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Q03EM9

- DDL_PEDPA

UniProt

Q03EM9 - DDL_PEDPA

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Pediococcus pentosaceus (strain ATCC 25745 / 183-1w)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 58 (01 Oct 2014)
      Sequence version 1 (14 Nov 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 bindingi295 – 2951Magnesium or manganese 1UniRule annotation
    Metal bindingi307 – 3071Magnesium or manganese 1UniRule annotation
    Metal bindingi307 – 3071Magnesium or manganese 2UniRule annotation
    Metal bindingi309 – 3091Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi173 – 22654ATPUniRule 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

    BioCyciPPEN278197:GI4Y-1302-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:PEPE_1302
    OrganismiPediococcus pentosaceus (strain ATCC 25745 / 183-1w)
    Taxonomic identifieri278197 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaePediococcus
    ProteomesiUP000000773: 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 – 351351D-alanine--D-alanine ligasePRO_1000030476Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi278197.PEPE_1302.

    Structurei

    3D structure databases

    ProteinModelPortaliQ03EM9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini146 – 340195ATP-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.
    OMAiDRIQAND.
    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. 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.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q03EM9-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKIAVLAGGK STERNVSLSS GSKITNALRS KGYDATMIDL FLGYELEDGQ    50
    SYEDVFKSSN TSTDYEISDA VLTEEDIEEL RTDGTVGLFG KNVLPILQAA 100
    DFVFLALHGG DGENGKVQAV LDLNHIKYTG SGSLASGIAM DKAISKEIML 150
    YNNIKTAQFA VLHAKDGIHP QLAFDYPMVV KPNSGGSSIG TRIVHDEAEL 200
    AESLKDAYRF DDEIIVEEFI TGREFSLGVV NGQAMPAIEI VVNDGWYDYE 250
    HKFQTGSTTK FVTPPEIEDD VHDEMKRVAV QTMDALGMTN YGRVDFLTND 300
    TGVYVIEANN LPGMTPLSLL PQEAEAAGIS YEDLCESIVL GKQKLYDELK 350
    K 351
    Length:351
    Mass (Da):38,351
    Last modified:November 14, 2006 - v1
    Checksum:iDB5C222F9E3FFE6C
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000422 Genomic DNA. Translation: ABJ68343.1.
    RefSeqiYP_804785.1. NC_008525.1.

    Genome annotation databases

    EnsemblBacteriaiABJ68343; ABJ68343; PEPE_1302.
    GeneIDi4417557.
    KEGGippe:PEPE_1302.
    PATRICi22875922. VBIPedPen34213_1231.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000422 Genomic DNA. Translation: ABJ68343.1 .
    RefSeqi YP_804785.1. NC_008525.1.

    3D structure databases

    ProteinModelPortali Q03EM9.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 278197.PEPE_1302.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABJ68343 ; ABJ68343 ; PEPE_1302 .
    GeneIDi 4417557.
    KEGGi ppe:PEPE_1302.
    PATRICi 22875922. VBIPedPen34213_1231.

    Phylogenomic databases

    eggNOGi COG1181.
    HOGENOMi HOG000011592.
    OMAi DRIQAND.
    OrthoDBi EOG6ND0KB.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci PPEN278197:GI4Y-1302-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.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 25745 / 183-1w.

    Entry informationi

    Entry nameiDDL_PEDPA
    AccessioniPrimary (citable) accession number: Q03EM9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: November 14, 2006
    Last modified: October 1, 2014
    This is version 58 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