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Entry version 47 (16 Oct 2019)
Sequence version 1 (11 Jan 2011)
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Protein

Lysine 5,6-aminomutase alpha subunit

Gene

kamD

Organism
Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654) (Clostridium sticklandii)
Status
Reviewed-Annotation score:

Annotation score:5 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

Catalyzes the migration of the L-beta-lysine and D-lysine epsilon amino group to the delta carbon to produce 3,5-diaminohexanoate and 2,5-diaminohexanoate, respectively.2 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 <a href="http://www.uniprot.org/help/function_section">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity 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

<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

  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

    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei241Pyridoxal phosphate1 Publication1
    Binding sitei266Pyridoxal phosphate1 Publication1
    Binding sitei271Pyridoxal phosphate1 Publication1
    Binding sitei302Pyridoxal phosphate1 Publication1

    <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

    <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
    LigandCobalamin, Cobalt, Pyridoxal phosphate

    Enzyme and pathway databases

    SABIO-RK: Biochemical Reaction Kinetics Database

    More...
    SABIO-RKi
    E3PRJ5

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00225

    <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:
    Lysine 5,6-aminomutase alpha subunitCurated (EC:5.4.3.32 Publications)
    Short name:
    5,6-LAM2 Publications
    Alternative name(s):
    D-lysine 5,6-aminomutase alpha subunitImported
    L-beta-lysine 5,6-aminomutase alpha subunitCurated
    <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:kamD
    Ordered Locus Names:CLOST_1379
    <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>OrganismiAcetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIMB 10654) (Clostridium sticklandii)
    <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 identifieri499177 [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 lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaeAcetoanaerobium
    <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
    • UP000007041 <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

    <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_00004169821 – 519Lysine 5,6-aminomutase alpha subunitAdd BLAST519

    <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

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Heterotetramer of 2 alpha and 2 beta subunits.

    1 Publication

    Protein-protein interaction databases

    Protein interaction database and analysis system

    More...
    IntActi
    E3PRJ5, 1 interactor

    STRING: functional protein association networks

    More...
    STRINGi
    1511.CLOST_1379

    <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

    Secondary structure

    1519
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

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

    More...
    SMRi
    E3PRJ5

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    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

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni57 – 59Adenosylcobalamin binding1 Publication3
    Regioni187 – 192Pyridoxal phosphate binding1 Publication6

    <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 KamD family.Sequence analysis

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4105EQ5 Bacteria
    ENOG410XSK3 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000223893

    KEGG Orthology (KO)

    More...
    KOi
    K01844

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    SGLCMPE

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.20.20.440, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR016176 Cbl-dep_enz_cat
    IPR015130 Lys-AminoMut_A
    IPR037086 Lys-AminoMut_asu_sf

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF09043 Lys-AminoMut_A, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51703 SSF51703, 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.

    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
    <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:i6FE0DEB4EC481DB1
    GO

    <p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

    The sequence CBH21499 differs from that shown. Reason: Erroneous initiation. Truncated N-terminus.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti4V → M in AAC79717 (PubMed:10617592).Curated1

    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
    AF104259 Genomic DNA Translation: AAC79717.1
    FP565809 Genomic DNA Translation: CBH21499.1 Different initiation.

    NCBI Reference Sequences

    More...
    RefSeqi
    WP_041487138.1, NC_014614.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    CBH21499; CBH21499; CLOST_1379

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    35557634

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    cst:CLOST_1379

    <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
    AF104259 Genomic DNA Translation: AAC79717.1
    FP565809 Genomic DNA Translation: CBH21499.1 Different initiation.
    RefSeqiWP_041487138.1, NC_014614.1

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1XRSX-ray2.80A5-519[»]
    SMRiE3PRJ5
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    IntActiE3PRJ5, 1 interactor
    STRINGi1511.CLOST_1379

    Genome annotation databases

    EnsemblBacteriaiCBH21499; CBH21499; CLOST_1379
    GeneIDi35557634
    KEGGicst:CLOST_1379

    Phylogenomic databases

    eggNOGiENOG4105EQ5 Bacteria
    ENOG410XSK3 LUCA
    HOGENOMiHOG000223893
    KOiK01844
    OMAiSGLCMPE

    Enzyme and pathway databases

    UniPathwayiUPA00225
    SABIO-RKiE3PRJ5

    Family and domain databases

    Gene3Di3.20.20.440, 1 hit
    InterProiView protein in InterPro
    IPR016176 Cbl-dep_enz_cat
    IPR015130 Lys-AminoMut_A
    IPR037086 Lys-AminoMut_asu_sf
    PfamiView protein in Pfam
    PF09043 Lys-AminoMut_A, 1 hit
    SUPFAMiSSF51703 SSF51703, 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 nameiKAMD_ACESD
    <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: E3PRJ5
    Secondary accession number(s): Q9ZFE6
    <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: April 18, 2012
    Last sequence update: January 11, 2011
    Last modified: October 16, 2019
    This is version 47 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

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
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