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E3PRJ4

- KAMED_CLOSD

UniProt

E3PRJ4 - KAMED_CLOSD

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: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 23 (01 Oct 2014)
      Sequence version 1 (08 Mar 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 presence of corrinoids in native system)1 Publication

    Pathwayi

    Sites

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

    GO - Molecular functioni

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

    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: 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.

    Structurei

    Secondary structure

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

    3D structure databases

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

    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.
    OMAiPYGDRRD.

    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

    MSSGLYSMEK KEFDKVLDLE RVKPYGDTMN DGKVQLSFTL PLKNNERSAE    50
    AAKQIALKMG LEEPSVVMQQ SLDEEFTFFV VYGNFVQSVN YNEIHVEAVN 100
    SEILSMEETD EYIKENIGRK IVVVGASTGT DAHTVGIDAI MNMKGYAGHY 150
    GLERYEMIDA YNLGSQVANE DFIKKAVELE ADVLLVSQTV TQKNVHIQNM 200
    THLIELLEAE GLRDRFVLLC GGPRINNEIA KELGYDAGFG PGRFADDVAT 250
    FAVKTLNDRM NS 262
    Length:262
    Mass (Da):29,224
    Last modified:March 8, 2011 - v1
    Checksum:i248765160F6EF46F
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF104259 Genomic DNA. Translation: AAC79718.1.
    FP565809 Genomic DNA. Translation: CBH21498.1.
    RefSeqiYP_003936403.1. NC_014614.1.

    Genome annotation databases

    EnsemblBacteriaiCBH21498; CBH21498; CLOST_1378.
    GeneIDi9854875.
    KEGGicst:CLOST_1378.
    PATRICi42273391. VBICloSti32817_1367.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF104259 Genomic DNA. Translation: AAC79718.1 .
    FP565809 Genomic DNA. Translation: CBH21498.1 .
    RefSeqi YP_003936403.1. 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 B 1-262 [» ]
    ProteinModelPortali E3PRJ4.
    SMRi E3PRJ4. Positions 33-261.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi E3PRJ4. 1 interaction.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CBH21498 ; CBH21498 ; CLOST_1378 .
    GeneIDi 9854875.
    KEGGi cst:CLOST_1378.
    PATRICi 42273391. VBICloSti32817_1367.

    Phylogenomic databases

    HOGENOMi HOG000223896.
    KOi K18011.
    OMAi PYGDRRD.

    Enzyme and pathway databases

    UniPathwayi UPA00225 .
    BioCyci CSTI499177:GJE9-1427-MONOMER.

    Family and domain databases

    Gene3Di 3.30.30.60. 1 hit.
    3.40.50.280. 1 hit.
    InterProi IPR006158. Cobalamin-bd.
    IPR028991. KamE_N.
    [Graphical view ]
    Pfami PF02310. B12-binding. 1 hit.
    [Graphical view ]
    SUPFAMi SSF117778. SSF117778. 1 hit.
    SSF52242. SSF52242. 1 hit.
    PROSITEi PS51332. B12_BINDING. 1 hit.
    [Graphical view ]
    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 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: October 1, 2014
    This is version 23 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