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Q8ZIE7

- DDL_YERPE

UniProt

Q8ZIE7 - DDL_YERPE

Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Yersinia pestis
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 101 (01 Oct 2014)
      Sequence version 1 (01 Mar 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 bindingi257 – 2571Magnesium or manganese 1UniRule annotation
    Metal bindingi270 – 2701Magnesium or manganese 1UniRule annotation
    Metal bindingi270 – 2701Magnesium or manganese 2UniRule annotation
    Metal bindingi272 – 2721Magnesium or manganese 2UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi134 – 18956ATPUniRule 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

    BioCyciYPES214092:GKDD-551-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
    Synonyms:ddlB
    Ordered Locus Names:YPO0557, y3624, YP_3627
    OrganismiYersinia pestis
    Taxonomic identifieri632 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
    ProteomesiUP000000815: Chromosome, UP000001019: Chromosome, UP000002490: 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 – 306306D-alanine--D-alanine ligasePRO_0000177912Add
    BLAST

    Proteomic databases

    PRIDEiQ8ZIE7.

    Interactioni

    Protein-protein interaction databases

    IntActiQ8ZIE7. 3 interactions.
    STRINGi214092.YPO0557.

    Structurei

    Secondary structure

    1
    306
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 95
    Helixi16 – 3318
    Beta strandi37 – 415
    Turni42 – 443
    Helixi47 – 493
    Turni50 – 545
    Beta strandi57 – 604
    Turni65 – 673
    Beta strandi68 – 703
    Helixi71 – 799
    Beta strandi83 – 853
    Helixi88 – 947
    Helixi97 – 10610
    Beta strandi114 – 1185
    Helixi119 – 1224
    Helixi127 – 1348
    Helixi135 – 1373
    Beta strandi139 – 1479
    Beta strandi155 – 1573
    Helixi160 – 1623
    Helixi163 – 1719
    Beta strandi175 – 1817
    Beta strandi187 – 1937
    Beta strandi201 – 2044
    Beta strandi222 – 2265
    Helixi231 – 24616
    Turni247 – 2493
    Beta strandi252 – 2609
    Beta strandi266 – 2749
    Beta strandi278 – 2814
    Helixi282 – 2909
    Helixi294 – 30310

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3V4ZX-ray2.69A/B1-306[»]
    ProteinModelPortaliQ8ZIE7.
    SMRiQ8ZIE7. Positions 1-306.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini101 – 303203ATP-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.
    KOiK01921.
    OMAiEDPARES.
    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.
    PS00844. DALA_DALA_LIGASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q8ZIE7-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAEKVAVLLG GTSAEREVSL LSGQAVLAGL KEAGIDAYGV DTKDFPVTQL    50
    KEQGFDKVFI ALHGRGGEDG TLQGVLEFLQ LPYTGSGVMA SALTMDKLRT 100
    KLVWQALGLP ISPYVALNRQ QFETLSPEEL VACVAKLGLP LIVKPSHEGS 150
    SVGMSKVDHA SELQKALVEA FQHDSDVLIE KWLSGPEFTV AILGDEVLPS 200
    IRIQPPGVFY DYDAKYLSDK TQYFCPSGLS DESEQQLAAL ALQAYHALDC 250
    SGWGRVDVMQ DRDGHFYLLE VNTSPGMTSH SLVPMAARQY GLSFSQLVAR 300
    ILMLAD 306
    Length:306
    Mass (Da):33,150
    Last modified:March 1, 2002 - v1
    Checksum:iC78CFF3D2E11F846
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL590842 Genomic DNA. Translation: CAL19236.1.
    AE009952 Genomic DNA. Translation: AAM87172.1.
    AE017042 Genomic DNA. Translation: AAS63775.1.
    PIRiAB0069.
    RefSeqiNP_670921.1. NC_004088.1.
    NP_994898.1. NC_005810.1.
    YP_002345628.1. NC_003143.1.

    Genome annotation databases

    EnsemblBacteriaiAAM87172; AAM87172; y3624.
    AAS63775; AAS63775; YP_3627.
    GeneIDi1148571.
    1173401.
    2763379.
    KEGGiype:YPO0557.
    ypk:y3624.
    ypm:YP_3627.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL590842 Genomic DNA. Translation: CAL19236.1 .
    AE009952 Genomic DNA. Translation: AAM87172.1 .
    AE017042 Genomic DNA. Translation: AAS63775.1 .
    PIRi AB0069.
    RefSeqi NP_670921.1. NC_004088.1.
    NP_994898.1. NC_005810.1.
    YP_002345628.1. NC_003143.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3V4Z X-ray 2.69 A/B 1-306 [» ]
    ProteinModelPortali Q8ZIE7.
    SMRi Q8ZIE7. Positions 1-306.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q8ZIE7. 3 interactions.
    STRINGi 214092.YPO0557.

    Proteomic databases

    PRIDEi Q8ZIE7.

    Protocols and materials databases

    DNASUi 1148571.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAM87172 ; AAM87172 ; y3624 .
    AAS63775 ; AAS63775 ; YP_3627 .
    GeneIDi 1148571.
    1173401.
    2763379.
    KEGGi ype:YPO0557.
    ypk:y3624.
    ypm:YP_3627.

    Phylogenomic databases

    eggNOGi COG1181.
    HOGENOMi HOG000011592.
    KOi K01921.
    OMAi EDPARES.
    OrthoDBi EOG6ND0KB.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci YPES214092:GKDD-551-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: CO-92 / Biovar Orientalis.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: KIM10+ / Biovar Mediaevalis.
    3. "Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans."
      Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D., Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L., Dai R.
      , Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H., Wang J., Huang P., Yang R.
      DNA Res. 11:179-197(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 91001 / Biovar Mediaevalis.

    Entry informationi

    Entry nameiDDL_YERPE
    AccessioniPrimary (citable) accession number: Q8ZIE7
    Secondary accession number(s): Q0WJB0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 2, 2002
    Last sequence update: March 1, 2002
    Last modified: October 1, 2014
    This is version 101 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