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UniProtKB - P39280 (EPMB_ECOLI)

Entry version 130 (13 Nov 2019)
Sequence version 1 (01 Feb 1995)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>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)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi120Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1
    Metal bindingi124Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1
    Metal bindingi127Iron-sulfur (4Fe-4S-S-AdoMet)Sequence analysis1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    Complete GO annotation on QuickGO ...

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionIsomerase
    Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, Pyridoxal phosphate, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...    BioCyci    		EcoCyc:G7836-MONOMER
    ECOL316407:JW4106-MONOMER
    MetaCyc:G7836-MONOMER

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:epmB
    Synonyms:yjeK
    Ordered Locus Names:b4146, JW4106
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    <p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

    Cells lack CadA activity (lysine decarboxylase).1 Publication

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001722881 – 342L-lysine 2,3-aminomutaseAdd BLAST342

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei332N6-(pyridoxal phosphate)lysineBy similarity1

    Proteomic databases

    jPOST - Japan Proteome Standard Repository/Database

    More...    jPOSTi    		P39280

    PaxDb, a database of protein abundance averages across all three domains of life

    More...    PaxDbi    		P39280

    PRoteomics IDEntifications database

    More...    PRIDEi    		P39280

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    Protein-protein interaction databases

    The Biological General Repository for Interaction Datasets (BioGrid)

    More...    BioGridi    		852954, 1 interactor

    Protein interaction database and analysis system

    More...    IntActi    		P39280, 16 interactors

    STRING: functional protein association networks

    More...    STRINGi    		511145.b4146

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...    SMRi    		P39280

    Database of comparative protein structure models

    More...    ModBasei    		Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    <p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Belongs to the radical SAM superfamily. KamA family.Curated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...    eggNOGi    		ENOG4105CK3 Bacteria
    COG1509 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...    HOGENOMi    		HOG000223517

    InParanoid: Eukaryotic Ortholog Groups

    More...    InParanoidi    		P39280

    KEGG Orthology (KO)

    More...    KOi    		K19810

    Database for complete collections of gene phylogenies

    More...    PhylomeDBi    		P39280

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...    Gene3Di    		3.20.20.70, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...    InterProi    		View protein in InterPro
    IPR013785 Aldolase_TIM
    IPR022462 EpmB
    IPR003739 Lys_aminomutase/Glu_NH3_mut
    IPR007197 rSAM

    The PANTHER Classification System

    More...    PANTHERi    		PTHR30538 PTHR30538, 1 hit

    Pfam protein domain database

    More...    Pfami    		View protein in Pfam
    PF04055 Radical_SAM, 1 hit

    PIRSF; a whole-protein classification database

    More...    PIRSFi    		PIRSF004911 DUF160, 1 hit

    Structure-Function Linkage Database

    More...    SFLDi    		SFLDF00314 L-lysine_2_3-aminomutase_(yjeK, 1 hit
    SFLDS00029 Radical_SAM, 1 hit

    TIGRFAMs; a protein family database

    More...    TIGRFAMsi    		TIGR03821 EFP_modif_epmB, 1 hit
    TIGR00238 TIGR00238, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iC35F066281588CD3
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...    EMBLi

    GenBank nucleotide sequence database

    More...    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...    DDBJi
    Links Updated
    		U14003 Genomic DNA Translation: AAA97045.1
    U00096 Genomic DNA Translation: AAC77106.1
    AP009048 Genomic DNA Translation: BAE78148.1

    Protein sequence database of the Protein Information Resource

    More...    PIRi    		S56374

    NCBI Reference Sequences

    More...    RefSeqi    		NP_418570.1, NC_000913.3
    WP_000940549.1, NZ_LN832404.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...    EnsemblBacteriai    		AAC77106; AAC77106; b4146
    BAE78148; BAE78148; BAE78148

    Database of genes from NCBI RefSeq genomes

    More...    GeneIDi    		948662

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...    KEGGi    		ecj:JW4106
    eco:b4146

    Pathosystems Resource Integration Center (PATRIC)

    More...    PATRICi    		fig|1411691.4.peg.2554

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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

    SMRiP39280
    ModBaseiSearch...

    Protein-protein interaction databases

    BioGridi852954, 1 interactor
    IntActiP39280, 16 interactors
    STRINGi511145.b4146

    Proteomic databases

    jPOSTiP39280
    PaxDbiP39280
    PRIDEiP39280

    Genome annotation databases

    EnsemblBacteriaiAAC77106; AAC77106; b4146
    BAE78148; BAE78148; BAE78148
    GeneIDi948662
    KEGGiecj:JW4106
    eco:b4146
    PATRICifig|1411691.4.peg.2554

    Organism-specific databases

    EchoBASE - an integrated post-genomic database for E. coli

    More...    EchoBASEi    		EB2366

    Phylogenomic databases

    eggNOGiENOG4105CK3 Bacteria
    COG1509 LUCA
    HOGENOMiHOG000223517
    InParanoidiP39280
    KOiK19810
    PhylomeDBiP39280

    Enzyme and pathway databases

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

    Miscellaneous databases

    Protein Ontology

    More...    PROi    		PR:P39280

    Family and domain databases

    Gene3Di3.20.20.70, 1 hit
    InterProiView protein in InterPro
    IPR013785 Aldolase_TIM
    IPR022462 EpmB
    IPR003739 Lys_aminomutase/Glu_NH3_mut
    IPR007197 rSAM
    PANTHERiPTHR30538 PTHR30538, 1 hit
    PfamiView protein in Pfam
    PF04055 Radical_SAM, 1 hit
    PIRSFiPIRSF004911 DUF160, 1 hit
    SFLDiSFLDF00314 L-lysine_2_3-aminomutase_(yjeK, 1 hit
    SFLDS00029 Radical_SAM, 1 hit
    TIGRFAMsiTIGR03821 EFP_modif_epmB, 1 hit
    TIGR00238 TIGR00238, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...    ProtoNeti    		Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...    MobiDBi    		Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiEPMB_ECOLI
    <p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P39280
    Secondary accession number(s): Q2M6F8
    <p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: November 13, 2019
    This is version 130 of the entry and version 1 of the sequence. See complete history.
    <p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
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