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Q3J4L8

- DDL_RHOS4

UniProt

Q3J4L8 - DDL_RHOS4

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 70 (01 Oct 2014)
      Sequence version 1 (08 Nov 2005)
      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 bindingi268 – 2681Magnesium or manganese 1UniRule annotation
    Metal bindingi268 – 2681Magnesium or manganese 2UniRule annotation
    Metal bindingi270 – 2701Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi135 – 18551ATPUniRule 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

    BioCyciRSPH272943:GJAS-719-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:RHOS4_06980
    ORF Names:RSP_2111
    OrganismiRhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
    Taxonomic identifieri272943 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRhodobacter
    ProteomesiUP000002703: Chromosome 1

    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 – 307307D-alanine--D-alanine ligasePRO_0000341161Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi272943.RSP_2111.

    Structurei

    3D structure databases

    ProteinModelPortaliQ3J4L8.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini108 – 301194ATP-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.
    OMAiCSGYSRV.
    OrthoDBiEOG6ND0KB.
    PhylomeDBiQ3J4L8.

    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.

    Q3J4L8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAGQSGRTFP RVAVLMGGAS TEREVSLSSG HSCSAALRDA GYEVTEVDAG    50
    PDLARVLAEL SPDAVFNALH GRWGEDGCVQ GLLEWLRIPY THSGVLASAL 100
    AMDKARAKEV FAAAGLPVTQ SVLATPEEVR ARHILPPPYV VKPNAEGSSV 150
    GVYIVHEDAN GPPQLAADMP QDLMVETYVP GRELTVTVMG DRVLAVTDIL 200
    SDGWYDYDAK YRPGGSRHIV PADLPAEITE ACHDIALRAH RALGCRGISR 250
    SDLRWDEARG LAGLILLETN TQPGMTPTSL SPEQAAHCGY SFPEFCAWLV 300
    EDASCSR 307
    Length:307
    Mass (Da):32,847
    Last modified:November 8, 2005 - v1
    Checksum:iAD33BA63F75762E9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000143 Genomic DNA. Translation: ABA78266.1.
    RefSeqiYP_352167.1. NC_007493.2.

    Genome annotation databases

    EnsemblBacteriaiABA78266; ABA78266; RSP_2111.
    GeneIDi3719582.
    KEGGirsp:RSP_2111.
    PATRICi23151218. VBIRhoSph57909_1004.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000143 Genomic DNA. Translation: ABA78266.1 .
    RefSeqi YP_352167.1. NC_007493.2.

    3D structure databases

    ProteinModelPortali Q3J4L8.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 272943.RSP_2111.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABA78266 ; ABA78266 ; RSP_2111 .
    GeneIDi 3719582.
    KEGGi rsp:RSP_2111.
    PATRICi 23151218. VBIRhoSph57909_1004.

    Phylogenomic databases

    eggNOGi COG1181.
    HOGENOMi HOG000011592.
    KOi K01921.
    OMAi CSGYSRV.
    OrthoDBi EOG6ND0KB.
    PhylomeDBi Q3J4L8.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci RSPH272943:GJAS-719-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 sequence of chromosome 1 of Rhodobacter sphaeroides 2.4.1."
      Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Richardson P., Mackenzie C., Choudhary M., Larimer F., Hauser L.J., Land M., Donohue T.J., Kaplan S.
      Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158.

    Entry informationi

    Entry nameiDDL_RHOS4
    AccessioniPrimary (citable) accession number: Q3J4L8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 10, 2008
    Last sequence update: November 8, 2005
    Last modified: October 1, 2014
    This is version 70 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