RegulonDB RegulonDB 10.10: Gene Form
   

dacD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

sbcB dacD sbmC CRP LexA TSS_2319 TSS_2319 TSS_2318 TSS_2318 sbcBp sbcBp TSS_2317 TSS_2317 TSS_2316 TSS_2316 sbmCp1 sbmCp1 sbmCp2 sbmCp2

Gene      
Name: dacD    Texpresso search in the literature
Synonym(s): ECK2004, EG11893, b2010, phsE, yeeC
Genome position(nucleotides): 2081381 <-- 2082547 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.27
External database links:  
ASAP:
 ABE-0006680
ECHOBASE:
 EB1839
ECOLIHUB:
 dacD
OU-MICROARRAY:
 b2010
STRING:
 511145.b2010
COLOMBOS: dacD


Product      
Name: D-alanyl-D-alanine carboxypeptidase DacD
Synonym(s): DacD, PBP6b, PhsE, YeeC, murein D,D-carboxypeptidase DacD, penicillin-binding protein 6b
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space,inner membrane
Molecular weight: 43.346
Isoelectric point: 6.722
Motif(s):
 
Type Positions Sequence
282 -> 372 FTTVQILHRGKKVGTERIWYGDKENIDLGTEQEFWMVLPKAEIPHIKAKYTLDGKELTAPISAHQRVGEIELYDRDKQVAHWPLVTLESVG
375 -> 388 SMFSRLSDYFHHKA
28 -> 262 SPQPPEIHAGSWVLMDYTTGQILTAGNEHQQRNPASLTKLMTGYVVDRAIDSHRITPDDIVTVGRDAWAKDNPVFVGSSLMFLKEGDRVSVRDLSRGLIVDSGNDACVALADYIAGGQRQFVEMMNNYAEKLHLKDTHFETVHGLDAPGQHSSAYDLAVLSRAIIHGEPEFYHMYSEKSLTWNGITQQNRNGLLWDKTMNVDGLKTGHTSGAGFNLIASAVDGQRRLIAVVMGAD
1 -> 21 MKRRLIIAASLFVFNLSSGFA
63 -> 67 SLTKL

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.7 - murein (peptidoglycan)
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005886 - plasma membrane
molecular_function GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0004180 - carboxypeptidase activity
GO:0004175 - endopeptidase activity
GO:0008800 - beta-lactamase activity
GO:0009002 - serine-type D-Ala-D-Ala carboxypeptidase activity
GO:0008658 - penicillin binding
biological_process GO:0000270 - peptidoglycan metabolic process
GO:0006508 - proteolysis
GO:0009252 - peptidoglycan biosynthetic process
GO:0008360 - regulation of cell shape
GO:0071555 - cell wall organization
Note(s): Note(s): ...[more].
Reference(s): [1] Ghosh AS., et al., 2003
[2] Harris F., et al., 2002
[3] Hayes ET., et al., 2006
[4] Meiresonne NY., et al., 2017
[5] Monton Silva A., et al., 2018
[6] Priyadarshini R., et al., 2006
[7] Varma A., et al., 2004
[8] de Pedro MA., et al., 2003
External database links:  
ECOCYC:
 RPOA-MONOMER
ECOLIWIKI:
 b2010
INTERPRO:
 IPR001967
INTERPRO:
 IPR037167
INTERPRO:
 IPR018044
INTERPRO:
 IPR015956
INTERPRO:
 IPR012907
INTERPRO:
 IPR012338
MODBASE:
 P33013
PDB:
 5FSR
PFAM:
 PF00768
PFAM:
 PF07943
PRIDE:
 P33013
PRINTS:
 PR00725
PRODB:
 PRO_000022395
REFSEQ:
 NP_416514
SMART:
 SM00936
SMR:
 P33013
SWISSMODEL:
 P33013
UNIPROT:
 P33013


Operon      
Name: dacD         
Operon arrangement:
Transcription unit        Promoter
dacD


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_2316 2081326 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_2317 2081705 reverse nd [RS-EPT-CBR] [9]
  promoter TSS_2318 2082732 forward nd [RS-EPT-CBR] [9]
  promoter TSS_2319 2083283 forward nd [RS-EPT-CBR] [9]


Evidence    

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


Reference(s)    

 [1] Ghosh AS., Young KD., 2003, Sequences near the active site in chimeric penicillin binding proteins 5 and 6 affect uniform morphology of Escherichia coli., J Bacteriol 185(7):2178-86

 [2] Harris F., Brandenburg K., Seydel U., Phoenix D., 2002, Investigations into the mechanisms used by the C-terminal anchors of Escherichia coli penicillin-binding proteins 4, 5, 6 and 6b for membrane interaction., Eur J Biochem 269(23):5821-9

 [3] Hayes ET., Wilks JC., Sanfilippo P., Yohannes E., Tate DP., Jones BD., Radmacher MD., BonDurant SS., Slonczewski JL., 2006, Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12., BMC Microbiol 6:89

 [4] Meiresonne NY., van der Ploeg R., Hink MA., den Blaauwen T., 2017, Activity-Related Conformational Changes in d,d-Carboxypeptidases Revealed by In Vivo Periplasmic Forster Resonance Energy Transfer Assay in Escherichia coli., MBio 8(5)

 [5] Monton Silva A., Otten C., Biboy J., Breukink E., VanNieuwenhze M., Vollmer W., den Blaauwen T., 2018, The Fluorescent D-Amino Acid NADA as a Tool to Study the Conditional Activity of Transpeptidases in Escherichia coli., Front Microbiol 9:2101

 [6] Priyadarshini R., Popham DL., Young KD., 2006, Daughter cell separation by penicillin-binding proteins and peptidoglycan amidases in Escherichia coli., J Bacteriol 188(15):5345-55

 [7] Varma A., Young KD., 2004, FtsZ collaborates with penicillin binding proteins to generate bacterial cell shape in Escherichia coli., J Bacteriol 186(20):6768-74

 [8] de Pedro MA., Young KD., Holtje JV., Schwarz H., 2003, Branching of Escherichia coli cells arises from multiple sites of inert peptidoglycan., J Bacteriol 185(4):1147-52

 [9] 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.

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