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C1B2N8

- DDL_RHOOB

UniProt

C1B2N8 - DDL_RHOOB

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Rhodococcus opacus (strain B4)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 39 (01 Oct 2014)
      Sequence version 1 (26 May 2009)
      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 bindingi313 – 3131Magnesium or manganese 1UniRule annotation
    Metal bindingi325 – 3251Magnesium or manganese 1UniRule annotation
    Metal bindingi325 – 3251Magnesium or manganese 2UniRule annotation
    Metal bindingi327 – 3271Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi179 – 23456ATPUniRule 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

    BioCyciROPA632772:GH0Q-6608-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:ROP_65580
    OrganismiRhodococcus opacus (strain B4)
    Taxonomic identifieri632772 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeNocardiaceaeRhodococcus
    ProteomesiUP000002212: 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 – 368368D-alanine--D-alanine ligasePRO_1000189743Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi632772.ROP_65580.

    Structurei

    3D structure databases

    ProteinModelPortaliC1B2N8.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini151 – 358208ATP-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.
    HOGENOMiHOG000011593.
    KOiK01921.
    OMAiIECGVLG.
    OrthoDBiEOG64BQ73.

    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. 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.

    C1B2N8-1 [UniParc]FASTAAdd to Basket

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    MSKPRTRVAV IFGGRSNEHS VSCVSAGSVL RNLDPERYEV VPIGITTEGS    50
    WVLGSTDPES LSIRGRSLPS VDADGSALAL TADPTRSGDL VALDDGEAGK 100
    ILASVDVVFP VLHGAYGEDG TIQGLLELAG VPYVGPGVLA SAAGMDKEFT 150
    KKLLAAEGLP IGFQVVLRPG TATLTDEQRS RLHLPVFVKP ARGGSSIGIT 200
    RVAEWAALDD AIAHARRHDP KVIVESGIAG REVECGVLEF PDGDVRASVI 250
    AEIRMPEGAD DDEAFYDFDS KYLDDVCEFD VPAKLEDSVS DEIRALAVRA 300
    FSALDCQGLA RVDFFVTEDG PVINEINTMP GFTSISMYPR MWDAVGVDYG 350
    TLVSTLVDTA LARGTGLR 368
    Length:368
    Mass (Da):39,036
    Last modified:May 26, 2009 - v1
    Checksum:i8444A75BCA579AF0
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP011115 Genomic DNA. Translation: BAH54805.1.
    RefSeqiYP_002783750.1. NC_012522.1.

    Genome annotation databases

    EnsemblBacteriaiBAH54805; BAH54805; ROP_65580.
    GeneIDi7745281.
    KEGGirop:ROP_65580.
    PATRICi23230549. VBIRhoOpa21106_6639.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP011115 Genomic DNA. Translation: BAH54805.1 .
    RefSeqi YP_002783750.1. NC_012522.1.

    3D structure databases

    ProteinModelPortali C1B2N8.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 632772.ROP_65580.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAH54805 ; BAH54805 ; ROP_65580 .
    GeneIDi 7745281.
    KEGGi rop:ROP_65580.
    PATRICi 23230549. VBIRhoOpa21106_6639.

    Phylogenomic databases

    eggNOGi COG1181.
    HOGENOMi HOG000011593.
    KOi K01921.
    OMAi IECGVLG.
    OrthoDBi EOG64BQ73.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci ROPA632772:GH0Q-6608-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. 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. "Comparison of the complete genome sequences of Rhodococcus erythropolis PR4 and Rhodococcus opacus B4."
      Takarada H., Sekine M., Hosoyama A., Yamada R., Fujisawa T., Omata S., Shimizu A., Tsukatani N., Tanikawa S., Fujita N., Harayama S.
      Submitted (MAR-2009) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: B4.

    Entry informationi

    Entry nameiDDL_RHOOB
    AccessioniPrimary (citable) accession number: C1B2N8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 28, 2009
    Last sequence update: May 26, 2009
    Last modified: October 1, 2014
    This is version 39 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

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3