Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P07862

- DDLB_ECOLI

UniProt

P07862 - DDLB_ECOLI

Protein

D-alanine--D-alanine ligase B

Gene

ddlB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 146 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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
    Active sitei15 – 151
    Active sitei150 – 1501
    Metal bindingi257 – 2571Magnesium or manganese 1By similarity
    Metal bindingi270 – 2701Magnesium or manganese 1By similarity
    Metal bindingi270 – 2701Magnesium or manganese 2By similarity
    Metal bindingi272 – 2721Magnesium or manganese 2By similarity
    Active sitei281 – 2811

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi134 – 18956ATPBy similarityAdd
    BLAST

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-HAMAP
    2. D-alanine-D-alanine ligase activity Source: EcoCyc
    3. magnesium ion binding Source: UniProtKB-HAMAP
    4. manganese ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. peptidoglycan biosynthetic process Source: EcoCyc
    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

    BioCyciEcoCyc:DALADALALIGB-MONOMER.
    ECOL316407:JW0090-MONOMER.
    MetaCyc:DALADALALIGB-MONOMER.
    UniPathwayiUPA00219.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-alanine--D-alanine ligase B (EC:6.3.2.4)
    Alternative name(s):
    D-Ala-D-Ala ligase B
    D-alanylalanine synthetase B
    Gene namesi
    Name:ddlB
    Synonyms:ddl
    Ordered Locus Names:b0092, JW0090
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10214. ddlB.

    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 – 11Removed
    Chaini2 – 306305D-alanine--D-alanine ligase BPRO_0000177818Add
    BLAST

    Proteomic databases

    PaxDbiP07862.
    PRIDEiP07862.

    Expressioni

    Gene expression databases

    GenevestigatoriP07862.

    Interactioni

    Subunit structurei

    Monomer.

    Protein-protein interaction databases

    IntActiP07862. 4 interactions.
    STRINGi511145.b0092.

    Structurei

    Secondary structure

    1
    306
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 85
    Helixi16 – 3217
    Beta strandi36 – 405
    Turni42 – 443
    Helixi47 – 493
    Turni50 – 545
    Beta strandi55 – 606
    Turni65 – 673
    Beta strandi68 – 703
    Helixi71 – 799
    Beta strandi83 – 853
    Helixi88 – 958
    Helixi97 – 10610
    Beta strandi114 – 1185
    Helixi119 – 1246
    Helixi129 – 1357
    Beta strandi139 – 1457
    Turni150 – 1534
    Beta strandi155 – 1595
    Helixi160 – 1623
    Helixi163 – 1708
    Turni171 – 1733
    Beta strandi175 – 1817
    Beta strandi187 – 1937
    Beta strandi201 – 2044
    Beta strandi206 – 2105
    Helixi212 – 2165
    Beta strandi222 – 2265
    Helixi231 – 24818
    Beta strandi252 – 2609
    Beta strandi266 – 2749
    Helixi282 – 2898
    Helixi294 – 30310

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1IOVX-ray2.20A1-306[»]
    1IOWX-ray1.90A1-306[»]
    2DLNX-ray2.30A1-306[»]
    ProteinModelPortaliP07862.
    SMRiP07862. Positions 1-306.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP07862.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini101 – 303203ATP-graspAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG1181.
    HOGENOMiHOG000011592.
    KOiK01921.
    OMAiEDPARES.
    OrthoDBiEOG6ND0KB.
    PhylomeDBiP07862.

    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. 2 hits.
    [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.

    P07862-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL    50
    KSMGFQKVFI ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSMDKLRS 100
    KLLWQGAGLP VAPWVALTRA EFEKGLSDKQ LAEISALGLP VIVKPSREGS 150
    SVGMSKVVAE NALQDALRLA FQHDEEVLIE KWLSGPEFTV AILGEEILPS 200
    IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL VLKAWTTLGC 250
    KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR 300
    ILELAD 306
    Length:306
    Mass (Da):32,840
    Last modified:January 23, 2007 - v3
    Checksum:iF2D401C323A04471
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M14029 Genomic DNA. Translation: AAA23672.1.
    K02668 Genomic DNA. Translation: AAA23815.1.
    X52644 Genomic DNA. Translation: CAA36869.1.
    X55034 Genomic DNA. Translation: CAA38869.1.
    U00096 Genomic DNA. Translation: AAC73203.1.
    AP009048 Genomic DNA. Translation: BAB96660.1.
    PIRiA30289. CEECDL.
    RefSeqiNP_414634.1. NC_000913.3.
    YP_488397.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73203; AAC73203; b0092.
    BAB96660; BAB96660; BAB96660.
    GeneIDi12932120.
    946324.
    KEGGiecj:Y75_p0091.
    eco:b0092.
    PATRICi32115289. VBIEscCol129921_0096.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M14029 Genomic DNA. Translation: AAA23672.1 .
    K02668 Genomic DNA. Translation: AAA23815.1 .
    X52644 Genomic DNA. Translation: CAA36869.1 .
    X55034 Genomic DNA. Translation: CAA38869.1 .
    U00096 Genomic DNA. Translation: AAC73203.1 .
    AP009048 Genomic DNA. Translation: BAB96660.1 .
    PIRi A30289. CEECDL.
    RefSeqi NP_414634.1. NC_000913.3.
    YP_488397.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1IOV X-ray 2.20 A 1-306 [» ]
    1IOW X-ray 1.90 A 1-306 [» ]
    2DLN X-ray 2.30 A 1-306 [» ]
    ProteinModelPortali P07862.
    SMRi P07862. Positions 1-306.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P07862. 4 interactions.
    STRINGi 511145.b0092.

    Chemistry

    ChEMBLi CHEMBL1956.

    Proteomic databases

    PaxDbi P07862.
    PRIDEi P07862.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73203 ; AAC73203 ; b0092 .
    BAB96660 ; BAB96660 ; BAB96660 .
    GeneIDi 12932120.
    946324.
    KEGGi ecj:Y75_p0091.
    eco:b0092.
    PATRICi 32115289. VBIEscCol129921_0096.

    Organism-specific databases

    EchoBASEi EB0210.
    EcoGenei EG10214. ddlB.

    Phylogenomic databases

    eggNOGi COG1181.
    HOGENOMi HOG000011592.
    KOi K01921.
    OMAi EDPARES.
    OrthoDBi EOG6ND0KB.
    PhylomeDBi P07862.

    Enzyme and pathway databases

    UniPathwayi UPA00219 .
    BioCyci EcoCyc:DALADALALIGB-MONOMER.
    ECOL316407:JW0090-MONOMER.
    MetaCyc:DALADALALIGB-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P07862.
    PROi P07862.

    Gene expression databases

    Genevestigatori P07862.

    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. 2 hits.
    [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. "Further evidence for overlapping transcriptional units in an Escherichia coli cell envelope-cell division gene cluster: DNA sequence and transcriptional organization of the ddl ftsQ region."
      Robinson A.C., Kenan D.J., Sweeney J., Donachie W.D.
      J. Bacteriol. 167:809-817(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region."
      Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A.
      Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Nucleotide sequence involving murG and murC in the mra gene cluster region of Escherichia coli."
      Ikeda M., Wachi M., Jung H.K., Ishino F., Matsuhashi M.
      Nucleic Acids Res. 18:4014-4014(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-41.
      Strain: K12.
    6. "Regulation of expression of the ftsA cell division gene by sequences in upstream genes."
      Dewar S.J., Donachie W.D.
      J. Bacteriol. 172:6611-6614(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 300-306.
    7. "D-alanine:D-alanine ligase of Escherichia coli. Expression, purification and inhibitory studies on the cloned enzyme."
      Al-Bar O.A., O'Connor C.D., Giles I.G., Akhtar M.
      Biochem. J. 282:747-752(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION, PARTIAL PROTEIN SEQUENCE.
    8. "Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3-A resolution."
      Fan C., Moews P.C., Walsh C.T., Knox J.R.
      Science 266:439-443(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
    9. "D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant."
      Fan C., Park I.-S., Walsh C.T., Knox J.R.
      Biochemistry 36:2531-2538(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).

    Entry informationi

    Entry nameiDDLB_ECOLI
    AccessioniPrimary (citable) accession number: P07862
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 146 of the entry and version 3 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3