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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: 5 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

    Pathwayi: lysine 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)DescriptionActionsGraphical viewLength
    Binding sitei238Pyridoxal phosphate1 Publication1
    Binding sitei263Pyridoxal phosphate1 Publication1
    Binding sitei268Pyridoxal phosphate1 Publication1
    Binding sitei299Pyridoxal phosphate1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    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 lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaeAcetoanaerobium
    Proteomesi
    • UP000007041 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004169821 – 519D-lysine 5,6-aminomutase alpha subunitAdd BLAST519

    Interactioni

    Subunit structurei

    Heterotetramer of 2 alpha and 2 beta subunits.1 Publication

    Protein-protein interaction databases

    IntActiE3PRJ5. 1 interactor.
    STRINGi499177.CLOST_1379.

    Structurei

    Secondary structure

    1519
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi12 – 34Combined sources23
    Beta strandi36 – 38Combined sources3
    Helixi39 – 48Combined sources10
    Helixi61 – 71Combined sources11
    Turni75 – 77Combined sources3
    Helixi79 – 88Combined sources10
    Helixi94 – 103Combined sources10
    Turni108 – 110Combined sources3
    Helixi116 – 148Combined sources33
    Beta strandi155 – 160Combined sources6
    Helixi165 – 177Combined sources13
    Beta strandi181 – 185Combined sources5
    Helixi191 – 193Combined sources3
    Helixi213 – 230Combined sources18
    Beta strandi235 – 239Combined sources5
    Helixi245 – 255Combined sources11
    Beta strandi258 – 261Combined sources4
    Helixi266 – 271Combined sources6
    Helixi275 – 291Combined sources17
    Beta strandi295 – 297Combined sources3
    Helixi301 – 304Combined sources4
    Beta strandi305 – 307Combined sources3
    Turni309 – 311Combined sources3
    Helixi313 – 329Combined sources17
    Helixi334 – 336Combined sources3
    Beta strandi340 – 342Combined sources3
    Helixi352 – 366Combined sources15
    Beta strandi373 – 375Combined sources3
    Helixi385 – 402Combined sources18
    Beta strandi405 – 408Combined sources4
    Turni412 – 416Combined sources5
    Helixi421 – 437Combined sources17
    Turni438 – 440Combined sources3
    Helixi441 – 444Combined sources4
    Helixi452 – 481Combined sources30
    Turni482 – 487Combined sources6
    Helixi498 – 500Combined sources3
    Beta strandi501 – 503Combined sources3
    Helixi511 – 516Combined sources6

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1XRSX-ray2.80A5-519[»]
    SMRiE3PRJ5.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni54 – 56Adenosylcobalamin binding1 Publication3
    Regioni184 – 189Pyridoxal phosphate binding1 Publication6

    Sequence similaritiesi

    Belongs to the KamD family.Sequence analysis

    Phylogenomic databases

    eggNOGiENOG4105EQ5. Bacteria.
    ENOG410XSK3. LUCA.
    HOGENOMiHOG000223893.
    KOiK01844.
    OMAiSGLCMPE.
    OrthoDBiPOG091H0UXE.

    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 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti4V → M in AAC79717 (PubMed:10617592).Curated1

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1XRSX-ray2.80A5-519[»]
    SMRiE3PRJ5.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiE3PRJ5. 1 interactor.
    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

    eggNOGiENOG4105EQ5. Bacteria.
    ENOG410XSK3. LUCA.
    HOGENOMiHOG000223893.
    KOiK01844.
    OMAiSGLCMPE.
    OrthoDBiPOG091H0UXE.

    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...

    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: November 30, 2016
    This is version 30 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

    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.