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Q03ZI1

- DDL_LEUMM

UniProt

Q03ZI1 - DDL_LEUMM

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Leuconostoc mesenteroides subsp. mesenteroides (strain ATCC 8293 / NCDO 523)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 62 (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 bindingi303 – 3031Magnesium or manganese 1UniRule annotation
    Metal bindingi316 – 3161Magnesium or manganese 1UniRule annotation
    Metal bindingi316 – 3161Magnesium or manganese 2UniRule annotation
    Metal bindingi318 – 3181Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi170 – 22556ATPUniRule 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

    BioCyciLMES203120:GJ8T-264-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:LEUM_0264
    OrganismiLeuconostoc mesenteroides subsp. mesenteroides (strain ATCC 8293 / NCDO 523)
    Taxonomic identifieri203120 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLeuconostocaceaeLeuconostoc
    ProteomesiUP000000362: 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 – 377377D-alanine--D-alanine ligasePRO_1000030463Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi203120.LEUM_0264.

    Structurei

    Secondary structure

    1
    377
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 118
    Helixi17 – 3418
    Beta strandi35 – 4410
    Helixi53 – 608
    Helixi65 – 739
    Helixi86 – 894
    Beta strandi95 – 1006
    Turni104 – 1063
    Beta strandi107 – 1093
    Helixi110 – 1178
    Beta strandi122 – 1243
    Helixi127 – 1348
    Helixi136 – 1449
    Turni145 – 1473
    Beta strandi153 – 1564
    Helixi160 – 1634
    Helixi166 – 1738
    Beta strandi177 – 1837
    Turni186 – 1894
    Beta strandi190 – 1934
    Helixi196 – 20611
    Turni207 – 2093
    Beta strandi213 – 2175
    Beta strandi224 – 23411
    Beta strandi236 – 2449
    Beta strandi248 – 2525
    Helixi257 – 2604
    Beta strandi268 – 2725
    Helixi277 – 29317
    Beta strandi298 – 3069
    Beta strandi312 – 3209
    Helixi328 – 3303
    Helixi332 – 3365
    Helixi340 – 36021

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1EHIX-ray2.38A/B1-377[»]
    ProteinModelPortaliQ03ZI1.
    SMRiQ03ZI1. Positions 3-362.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ03ZI1.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini140 – 349210ATP-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.
    OMAiQIDVIFP.
    OrthoDBiEOG64BQ73.

    Family and domain databases

    Gene3Di3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    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.

    Q03ZI1-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTKKRVALIF GGNSSEHDVS KRSAQNFYNA IEATGKYEII VFAIAQNGFF    50
    LDTESSKKIL ALEDEQPIVD AFMKTVDASD PLARIHALKS AGDFDIFFPV 100
    VHGNLGEDGT LQGLFKLLDK PYVGAPLRGH AVSFDKALTK ELLTVNGIRN 150
    TKYIVVDPES ANNWSWDKIV AELGNIVFVK AANQGSSVGI SRVTNAEEYT 200
    EALSDSFQYD YKVLIEEAVN GARELEVGVI GNDQPLVSEI GAHTVPNQGS 250
    GDGWYDYNNK FVDNSAVHFE IPAQLSPEVT KEVKQMALDA YKVLNLRGEA 300
    RMDFLLDENN VPYLGEPNTL PGFTNMSLFK RLWDYSDINN AKLVDMLIDY 350
    GFEDFAQNKK LSYSFVSLGE EKIGKFN 377
    Length:377
    Mass (Da):41,826
    Last modified:November 14, 2006 - v1
    Checksum:iD1C6A40A6812AE01
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000414 Genomic DNA. Translation: ABJ61391.1.
    RefSeqiYP_817764.1. NC_008531.1.

    Genome annotation databases

    EnsemblBacteriaiABJ61391; ABJ61391; LEUM_0264.
    GeneIDi4422165.
    KEGGilme:LEUM_0264.
    PATRICi22408513. VBILeuMes50664_0271.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000414 Genomic DNA. Translation: ABJ61391.1 .
    RefSeqi YP_817764.1. NC_008531.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1EHI X-ray 2.38 A/B 1-377 [» ]
    ProteinModelPortali Q03ZI1.
    SMRi Q03ZI1. Positions 3-362.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 203120.LEUM_0264.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABJ61391 ; ABJ61391 ; LEUM_0264 .
    GeneIDi 4422165.
    KEGGi lme:LEUM_0264.
    PATRICi 22408513. VBILeuMes50664_0271.

    Phylogenomic databases

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

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci LMES203120:GJ8T-264-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q03ZI1.

    Family and domain databases

    Gene3Di 3.30.1490.20. 1 hit.
    3.30.470.20. 1 hit.
    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: ATCC 8293 / NCDO 523.

    Entry informationi

    Entry nameiDDL_LEUMM
    AccessioniPrimary (citable) accession number: Q03ZI1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: November 14, 2006
    Last modified: October 1, 2014
    This is version 62 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3