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P0A1F0

- DDLA_SALTY

UniProt

P0A1F0 - DDLA_SALTY

Protein

D-alanine--D-alanine ligase A

Gene

ddlA

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 73 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Cell wall formation.

    Catalytic activityi

    ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.

    Cofactori

    Binds 2 magnesium or manganese ions per subunit.By similarity

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi302 – 3021Magnesium or manganese 1By similarity
    Metal bindingi315 – 3151Magnesium or manganese 1By similarity
    Metal bindingi315 – 3151Magnesium or manganese 2By similarity
    Metal bindingi317 – 3171Magnesium or manganese 2By similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi175 – 23056ATPBy similarityAdd
    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

    BioCyciSENT99287:GCTI-381-MONOMER.
    UniPathwayiUPA00219.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanine--D-alanine ligase A (EC:6.3.2.4)
    Alternative name(s):
    D-Ala-D-Ala ligase A
    D-alanylalanine synthetase A
    Gene namesi
    Name:ddlA
    Ordered Locus Names:STM0380
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    ProteomesiUP000001014: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 364363D-alanine--D-alanine ligase APRO_0000177868Add
    BLAST

    Proteomic databases

    PaxDbiP0A1F0.
    PRIDEiP0A1F0.

    Interactioni

    Protein-protein interaction databases

    STRINGi99287.STM0380.

    Structurei

    Secondary structure

    1
    364
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 118
    Helixi17 – 3014
    Turni33 – 353
    Beta strandi36 – 438
    Beta strandi49 – 524
    Beta strandi54 – 607
    Turni64 – 663
    Beta strandi75 – 784
    Beta strandi83 – 853
    Beta strandi87 – 893
    Turni90 – 923
    Beta strandi100 – 1045
    Turni109 – 1124
    Helixi115 – 1228
    Beta strandi127 – 1293
    Helixi132 – 1398
    Helixi141 – 15010
    Beta strandi158 – 1625
    Turni163 – 1653
    Helixi166 – 1683
    Helixi171 – 1788
    Beta strandi180 – 1867
    Turni191 – 1944
    Beta strandi196 – 2005
    Helixi201 – 21414
    Beta strandi216 – 2227
    Beta strandi226 – 23813
    Beta strandi240 – 2489
    Turni257 – 2604
    Helixi262 – 2654
    Beta strandi267 – 2715
    Helixi276 – 29217
    Beta strandi297 – 3059
    Beta strandi311 – 3199
    Helixi327 – 3337
    Turni334 – 3363
    Helixi339 – 35921

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3I12X-ray2.20A/B/C/D1-364[»]
    3Q1KX-ray2.20A/B/C/D1-364[»]
    ProteinModelPortaliP0A1F0.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A1F0.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini145 – 348204ATP-graspAdd
    BLAST

    Sequence similaritiesi

    Belongs to the D-alanine--D-alanine ligase family.Curated
    Contains 1 ATP-grasp domain.Curated

    Phylogenomic databases

    eggNOGiCOG1181.
    HOGENOMiHOG000011593.
    KOiK01921.
    OMAiQIDVIFP.
    OrthoDBiEOG64BQ73.
    PhylomeDBiP0A1F0.

    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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P0A1F0-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAKLRVGIVF GGKSAEHEVS LQSAKNIVDA IDKTRFDVVL LGIDKAGQWH    50
    VNDAENYLQN ADDPAHIALR PSAISLAQVP GKHQHQLINA QNGQPLPTVD 100
    VIFPIVHGTL GEDGSLQGML RVANLPFVGS DVLSSAACMD KDVAKRLLRD 150
    AGLNIAPFIT LTRTNRHAFS FAEVESRLGL PLFVKPANQG SSVGVSKVAN 200
    EAQYQQAVAL AFEFDHKVVV EQGIKGREIE CAVLGNDNPQ ASTCGEIVLN 250
    SEFYAYDTKY IDDNGAQVVV PAQIPSEVND KIRAIAIQAY QTLGCAGMAR 300
    VDVFLTADNE VVINEINTLP GFTNISMYPK LWQASGLGYT DLISRLIELA 350
    LERHTANNAL KTTM 364
    Length:364
    Mass (Da):39,357
    Last modified:January 23, 2007 - v2
    Checksum:i00AB43A06746E276
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti17 – 171H → A.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M20793 Genomic DNA. Translation: AAA27056.1.
    AE006468 Genomic DNA. Translation: AAL19334.1.
    PIRiA28642. CEEBDT.
    RefSeqiNP_459375.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL19334; AAL19334; STM0380.
    GeneIDi1251899.
    KEGGistm:STM0380.
    PATRICi32379083. VBISalEnt20916_0403.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M20793 Genomic DNA. Translation: AAA27056.1 .
    AE006468 Genomic DNA. Translation: AAL19334.1 .
    PIRi A28642. CEEBDT.
    RefSeqi NP_459375.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3I12 X-ray 2.20 A/B/C/D 1-364 [» ]
    3Q1K X-ray 2.20 A/B/C/D 1-364 [» ]
    ProteinModelPortali P0A1F0.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 99287.STM0380.

    Proteomic databases

    PaxDbi P0A1F0.
    PRIDEi P0A1F0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL19334 ; AAL19334 ; STM0380 .
    GeneIDi 1251899.
    KEGGi stm:STM0380.
    PATRICi 32379083. VBISalEnt20916_0403.

    Phylogenomic databases

    eggNOGi COG1181.
    HOGENOMi HOG000011593.
    KOi K01921.
    OMAi QIDVIFP.
    OrthoDBi EOG64BQ73.
    PhylomeDBi P0A1F0.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci SENT99287:GCTI-381-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0A1F0.

    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. "Isolation, cloning, and sequencing of the Salmonella typhimurium ddlA gene with purification and characterization of its product, D-alanine:D-alanine ligase (ADP forming)."
      Daub E., Zawadzke L.E., Botstein D., Walsh C.T.
      Biochemistry 27:3701-3708(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-36.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LT2 / SGSC1412 / ATCC 700720.

    Entry informationi

    Entry nameiDDLA_SALTY
    AccessioniPrimary (citable) accession number: P0A1F0
    Secondary accession number(s): P15051
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 1, 2005
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 73 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, Direct protein sequencing, 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