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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

    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
    Metal bindingi133Cobalt (adenosylcobalamin axial ligand); via tele nitrogenImported1

    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 lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaeAcetoanaerobium
    Proteomesi
    • UP000007041 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004169841 – 262D-lysine 5,6-aminomutase beta subunitAdd BLAST262

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei144N6-(pyridoxal phosphate)lysine1 Publication1

    Interactioni

    Subunit structurei

    Heterotetramer of 2 alpha and 2 beta subunits.1 Publication

    Protein-protein interaction databases

    IntActiE3PRJ4. 1 interactor.
    STRINGi499177.CLOST_1378.

    Structurei

    Secondary structure

    1262
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi34 – 42Combined sources9
    Helixi46 – 57Combined sources12
    Beta strandi65 – 73Combined sources9
    Beta strandi76 – 83Combined sources8
    Helixi106 – 116Combined sources11
    Beta strandi121 – 128Combined sources8
    Helixi135 – 141Combined sources7
    Helixi152 – 154Combined sources3
    Beta strandi158 – 162Combined sources5
    Beta strandi165 – 167Combined sources3
    Helixi169 – 178Combined sources10
    Beta strandi182 – 187Combined sources6
    Helixi195 – 209Combined sources15
    Helixi213 – 215Combined sources3
    Beta strandi216 – 221Combined sources6
    Helixi227 – 231Combined sources5
    Turni232 – 234Combined sources3
    Beta strandi236 – 239Combined sources4
    Helixi245 – 260Combined sources16

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiE3PRJ4.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini120 – 262B12-bindingPROSITE-ProRule annotationAdd BLAST143

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni130 – 136Adenosylcobalamin binding1 Publication7
    Regioni185 – 192Adenosylcobalamin binding1 Publication8
    Regioni219 – 223Adenosylcobalamin binding1 Publication5
    Regioni239 – 244Adenosylcobalamin binding1 Publication6

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4107CHF. Bacteria.
    COG5012. LUCA.
    HOGENOMiHOG000223896.
    KOiK18011.
    OMAiAIMNMKG.
    OrthoDBiPOG091H10H2.

    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.
    PF16554. OAM_dimer. 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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1XRSX-ray2.80B1-262[»]
    ProteinModelPortaliE3PRJ4.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiE3PRJ4. 1 interactor.
    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

    eggNOGiENOG4107CHF. Bacteria.
    COG5012. LUCA.
    HOGENOMiHOG000223896.
    KOiK18011.
    OMAiAIMNMKG.
    OrthoDBiPOG091H10H2.

    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.
    PF16554. OAM_dimer. 1 hit.
    [Graphical view]
    SUPFAMiSSF117778. SSF117778. 1 hit.
    SSF52242. SSF52242. 1 hit.
    PROSITEiPS51332. B12_BINDING. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    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: November 30, 2016
    This is version 35 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.