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Q2JLR0

- DAPF_SYNJB

UniProt

Q2JLR0 - DAPF_SYNJB

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Synechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium Yellowstone B-Prime)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 60 (01 Oct 2014)
      Sequence version 1 (07 Mar 2006)
      Previous versions | rss
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    Functioni

    Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan.UniRule annotation

    Catalytic activityi

    LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei15 – 151SubstrateUniRule annotation
    Binding sitei49 – 491SubstrateUniRule annotation
    Binding sitei68 – 681SubstrateUniRule annotation
    Active sitei77 – 771Proton donor/acceptorUniRule annotation
    Binding sitei165 – 1651SubstrateUniRule annotation
    Sitei167 – 1671Important for catalytic activityUniRule annotation
    Binding sitei201 – 2011SubstrateUniRule annotation
    Sitei219 – 2191Important for catalytic activityUniRule annotation
    Active sitei228 – 2281Proton donor/acceptorUniRule annotation

    GO - Molecular functioni

    1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Amino-acid biosynthesis, Lysine biosynthesis

    Enzyme and pathway databases

    BioCyciSSP321332:GH1B-1371-MONOMER.
    UniPathwayiUPA00034; UER00025.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
    Short name:
    DAP epimeraseUniRule annotation
    Gene namesi
    Name:dapFUniRule annotation
    Ordered Locus Names:CYB_1371
    OrganismiSynechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium Yellowstone B-Prime)
    Taxonomic identifieri321332 [NCBI]
    Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus
    ProteomesiUP000001938: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 285285Diaminopimelate epimerasePRO_1000011975Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi77 ↔ 228

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi321332.CYB_1371.

    Structurei

    3D structure databases

    ProteinModelPortaliQ2JLR0.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni12 – 132Substrate bindingUniRule annotation
    Regioni77 – 793Substrate bindingUniRule annotation
    Regioni219 – 2202Substrate bindingUniRule annotation
    Regioni229 – 2302Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220467.
    KOiK01778.
    OMAiVFDRYFL.
    OrthoDBiEOG6ND0M5.

    Family and domain databases

    HAMAPiMF_00197. DAP_epimerase.
    InterProiIPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view]
    PANTHERiPTHR31689. PTHR31689. 1 hit.
    PfamiPF01678. DAP_epimerase. 2 hits.
    [Graphical view]
    TIGRFAMsiTIGR00652. DapF. 1 hit.
    PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q2JLR0-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTPRLSFHKY QGLGNDFILV DNRWQSQPCL SPEEAVALCN RRFGVGADGV    50
    IFLLPGQEGA DFSMRLFNSD GSEAEMCGNG IRCLARFLQD LGIPGRDGAY 100
    QIHTLAGRIV PQVRADGLVT VDMGIPRLLA KQIPTTLVEP DEKVIRQPLA 150
    VAGREWRVTA VSMGNPHCVV FLEEEGSLEE LDLAAVGPLF EHHPAFPERT 200
    NTEFVQVLSP TRLRLRVWER GAGATLACGT GACAVLVAAV LEERAESQAT 250
    VELPGGNLEI RWDPSTQHVW MTGPALHVFS GTTAG 285
    Length:285
    Mass (Da):30,949
    Last modified:March 7, 2006 - v1
    Checksum:i73DAB469419A3471
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000240 Genomic DNA. Translation: ABD02344.1.
    RefSeqiWP_011432994.1. NC_007776.1.
    YP_477607.1. NC_007776.1.

    Genome annotation databases

    EnsemblBacteriaiABD02344; ABD02344; CYB_1371.
    GeneIDi3901238.
    KEGGicyb:CYB_1371.
    PATRICi23805070. VBISynSp29577_1388.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000240 Genomic DNA. Translation: ABD02344.1 .
    RefSeqi WP_011432994.1. NC_007776.1.
    YP_477607.1. NC_007776.1.

    3D structure databases

    ProteinModelPortali Q2JLR0.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 321332.CYB_1371.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABD02344 ; ABD02344 ; CYB_1371 .
    GeneIDi 3901238.
    KEGGi cyb:CYB_1371.
    PATRICi 23805070. VBISynSp29577_1388.

    Phylogenomic databases

    eggNOGi COG0253.
    HOGENOMi HOG000220467.
    KOi K01778.
    OMAi VFDRYFL.
    OrthoDBi EOG6ND0M5.

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci SSP321332:GH1B-1371-MONOMER.

    Family and domain databases

    HAMAPi MF_00197. DAP_epimerase.
    InterProi IPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view ]
    PANTHERi PTHR31689. PTHR31689. 1 hit.
    Pfami PF01678. DAP_epimerase. 2 hits.
    [Graphical view ]
    TIGRFAMsi TIGR00652. DapF. 1 hit.
    PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses."
      Bhaya D., Grossman A.R., Steunou A.-S., Khuri N., Cohan F.M., Hamamura N., Melendrez M.C., Bateson M.M., Ward D.M., Heidelberg J.F.
      ISME J. 1:703-713(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: JA-2-3B'a(2-13).

    Entry informationi

    Entry nameiDAPF_SYNJB
    AccessioniPrimary (citable) accession number: Q2JLR0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: March 7, 2006
    Last modified: October 1, 2014
    This is version 60 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3