MG1655
W3110
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Gene Report : ddlB
PEC Original Annotations
Essentiality
     Class non-essential
     References (PMID)
Escherichia coli and Salmonella, Cellular and Molecular Biology Second Edition. ASM Press. 1996
Neidhart, F.C.
     Deletion OCR30,31-3 (BK2-1 / AK1-1) (D)  
Related gene (W3110 PEC)
     Gene Search Search MG1655 PEC by gene name:  ddlB
Related strains
     Strains Search Search strains by gene name:  ddlB   Search strains by all related name:  ddlB b0092 ddl ECK0093 JW0090

General information  (Go to Linear View:)
 Gene Name ddlB  
 Alternative name b0092,ddl,ECK0093,JW0090  
 Location, Length 102,233 - 103,153 (  +  ) ;   2.20 min ; 921 (bp) ,   306 (aa) Go to Linear View
 Product D-alanine:D-alanine ligase  
 Operon Name mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC  
 Note D-alanine-D-alanine ligase B, affects cell division; GO_component: GO:0009274 - peptidoglycan-based cell wall; GO_component: GO:0005737 - cytoplasm; GO_process: GO:0009252 - peptidoglycan biosynthetic process  
 Function enzyme; Murein sacculus, peptidoglycan  
 Gene Ontology GO:0000166; nucleotide binding ( ddlB )
GO:0003824; catalytic activity ( ddlB )
GO:0005524; ATP binding ( ddlB )
GO:0005618; cell wall ( ddlB )
GO:0005737; cytoplasm ( ddlB )
GO:0007047; cell wall organization and biogenesis ( ddlB )
GO:0008360; regulation of cell shape ( ddlB )
GO:0008716; D-alanine-D-alanine ligase activity ( ddlB )
GO:0009252; peptidoglycan biosynthetic process ( ddlB )
GO:0016874; ligase activity ( ddlB )
GO:0030145; manganese ion binding ( ddlB )
GO:0046872; metal ion binding ( ddlB )
 PID 1786280  
 EC number
  (KEGG Pathway)
 
6.3.2.4  
Verified Protein Starts (data compiled from literature and appropriate citations are available from EcoGene)
     EcoGene ddlB ( EG10214 )  
    Number of removed 1 aa cleaved  
SWISS-PROT  ( Show simple )
  botton Entry name(Acc.no) DDLB_ECOLI ( P07862 )
    -  Protein name D-alanine--D-alanine ligase B  
    -  Synonyms EC 6.3.2.4, D-alanylalanine synthetase B, D-Ala-D-Ala ligase B  
    -  Gene name Name=ddlB; Synonyms=ddl; OrderedLocusNames=b0092;  
    -  Comments
  • FUNCTION:Cell wall formation.
  • CATALYTIC ACTIVITY:ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.
  • PATHWAY:D-alanine branch of peptidoglycan biosynthesis; second step.
  • SUBUNIT:Monomer.
  • SUBCELLULAR LOCATION:Cytoplasmic.
  • SIMILARITY:Belongs to the D-alanine--D-alanine ligase family.
  • SIMILARITY:Contains 1 ATP-grasp domain.  
  •   botton Entry name(Acc.no) DDLB_ECOL6 ( Q8FL63 )
        -  Protein name D-alanine--D-alanine ligase B  
        -  Synonyms EC 6.3.2.4, D-alanylalanine synthetase B, D-Ala-D-Ala ligase B  
        -  Gene name Name=ddlB; OrderedLocusNames=c0110;  
        -  Comments
  • FUNCTION:Cell wall formation (By similarity).
  • CATALYTIC ACTIVITY:ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.
  • PATHWAY:D-alanine branch of peptidoglycan biosynthesis; second step.
  • SUBUNIT:Monomer (By similarity).
  • SUBCELLULAR LOCATION:Cytoplasmic (By similarity).
  • SIMILARITY:Belongs to the D-alanine--D-alanine ligase family.
  • SIMILARITY:Contains 1 ATP-grasp domain.  
  •   botton Entry name(Acc.no) DDLB_ECO57 ( Q8X9Y6 )
        -  Protein name D-alanine--D-alanine ligase B  
        -  Synonyms EC 6.3.2.4, D-alanylalanine synthetase B, D-Ala-D-Ala ligase B  
        -  Gene name Name=ddlB; OrderedLocusNames=z0102, ECs0096;  
        -  Comments
  • FUNCTION:Cell wall formation (By similarity).
  • CATALYTIC ACTIVITY:ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.
  • PATHWAY:D-alanine branch of peptidoglycan biosynthesis; second step.
  • SUBUNIT:Monomer (By similarity).
  • SUBCELLULAR LOCATION:Cytoplasmic (By similarity).
  • SIMILARITY:Belongs to the D-alanine--D-alanine ligase family.
  • SIMILARITY:Contains 1 ATP-grasp domain.  

  •  Linear View (Whole Mode)
    View Location
       90.0  –  115.0 (KBP)

    Homology Analysis
    BLAST
        Bacteria
             GTOP ddlB (  homologous genes of other bacterias  )  
        PDB     (database updated : 2007.02.20 )
             PSI-BLAST Chain , Mol_id: 1; Molecule: D-Alanine--D-Alanine Ligase; Chain: Null; Ec: 6.3.2.4  
        SWISS-PROT     (database updated : 2007.02.20 )
             BLAST D-alanine--D-alanine ligase B  
             PSI-BLAST D-alanine--D-alanine ligase
        nr     (database updated : 2007.02.20 )
             BLAST D-alanylalanine synthetase [Escherichia coli K12]  
    Pfam 28.0   (database updated : 2015-05 )
        Pfam
    PROSITE
        PROSITE PKC_PHOSPHO_SITE    CK2_PHOSPHO_SITE    TYR_PHOSPHO_SITE    MYRISTYL    GRAM_POS_ANCHORING    DALA_DALA_LIGASE_1    DALA_DALA_LIGASE_2     

    Other Cross-Reference
        COG COG1181M 
        EcoCyc ddlB 

    MMBR References
    Nucleic Acids Res. 1990;18(13):4014
    Nucleotide sequence involving murG and murC in the mra gene cluster region of Escherichia coli.
    Ikeda M, Wachi M, Jung HK, Ishino F, Matsuhashi M. ( 2197603 )
    J Bacteriol. 1989;171(11):6379-82.
    Inhibition of growth of ftsQ, ftsA, and ftsZ mutant cells of Escherichia coli by amplification of a chromosomal region encompassing closely aligned cell division and cell growth genes.
    Jung HK, Ishino F, Matsuhashi M. ( 2553679 )
    J Bacteriol. 1980;142(2):615-20.
    Organization of genes in the ftsA-envA region of the Escherichia coli genetic map and identification of a new fts locus (ftsZ).
    Lutkenhaus JF, Wolf-Watz H, Donachie WD. ( 6991482 )
    J Bacteriol. 1980;143(3):1281-8.
    Determination of transcriptional units and gene products from the ftsA region of Escherichia coli.
    Lutkenhaus JF, Wu HC. ( 6447690 )
    Biochemistry. 1996;35(32):10464-71.
    Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B.
    Park IS, Lin CH, Walsh CT. ( 8756703 )
    J Bacteriol. 1986;167(3):809-17.
    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 AC, Kenan DJ, Sweeney J, Donachie WD. ( 3528126 )

    Sequences
    Amino acid
    FASTA format
    0001 MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL KSMGFQKVFI ALHGRGGEDG 
    0071 TLQGMLELMG LPYTGSGVMA SALSMDKLRS KLLWQGAGLP VAPWVALTRA EFEKGLSDKQ LAEISALGLP 
    0141 VIVKPSREGS SVGMSKVVAE NALQDALRLA FQHDEEVLIE KWLSGPEFTV AILGEEILPS IRIQPSGTFY 
    0211 DYEAKYLSDE TQYFCPAGLE ASQEANLQAL VLKAWTTLGC KGWGRIDVML DSDGQFYLLE ANTSPGMTSH 
    0281 SLVPMAARQA GMSFSQLVVR ILELAD
    
    
    Nucleotide
    FASTA format

    View sequence out neighbor 100bp
    -100                                             AACGACCTGA TTCTCGTTCA GGGGGCTGGT 
    -070 AATATTGGAA AAATTGCCCG TTCTTTAGCT GAAATCAAAC TGAAGCCGCA AACTCCGGAG GAAGAACAAC 
    0001 atgactgata aaatcgcggt cctgttgggt gggacctccg ctgagcggga agtttctctg aattctggcg 
    0071 cagcggtgtt agccggactg cgtgaaggcg gtattgacgc gtatcctgtc gacccgaaag aagtcgacgt 
    0141 gacgcaactg aagtcgatgg gctttcagaa agtgtttatc gcgctacacg gtcgcggcgg tgaagatggt 
    0211 acgctgcagg ggatgctcga gctgatgggc ttgccttata ccggaagcgg agtgatggca tctgcgcttt 
    0281 caatggataa actacgcagc aaacttctat ggcaaggtgc cggtttaccg gtcgcgccgt gggtagcgtt 
    0351 aacccgcgca gagtttgaaa aaggcctgag cgataagcag ttagcagaaa tttctgctct gggtttgccg 
    0421 gttatcgtta agccgagccg cgaaggttcc agtgtgggaa tgtcaaaagt agtagcagaa aatgctctac 
    0491 aagatgcatt aagattggca tttcagcacg atgaagaagt attgattgaa aaatggctaa gtgggccgga 
    0561 gttcacggtt gcgatactcg gtgaagaaat tttaccgtca atacgtattc aaccgtccgg aaccttctat 
    0631 gattatgagg cgaagtatct ctctgatgag acacagtatt tctgccccgc aggtctggaa gcgtcacaag 
    0701 aggccaattt gcaggcatta gtgctgaaag catggacgac gttaggttgc aaaggatggg gacgtattga 
    0771 cgttatgctg gacagcgatg gacagtttta tctgctggaa gccaatacct caccgggtat gaccagccac 
    0841 agcctggtgc cgatggcggc acgtcaggca ggtatgagct tctcgcagtt ggtagtacga attctggaac 
    0911 tggcggacta aTATGTCGCA GGCTGCTCTG AACACGCGAA ACAGCGAAGA AGAGGTTTCT TCTCGCCGCA 
    0981 ATAATGGAAC GCGTCTGGCG GGGATCCTTT TCCTGCTGAC C