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Q5YRY7

- DDL_NOCFA

UniProt

Q5YRY7 - DDL_NOCFA

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Nocardia farcinica (strain IFM 10152)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 74 (01 Oct 2014)
      Sequence version 1 (23 Nov 2004)
      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 bindingi308 – 3081Magnesium or manganese 1UniRule annotation
    Metal bindingi320 – 3201Magnesium or manganese 1UniRule annotation
    Metal bindingi320 – 3201Magnesium or manganese 2UniRule annotation
    Metal bindingi322 – 3221Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi176 – 23156ATPUniRule 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

    BioCyciNFAR247156:GJ9T-4263-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:NFA_42050
    OrganismiNocardia farcinica (strain IFM 10152)
    Taxonomic identifieri247156 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeNocardiaceaeNocardia
    ProteomesiUP000006820: 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 – 363363D-alanine--D-alanine ligasePRO_0000341140Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi247156.nfa42050.

    Structurei

    3D structure databases

    ProteinModelPortaliQ5YRY7.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini148 – 353206ATP-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.
    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.

    Q5YRY7-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTNRIRVAVV FGGRSNEHAV SCVSAGSVLR HLDPTRYEAV PIGITPQGGW    50
    VLANSDVAAI GLSHEALPSV DAGGTALTLT ADPTRGGELV ALDDAGAVLG 100
    TVDVVFPILH GPFGEDGTLQ GMLELAGVPY VGPGVLASAA GMDKEFTKKL 150
    LAAEGLPVGT QVVLRPGTAT LTEEQRERLG LPVFVKPARA GSSIGITKVD 200
    DWAALDTAIA AAREHDPKVI VEAGIVGREV ECGVLEFPDG RISASVLAEI 250
    RMPEGDGPQF YDFDTKYLDD VCEFDVPAKL DDDIAEQVRE LAVRAFQALD 300
    CQGLARVDFF VTADGPVINE INTMPGFTSI SMYPRMWEAT GIDYGTLVST 350
    LIETALARGT GLR 363
    Length:363
    Mass (Da):38,228
    Last modified:November 23, 2004 - v1
    Checksum:iEB08DE40900C2449
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP006618 Genomic DNA. Translation: BAD59054.1.
    RefSeqiYP_120418.1. NC_006361.1.

    Genome annotation databases

    EnsemblBacteriaiBAD59054; BAD59054; NFA_42050.
    GeneIDi3109811.
    KEGGinfa:nfa42050.
    PATRICi22737950. VBINocFar94200_4204.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP006618 Genomic DNA. Translation: BAD59054.1 .
    RefSeqi YP_120418.1. NC_006361.1.

    3D structure databases

    ProteinModelPortali Q5YRY7.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 247156.nfa42050.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD59054 ; BAD59054 ; NFA_42050 .
    GeneIDi 3109811.
    KEGGi nfa:nfa42050.
    PATRICi 22737950. VBINocFar94200_4204.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci NFAR247156:GJ9T-4263-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: IFM 10152.

    Entry informationi

    Entry nameiDDL_NOCFA
    AccessioniPrimary (citable) accession number: Q5YRY7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 10, 2008
    Last sequence update: November 23, 2004
    Last modified: October 1, 2014
    This is version 74 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