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A0M4U5

- DDL_GRAFK

UniProt

A0M4U5 - DDL_GRAFK

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Gramella forsetii (strain KT0803)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 59 (01 Oct 2014)
      Sequence version 1 (12 Dec 2006)
      Previous versions | rss
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    Functioni

    Cell wall formation.UniRule annotation

    Catalytic activityi

    ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotation

    Cofactori

    Binds 2 magnesium or manganese ions per subunit.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi275 – 2751Magnesium or manganese 1UniRule annotation
    Metal bindingi287 – 2871Magnesium or manganese 1UniRule annotation
    Metal bindingi287 – 2871Magnesium or manganese 2UniRule annotation
    Metal bindingi289 – 2891Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi149 – 20456ATPUniRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
    3. magnesium ion binding Source: UniProtKB-HAMAP
    4. manganese ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
    2. regulation of cell shape Source: UniProtKB-KW

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciGFOR411154:GI79-2684-MONOMER.
    UniPathwayiUPA00219.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanine--D-alanine ligaseUniRule annotation (EC:6.3.2.4UniRule annotation)
    Alternative name(s):
    D-Ala-D-Ala ligaseUniRule annotation
    D-alanylalanine synthetaseUniRule annotation
    Gene namesi
    Name:ddlUniRule annotation
    Ordered Locus Names:GFO_2684
    OrganismiGramella forsetii (strain KT0803)
    Taxonomic identifieri411154 [NCBI]
    Taxonomic lineageiBacteriaBacteroidetesFlavobacteriiaFlavobacterialesFlavobacteriaceaeGramella
    ProteomesiUP000000755: 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 – 326326D-alanine--D-alanine ligasePRO_0000341104Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi411154.GFO_2684.

    Structurei

    3D structure databases

    ProteinModelPortaliA0M4U5.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini121 – 320200ATP-graspUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
    Contains 1 ATP-grasp domain.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG1181.
    HOGENOMiHOG000011592.
    KOiK01921.
    OMAiKLAFQYD.
    OrthoDBiEOG6ND0KB.

    Family and domain databases

    Gene3Di3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    3.40.50.20. 1 hit.
    HAMAPiMF_00047. Dala_Dala_lig.
    InterProiIPR011761. ATP-grasp.
    IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR000291. D-Ala_lig_Van_CS.
    IPR005905. D_ala_D_ala.
    IPR011095. Dala_Dala_lig_C.
    IPR011127. Dala_Dala_lig_N.
    IPR016185. PreATP-grasp_dom.
    [Graphical view]
    PANTHERiPTHR23132. PTHR23132. 1 hit.
    PfamiPF07478. Dala_Dala_lig_C. 1 hit.
    PF01820. Dala_Dala_lig_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF52440. SSF52440. 1 hit.
    TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
    PROSITEiPS50975. ATP_GRASP. 1 hit.
    PS00843. DALA_DALA_LIGASE_1. 1 hit.
    PS00844. DALA_DALA_LIGASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    A0M4U5-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKKKIAIAMG GYSSEYRISI NSGNIVYKHL DHDLYEPYRV HILKGEWFVV    50
    ADDDTPYPIN KSNFTVKIND KVIQFDCVFN TIHGTPGENG LLQAYLELIG 100
    IPQTSCDYYQ SALTFNKRDL ISVLRPYGIK AATNYFLNKD QEINTKEIVD 150
    KVGLPCFVKA NRAGSSFGVT KVKTEDEIIS AAKTAFTEDD EAIIESFLDG 200
    TEVSVGVITY KGKVLALPVT EIIPDGEFFD YEAKYLGKSQ EITPARISEE 250
    DTKKVQDIAI MIYKKLKMKG LSRSEFIFHE GEPHFIEMNT NPGISQASIL 300
    PQQAEKAGIS LKDLFGSTIE AALNQK 326
    Length:326
    Mass (Da):36,436
    Last modified:December 12, 2006 - v1
    Checksum:i15D631E2BC685E20
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CU207366 Genomic DNA. Translation: CAL67640.1.
    RefSeqiWP_011710543.1. NC_008571.1.
    YP_862707.1. NC_008571.1.

    Genome annotation databases

    EnsemblBacteriaiCAL67640; CAL67640; GFO_2684.
    GeneIDi4650906.
    KEGGigfo:GFO_2684.
    PATRICi22074122. VBIGraFor5527_2589.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CU207366 Genomic DNA. Translation: CAL67640.1 .
    RefSeqi WP_011710543.1. NC_008571.1.
    YP_862707.1. NC_008571.1.

    3D structure databases

    ProteinModelPortali A0M4U5.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 411154.GFO_2684.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAL67640 ; CAL67640 ; GFO_2684 .
    GeneIDi 4650906.
    KEGGi gfo:GFO_2684.
    PATRICi 22074122. VBIGraFor5527_2589.

    Phylogenomic databases

    eggNOGi COG1181.
    HOGENOMi HOG000011592.
    KOi K01921.
    OMAi KLAFQYD.
    OrthoDBi EOG6ND0KB.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci GFOR411154:GI79-2684-MONOMER.

    Family and domain databases

    Gene3Di 3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    3.40.50.20. 1 hit.
    HAMAPi MF_00047. Dala_Dala_lig.
    InterProi IPR011761. ATP-grasp.
    IPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR000291. D-Ala_lig_Van_CS.
    IPR005905. D_ala_D_ala.
    IPR011095. Dala_Dala_lig_C.
    IPR011127. Dala_Dala_lig_N.
    IPR016185. PreATP-grasp_dom.
    [Graphical view ]
    PANTHERi PTHR23132. PTHR23132. 1 hit.
    Pfami PF07478. Dala_Dala_lig_C. 1 hit.
    PF01820. Dala_Dala_lig_N. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52440. SSF52440. 1 hit.
    TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
    PROSITEi PS50975. ATP_GRASP. 1 hit.
    PS00843. DALA_DALA_LIGASE_1. 1 hit.
    PS00844. DALA_DALA_LIGASE_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter."
      Bauer M., Kube M., Teeling H., Richter M., Lombardot T., Allers E., Wuerdemann C.A., Quast C., Kuhl H., Knaust F., Woebken D., Bischof K., Mussmann M., Choudhuri J.V., Meyer F., Reinhardt R., Amann R.I., Gloeckner F.O.
      Environ. Microbiol. 8:2201-2213(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: KT0803.

    Entry informationi

    Entry nameiDDL_GRAFK
    AccessioniPrimary (citable) accession number: A0M4U5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 10, 2008
    Last sequence update: December 12, 2006
    Last modified: October 1, 2014
    This is version 59 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