RegulonDB RegulonDB 10.9: Gene Form
   

ddlB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

murC murG ddlB ftsQ ftsW ftsA RcsB SdiA SdiA SdiA ppGpp TSS_183 TSS_183 TSS_182 TSS_182 TSS_181 TSS_181 ftsAp1 ftsAp1 TSS_180 TSS_180 TSS_179 (cluster) TSS_179 (cluster) TSS_178 TSS_178 TSS_177 TSS_177 TSS_176 TSS_176 ftsQp1 ftsQp1 TSS_175 TSS_175 ftsQp2 ftsQp2 TSS_174 TSS_174 TSS_173 (cluster) TSS_173 (cluster) TSS_172 TSS_172

Gene      
Name: ddlB    Texpresso search in the literature
Synonym(s): ECK0093, EG10214, b0092, ddl
Genome position(nucleotides): 102233 --> 103153 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.57
External database links:  
ASAP:
ABE-0000326
CGSC:
870
ECHOBASE:
EB0210
ECOLIHUB:
ddlB
OU-MICROARRAY:
b0092
STRING:
511145.b0092
COLOMBOS: ddlB


Product      
Name: D-alanine—D-alanine ligase B
Synonym(s): Ddl, DdlB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 32.84
Isoelectric point: 4.482
Motif(s):
 
Type Positions Sequence
101 -> 303 KLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILE
134 -> 189 ISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFT
4 -> 86 KIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGS
103 -> 303 LWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILE
2 -> 306 TDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILELAD

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.7 - murein (peptidoglycan)
  6 - cell structure --> 6.2 - murein
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0046872 - metal ion binding
GO:0016874 - ligase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0008716 - D-alanine-D-alanine ligase activity
GO:0042803 - protein homodimerization activity
biological_process GO:0009252 - peptidoglycan biosynthetic process
GO:0008360 - regulation of cell shape
GO:0071555 - cell wall organization
Note(s): Note(s): ...[more].
Reference(s): [1] Besong GE., et al., 2005
[2] Hersch SJ., et al., 2020
[3] Kovac A., et al., 2008
[4] Kovac A., et al., 2007
[5] Lugtenberg EJ., et al., 1973
[6] Murakami R., et al., 2009
[7] Putty S., et al., 2011
[8] Skedelj V., et al., 2012
[9] Sova M., et al., 2009
[10] Vehar B., et al., 2011
[11] Wu D., et al., 2008
External database links:  
ECOCYC:
DALADALALIGB-MONOMER
ECOLIWIKI:
b0092
INTERPRO:
IPR013815
INTERPRO:
IPR005905
INTERPRO:
IPR011761
INTERPRO:
IPR000291
INTERPRO:
IPR016185
INTERPRO:
IPR011127
INTERPRO:
IPR011095
MODBASE:
P07862
PDB:
4C5C
PDB:
2DLN
PDB:
4C5A
PDB:
1IOW
PDB:
4C5B
PDB:
1IOV
PFAM:
PF07478
PFAM:
PF01820
PRIDE:
P07862
PRODB:
PRO_000022420
PROSITE:
PS50975
PROSITE:
PS00844
PROSITE:
PS00843
REFSEQ:
NP_414634
SMR:
P07862
UNIPROT:
P07862


Operon      
Name: mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC         
Operon arrangement:
Transcription unit        Promoter
mraZW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
mraW-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC
ftsQ
ftsQAZ
ftsQAZ
ftsAZ
ftsZ
ftsZ
ftsZ
lpxC
lpxC


Transcriptional Regulation      
Display Regulation             
Repressed by: MraZ, LexA, PdhR


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_172 100621 forward nd [RS-EPT-CBR] [12]
  promoter TSS_173 (cluster) 102049 forward For this promoter, there
Read more >
[RS-EPT-CBR] [12]
  promoter TSS_174 102679 forward nd [RS-EPT-CBR] [12]
  promoter TSS_175 102865 forward nd [RS-EPT-CBR] [12]
  promoter TSS_176 102872 forward nd [RS-EPT-CBR] [12]
  promoter TSS_177 103019 forward nd [RS-EPT-CBR] [12]
  promoter TSS_178 103024 forward nd [RS-EPT-CBR] [12]
  promoter TSS_179 (cluster) 103028 forward For this promoter, there
Read more >
[RS-EPT-CBR] [12]
  promoter TSS_180 103133 forward nd [RS-EPT-CBR] [12]
  promoter TSS_181 103608 forward nd [RS-EPT-CBR] [12]
  promoter TSS_182 103889 forward nd [RS-EPT-CBR] [12]
  promoter TSS_183 103960 forward nd [RS-EPT-CBR] [12]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Besong GE., Bostock JM., Stubbings W., Chopra I., Roper DI., Lloyd AJ., Fishwick CW., Johnson AP., 2005, A de novo designed inhibitor of D-Ala-D-Ala ligase from E. coli., Angew Chem Int Ed Engl 44(39):6403-6

 [2] Hersch SJ., Watanabe N., Stietz MS., Manera K., Kamal F., Burkinshaw B., Lam L., Pun A., Li M., Savchenko A., Dong TG., 2020, Envelope stress responses defend against type six secretion system attacks independently of immunity proteins., Nat Microbiol 5(5):706-714

 [3] Kovac A., Konc J., Vehar B., Bostock JM., Chopra I., Janezic D., Gobec S., 2008, Discovery of new inhibitors of D-alanine:D-alanine ligase by structure-based virtual screening., J Med Chem 51(23):7442-8

 [4] Kovac A., Majce V., Lenarsic R., Bombek S., Bostock JM., Chopra I., Polanc S., Gobec S., 2007, Diazenedicarboxamides as inhibitors of D-alanine-D-alanine ligase (Ddl)., Bioorg Med Chem Lett 17(7):2047-54

 [5] Lugtenberg EJ., v Schijndel-van Dam A., 1973, Temperature-sensitive mutant of Escherichia coli K-12 with an impaired D-alanine:D-alanine ligase., J Bacteriol 113(1):96-104

 [6] Murakami R., Muramatsu Y., Minami E., Masuda K., Sakaida Y., Endo S., Suzuki T., Ishida O., Takatsu T., Miyakoshi S., Inukai M., Isono F., 2009, A novel assay of bacterial peptidoglycan synthesis for natural product screening., J Antibiot (Tokyo) 62(3):153-8

 [7] Putty S., Rai A., Jamindar D., Pagano P., Quinn CL., Mima T., Schweizer HP., Gutheil WG., 2011, Characterization of d-boroAla as a novel broad-spectrum antibacterial agent targeting d-Ala-d-Ala ligase., Chem Biol Drug Des 78(5):757-63

 [8] Skedelj V., Arsovska E., Tomasic T., Kroflic A., Hodnik V., Hrast M., Bester-Rogac M., Anderluh G., Gobec S., Bostock J., Chopra I., O'Neill AJ., Randall C., Zega A., 2012, 6-Arylpyrido[2,3-d]pyrimidines as Novel ATP-Competitive Inhibitors of Bacterial D-Alanine:D-Alanine Ligase., PLoS One 7(8):e39922

 [9] Sova M., Cadez G., Turk S., Majce V., Polanc S., Batson S., Lloyd AJ., Roper DI., Fishwick CW., Gobec S., 2009, Design and synthesis of new hydroxyethylamines as inhibitors of D-alanyl-D-lactate ligase (VanA) and D-alanyl-D-alanine ligase (DdlB)., Bioorg Med Chem Lett 19(5):1376-9

 [10] Vehar B., Hrast M., Kovac A., Konc J., Mariner K., Chopra I., O'Neill A., Janezic D., Gobec S., 2011, Ellipticines and 9-acridinylamines as inhibitors of D-alanine:D-alanine ligase., Bioorg Med Chem 19(17):5137-46

 [11] Wu D., Kong Y., Han C., Chen J., Hu L., Jiang H., Shen X., 2008, D-Alanine:D-alanine ligase as a new target for the flavonoids quercetin and apigenin., Int J Antimicrob Agents 32(5):421-6

 [12] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.


RegulonDB