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Protein

L-lysine 2,3-aminomutase

Gene

epmB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

With EpmA is involved in the beta-lysylation step of the post-translational modification of translation elongation factor P (EF-P) on 'Lys-34'. EpmB appears to act before EpmA. Displays lysine 2,3-aminomutase activity, producing (R)-beta-lysine from (S)-alpha-lysine (L-lysine). Cannot use (S)-ornithine or (R)-alpha-lysine as a substrate.3 Publications

Catalytic activityi

L-lysine = (3R)-3,6-diaminohexanoate.1 Publication

Cofactori

Protein has several cofactor binding sites:

Kineticsi

kcat is 4.8 min(-1) (at pH 8 and 25 degrees Celsius).

  1. KM=5 mM for L-lysine (at pH 8 and 25 degrees Celsius)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi120 – 1201Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
    Metal bindingi124 – 1241Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis
    Metal bindingi127 – 1271Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis

    GO - Molecular functioni

    • 4 iron, 4 sulfur cluster binding Source: EcoCyc
    • intramolecular transferase activity, transferring amino groups Source: EcoCyc
    • metal ion binding Source: UniProtKB-KW
    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Ligandi

    4Fe-4S, Iron, Iron-sulfur, Metal-binding, Pyridoxal phosphate, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciEcoCyc:G7836-MONOMER.
    ECOL316407:JW4106-MONOMER.
    MetaCyc:G7836-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    L-lysine 2,3-aminomutase (EC:5.4.3.-)
    Short name:
    LAM
    Alternative name(s):
    EF-P post-translational modification enzyme B
    Gene namesi
    Name:epmB
    Synonyms:yjeK
    Ordered Locus Names:b4146, JW4106
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG12473. epmB.

    Pathology & Biotechi

    Disruption phenotypei

    Cells lack CadA activity (lysine decarboxylase).1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 342342L-lysine 2,3-aminomutasePRO_0000172288Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei332 – 3321N6-(pyridoxal phosphate)lysineBy similarity

    Proteomic databases

    PaxDbiP39280.
    PRIDEiP39280.

    Interactioni

    Protein-protein interaction databases

    IntActiP39280. 16 interactions.
    STRINGi511145.b4146.

    Structurei

    3D structure databases

    ProteinModelPortaliP39280.
    SMRiP39280. Positions 14-335.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the radical SAM superfamily. KamA family.Curated

    Phylogenomic databases

    eggNOGiENOG4105CK3. Bacteria.
    COG1509. LUCA.
    HOGENOMiHOG000223517.
    InParanoidiP39280.
    KOiK19810.
    OMAiHFPYADN.
    PhylomeDBiP39280.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR022462. EpmB.
    IPR003739. Lys_aminomutase/Glu_NH3_mut.
    IPR007197. rSAM.
    [Graphical view]
    PfamiPF04055. Radical_SAM. 1 hit.
    [Graphical view]
    PIRSFiPIRSF004911. DUF160. 1 hit.
    TIGRFAMsiTIGR03821. EFP_modif_epmB. 1 hit.
    TIGR00238. TIGR00238. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P39280-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAHIVTLNTP SREDWLTQLA DVVTDPDELL RLLNIDAEEK LLAGRSAKKL
    60 70 80 90 100
    FALRVPRSFI DRMEKGNPDD PLLRQVLTSQ DEFVIAPGFS TDPLEEQHSV
    110 120 130 140 150
    VPGLLHKYHN RALLLVKGGC AVNCRYCFRR HFPYAENQGN KRNWQTALEY
    160 170 180 190 200
    VAAHPELDEM IFSGGDPLMA KDHELDWLLT QLEAIPHIKR LRIHSRLPIV
    210 220 230 240 250
    IPARITEALV ECFARSTLQI LLVNHINHAN EVDETFRQAM AKLRRVGVTL
    260 270 280 290 300
    LNQSVLLRDV NDNAQTLANL SNALFDAGVM PYYLHVLDKV QGAAHFMVSD
    310 320 330 340
    DEARQIMREL LTLVSGYLVP KLAREIGGEP SKTPLDLQLR QQ
    Length:342
    Mass (Da):38,750
    Last modified:February 1, 1995 - v1
    Checksum:iC35F066281588CD3
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U14003 Genomic DNA. Translation: AAA97045.1.
    U00096 Genomic DNA. Translation: AAC77106.1.
    AP009048 Genomic DNA. Translation: BAE78148.1.
    PIRiS56374.
    RefSeqiNP_418570.1. NC_000913.3.
    WP_000940549.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77106; AAC77106; b4146.
    BAE78148; BAE78148; BAE78148.
    GeneIDi948662.
    KEGGiecj:JW4106.
    eco:b4146.
    PATRICi32123861. VBIEscCol129921_4278.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U14003 Genomic DNA. Translation: AAA97045.1.
    U00096 Genomic DNA. Translation: AAC77106.1.
    AP009048 Genomic DNA. Translation: BAE78148.1.
    PIRiS56374.
    RefSeqiNP_418570.1. NC_000913.3.
    WP_000940549.1. NZ_LN832404.1.

    3D structure databases

    ProteinModelPortaliP39280.
    SMRiP39280. Positions 14-335.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP39280. 16 interactions.
    STRINGi511145.b4146.

    Proteomic databases

    PaxDbiP39280.
    PRIDEiP39280.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77106; AAC77106; b4146.
    BAE78148; BAE78148; BAE78148.
    GeneIDi948662.
    KEGGiecj:JW4106.
    eco:b4146.
    PATRICi32123861. VBIEscCol129921_4278.

    Organism-specific databases

    EchoBASEiEB2366.
    EcoGeneiEG12473. epmB.

    Phylogenomic databases

    eggNOGiENOG4105CK3. Bacteria.
    COG1509. LUCA.
    HOGENOMiHOG000223517.
    InParanoidiP39280.
    KOiK19810.
    OMAiHFPYADN.
    PhylomeDBiP39280.

    Enzyme and pathway databases

    BioCyciEcoCyc:G7836-MONOMER.
    ECOL316407:JW4106-MONOMER.
    MetaCyc:G7836-MONOMER.

    Miscellaneous databases

    PROiP39280.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR022462. EpmB.
    IPR003739. Lys_aminomutase/Glu_NH3_mut.
    IPR007197. rSAM.
    [Graphical view]
    PfamiPF04055. Radical_SAM. 1 hit.
    [Graphical view]
    PIRSFiPIRSF004911. DUF160. 1 hit.
    TIGRFAMsiTIGR03821. EFP_modif_epmB. 1 hit.
    TIGR00238. TIGR00238. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiEPMB_ECOLI
    AccessioniPrimary (citable) accession number: P39280
    Secondary accession number(s): Q2M6F8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: September 7, 2016
    This is version 114 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

    Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. 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.