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A7HVV0

- DDL_PARL1

UniProt

A7HVV0 - DDL_PARL1

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Parvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 51 (01 Oct 2014)
      Sequence version 1 (11 Sep 2007)
      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 bindingi252 – 2521Magnesium or manganese 1UniRule annotation
    Metal bindingi269 – 2691Magnesium or manganese 1UniRule annotation
    Metal bindingi269 – 2691Magnesium or manganese 2UniRule annotation
    Metal bindingi271 – 2711Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi130 – 18455ATPUniRule 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

    BioCyciPLAV402881:GHQA-2452-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:Plav_2424
    OrganismiParvibaculum lavamentivorans (strain DS-1 / DSM 13023 / NCIMB 13966)
    Taxonomic identifieri402881 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhodobiaceaeParvibaculum
    ProteomesiUP000006377: 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 – 308308D-alanine--D-alanine ligasePRO_0000341144Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi402881.Plav_2424.

    Structurei

    3D structure databases

    ProteinModelPortaliA7HVV0.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini103 – 302200ATP-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.
    OMAiANDTQYR.
    OrthoDBiEOG6ND0KB.

    Family and domain databases

    Gene3Di3.30.1490.20. 1 hit.
    3.30.470.20. 2 hits.
    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. 2 hits.
    [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.

    A7HVV0-1 [UniParc]FASTAAdd to Basket

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    MSQAKHVAVL KGGWSAEREV SLVSGKGCAE ALRKHGYRVT EIDAGRDLAD    50
    QILKVKPDVA FNALHGRWGE DGCVQGLLEI LRVPYTHSGV LASALAMHKE 100
    RAKFVFRAAG LPVAESVVVP REQAAHGHVM DPPYVIKPVS EGSSVGVFIV 150
    RAGDNRPPAE LTSAEWNLGD EVMAERYIAG RELTCAVMGE EIFGVTEIIA 200
    NTTFYDYEAK YQTGGSRHII PAPIDADIYA EVQRVTLAAH KALGCRGVSR 250
    ADFRFDDTRP GKPELILLEV NTQPGMTPTS LVPELANLAG YSYGELVSWM 300
    VEEASCDR 308
    Length:308
    Mass (Da):33,445
    Last modified:September 11, 2007 - v1
    Checksum:i03F417AD70EDBFEA
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000774 Genomic DNA. Translation: ABS64033.1.
    RefSeqiYP_001413690.1. NC_009719.1.

    Genome annotation databases

    EnsemblBacteriaiABS64033; ABS64033; Plav_2424.
    GeneIDi5454049.
    KEGGipla:Plav_2424.
    PATRICi22866559. VBIParLav90819_2502.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000774 Genomic DNA. Translation: ABS64033.1 .
    RefSeqi YP_001413690.1. NC_009719.1.

    3D structure databases

    ProteinModelPortali A7HVV0.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 402881.Plav_2424.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABS64033 ; ABS64033 ; Plav_2424 .
    GeneIDi 5454049.
    KEGGi pla:Plav_2424.
    PATRICi 22866559. VBIParLav90819_2502.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci PLAV402881:GHQA-2452-MONOMER.

    Family and domain databases

    Gene3Di 3.30.1490.20. 1 hit.
    3.30.470.20. 2 hits.
    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. 2 hits.
    [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. "Complete genome sequence and annotation of Parvibaculum lavamentivorans DS-1."
      Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Saunders E., Brettin T., Bruce D., Detter J.C., Han C., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Richardson P.
      Submitted (JUL-2007) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: DS-1 / DSM 13023 / NCIMB 13966.

    Entry informationi

    Entry nameiDDL_PARL1
    AccessioniPrimary (citable) accession number: A7HVV0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 10, 2008
    Last sequence update: September 11, 2007
    Last modified: October 1, 2014
    This is version 51 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