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P95803

- DDL_STRMU

UniProt

P95803 - DDL_STRMU

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 109 (01 Oct 2014)
      Sequence version 2 (28 Nov 2002)
      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 bindingi289 – 2891Magnesium or manganese 1UniRule annotation
    Metal bindingi302 – 3021Magnesium or manganese 1UniRule annotation
    Metal bindingi302 – 3021Magnesium or manganese 2UniRule annotation
    Metal bindingi304 – 3041Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi163 – 21856ATPUniRule 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

    BioCyciSMUT210007:GC7Z-588-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:SMU_599
    OrganismiStreptococcus mutans serotype c (strain ATCC 700610 / UA159)
    Taxonomic identifieri210007 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
    ProteomesiUP000002512: 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 – 349349D-alanine--D-alanine ligasePRO_0000177886Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi210007.SMU.599.

    Structurei

    Secondary structure

    1
    349
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 118
    Helixi17 – 3014
    Turni33 – 353
    Beta strandi36 – 438
    Beta strandi49 – 579
    Helixi73 – 753
    Helixi79 – 824
    Beta strandi88 – 925
    Turni96 – 983
    Beta strandi99 – 1013
    Helixi102 – 1098
    Beta strandi114 – 1163
    Helixi119 – 1268
    Helixi128 – 13811
    Beta strandi146 – 1505
    Helixi155 – 16511
    Beta strandi168 – 1747
    Beta strandi184 – 1885
    Helixi189 – 20214
    Beta strandi204 – 2107
    Beta strandi214 – 22613
    Beta strandi233 – 2353
    Beta strandi255 – 2584
    Helixi263 – 27917
    Beta strandi284 – 2929
    Beta strandi298 – 3069
    Helixi314 – 3218
    Helixi326 – 34520

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3K3PX-ray2.23A/B1-349[»]
    ProteinModelPortaliP95803.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP95803.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini133 – 335203ATP-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.
    OMAiKLAFQYD.
    OrthoDBiEOG64BQ73.
    PhylomeDBiP95803.

    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.

    P95803-1 [UniParc]FASTAAdd to Basket

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    MSKETLVLLY GGRSAERDVS VLSAESVMRA INYDNFLVKT YFITQAGDFI    50
    KTQEFDSQPS ETDKLMTNDT IIASQKIKPS DIYEEEAVVF PVLHGPMGED 100
    GSIQGFLEVL KMPYVGTNIL SSSVAMDKIT TNQVLESATT IPQVAYVALI 150
    EGEPLESKLA EVEEKLIYPV FVKPANMGSS VGISKAENRT DLKQAIALAL 200
    KYDSRVLIEQ GVDAREIEVG ILGNTDVKTT LPGEIVKDVA FYDYEAKYID 250
    NKITMAIPAE IDPVIVEKMR DYAATAFRTL GCCGLSRCDF FLTEDGKVYL 300
    NELNTMPGFT QWSMYPLLWE NMGLSYSVLI EELVSLAKEM FDKRESHLV 349
    Length:349
    Mass (Da):38,838
    Last modified:November 28, 2002 - v2
    Checksum:iFFDAAD9942CAE7EF
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti132 – 1321N → K in AAB41854. 1 PublicationCurated
    Sequence conflicti238 – 2381D → V in AAB41854. 1 PublicationCurated
    Sequence conflicti273 – 2731A → R in AAB41854. 1 PublicationCurated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE014133 Genomic DNA. Translation: AAN58338.1.
    U69165 Genomic DNA. Translation: AAB41854.1.
    RefSeqiNP_721032.1. NC_004350.2.
    WP_002352219.1. NC_004350.2.

    Genome annotation databases

    EnsemblBacteriaiAAN58338; AAN58338; SMU_599.
    GeneIDi1029384.
    KEGGismu:SMU_599.
    PATRICi19663399. VBIStrMut61772_0532.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE014133 Genomic DNA. Translation: AAN58338.1 .
    U69165 Genomic DNA. Translation: AAB41854.1 .
    RefSeqi NP_721032.1. NC_004350.2.
    WP_002352219.1. NC_004350.2.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3K3P X-ray 2.23 A/B 1-349 [» ]
    ProteinModelPortali P95803.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 210007.SMU.599.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAN58338 ; AAN58338 ; SMU_599 .
    GeneIDi 1029384.
    KEGGi smu:SMU_599.
    PATRICi 19663399. VBIStrMut61772_0532.

    Phylogenomic databases

    eggNOGi COG1181.
    KOi K01921.
    OMAi KLAFQYD.
    OrthoDBi EOG64BQ73.
    PhylomeDBi P95803.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci SMUT210007:GC7Z-588-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P95803.

    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: ATCC 700610 / UA159.
    2. Garnier F., Gerbaud G., Courvalin P., Galimand M.
      Submitted (FEB-1997) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 106-303.
      Strain: ATCC 25175 / DSM 20523 / JCM 5705 / NBRC 13955 / NCIMB 702062 / NCTC 10449.

    Entry informationi

    Entry nameiDDL_STRMU
    AccessioniPrimary (citable) accession number: P95803
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 28, 2002
    Last modified: October 1, 2014
    This is version 109 of the entry and version 2 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