBH21499; CLOST_1379.
    GeneIDi9856102.
    KEGGicst:CLOST_1379.
    PATRICi42273393. VBICloSti32817_1368.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF104259 Genomic DNA. Translation: AAC79717.1 .
    FP565809 Genomic DNA. Translation: CBH21499.1 . Different initiation.
    RefSeqi YP_003936404.1. NC_014614.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1XRS X-ray 2.80 A 5-519 [» ]
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi E3PRJ5. 1 interaction.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CBH21499 ; CBH21499 ; CLOST_1379 .
    GeneIDi 9856102.
    KEGGi cst:CLOST_1379.
    PATRICi 42273393. VBICloSti32817_1368.

    Phylogenomic databases

    HOGENOMi HOG000223893.
    KOi K01844.
    OMAi FRDINMK.

    Enzyme and pathway databases

    UniPathwayi UPA00225 .
    BioCyci CSTI499177:GJE9-1428-MONOMER.

    Family and domain databases

    Gene3Di 3.20.20.440. 1 hit.
    InterProi IPR016176. Cbl-dep_enz_cat.
    IPR015130. Lys-AminoMut_A.
    [Graphical view ]
    Pfami PF09043. Lys-AminoMut_A. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51703. SSF51703. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 19 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