Escherichia coli K-12 substr. MG1655 Enzyme: DD-carboxypeptidase, penicillin-binding protein 6b

Gene: dacD Accession Numbers: EG11893 (EcoCyc), b2010, ECK2004

Synonyms: phsE, yeeC, PBP6b

Regulation Summary Diagram: ?

Regulation summary diagram for dacD

DacD, also called penicillin-binding protein 6b (PBP6b), is a D-alanyl-D-alanine carboxypeptidase and penicillin-binding protein with sequence similarity to DacA (PBP5) and DacC (PBP6) [Baquero96].

DacD contains the β-lactam/penicillin-binding domain motif sequences SxxK (SLTK), [S/Y]xN (SGN), and [K/H][T/S]G (KTG) and binds benzylpenicillin [Baquero96].

Increased expression of dacD in a dacA dacC mutant reduces the amount of pentapeptide muropeptides in peptidoglycan [Baquero96]. A dacA dacB dacC dacD quadruple deletion mutant has no growth defects [Baquero96]. Deletion of eight penicillin binding proteins, including DacD among them, leaves cells viable [Denome99]. The dacA dacB dacD, dacA pbpG dacD, dacA dacC dacD, and yrfE yrfF mrcA dacA dacB dacC pbpG ampC ampH mutants display morphological defects [Nelson01, Meberg04, dePedro03]. Overexpresssion of DacD in early exponential growth leads to cell lysis [Nelson01]. Attachment of the C-terminal membrane anchor of DacD to a mutant PBP5 with its own C-terminal anchor removed can complement the morphological defects of the PBP5 mutant [Nelson02].

Expression of dacD was upregulated under basic conditions with oxygen limitation [Hayes06].

Reviews: [Ghosh08, Scheffers05, Holtje98]

Citations: [Harris02, Ghosh03, Varma04, Priyadarshini06]

Locations: inner membrane

Map Position: [2,079,405 <- 2,080,571] (44.82 centisomes, 161°)
Length: 1167 bp / 388 aa

Molecular Weight of Polypeptide: 43.346 kD (from nucleotide sequence), 41.0 kD (experimental) [Baquero96 ]

Unification Links: ASAP:ABE-0006680 , EchoBASE:EB1839 , EcoGene:EG11893 , EcoliWiki:b2010 , ModBase:P33013 , OU-Microarray:b2010 , PortEco:dacD , PR:PRO_000022395 , Protein Model Portal:P33013 , RefSeq:NP_416514 , RegulonDB:EG11893 , SMR:P33013 , String:511145.b2010 , Swiss-Model:P33013 , UniProt:P33013

Relationship Links: InterPro:IN-FAMILY:IPR001967 , InterPro:IN-FAMILY:IPR012338 , InterPro:IN-FAMILY:IPR012907 , InterPro:IN-FAMILY:IPR015956 , InterPro:IN-FAMILY:IPR018044 , Pfam:IN-FAMILY:PF00768 , Pfam:IN-FAMILY:PF07943 , Prints:IN-FAMILY:PR00725 , Smart:IN-FAMILY:SM00936

In Paralogous Gene Group: 169 (4 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0008360 - regulation of cell shape Inferred from experiment Inferred by computational analysis [UniProtGOA11, dePedro03, Nelson01, Meberg04]
GO:0009252 - peptidoglycan biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, Baquero96]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0071555 - cell wall organization Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004180 - carboxypeptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Baquero96]
GO:0008658 - penicillin binding Inferred from experiment [Baquero96]
GO:0004175 - endopeptidase activity Inferred by computational analysis [Gaudet10]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11]
GO:0009002 - serine-type D-Ala-D-Ala carboxypeptidase activity Inferred by computational analysis [Gaudet10, GOA01a, GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Baquero96]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Gaudet10]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure murein

Essentiality data for dacD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Enzymatic reaction of: D-alanyl-D-alanine carboxypeptidase (DD-carboxypeptidase, penicillin-binding protein 6b)

EC Number:

a nascent [peptidoglycan]n with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine) pentapeptide[periplasmic space] + H2O[periplasmic space] <=> a nascent peptidoglycan with (L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanine) tetrapeptide[periplasmic space] + D-alanine[periplasmic space]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: peptidoglycan maturation (meso-diaminopimelate containing)

T(opt): 37 °C [Hsieh06, BRENDA14, Josephine06]

pH(opt): 7.2 [BRENDA14, Hsieh06], 8 [BRENDA14, Josephine06], 8.5 [BRENDA14, Josephine06], 9 [BRENDA14, Stefanova02]

Sequence Features

Protein sequence of DD-carboxypeptidase, penicillin-binding protein 6b with features indicated

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 21 DacD signal sequence
Chain 22 -> 388  
UniProt: D-alanyl-D-alanine carboxypeptidase dacD;
Active-Site 63  
UniProt: Acyl-ester intermediate; Non-Experimental Qualifier: by similarity;
Active-Site 63, 64, 65, 66, 129, 130, 131, 232, 233, 234 DacD penicillin-binding domain
Active-Site 66  
UniProt: Proton acceptor; Non-Experimental Qualifier: by similarity;
Active-Site 129  
UniProt: Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 232  
UniProt: Substrate; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b2010 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11893; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Baquero96: Baquero MR, Bouzon M, Quintela JC, Ayala JA, Moreno F (1996). "dacD, an Escherichia coli gene encoding a novel penicillin-binding protein (PBP6b) with DD-carboxypeptidase activity." J Bacteriol 178(24);7106-11. PMID: 8955390

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Denome99: Denome SA, Elf PK, Henderson TA, Nelson DE, Young KD (1999). "Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: viability, characteristics, and implications for peptidoglycan synthesis." J Bacteriol 181(13);3981-93. PMID: 10383966

dePedro03: 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. PMID: 12562782

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Ghosh03: 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. PMID: 12644487

Ghosh08: Ghosh AS, Chowdhury C, Nelson DE (2008). "Physiological functions of D-alanine carboxypeptidases in Escherichia coli." Trends Microbiol 16(7);309-17. PMID: 18539032

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Harris02: 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. PMID: 12444970

Hayes06: 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. PMID: 17026754

Holtje98: Holtje JV (1998). "Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli." Microbiol Mol Biol Rev 62(1);181-203. PMID: 9529891

Hsieh06: Hsieh ML, Tseng MJ, Tseng MC, Chu YH (2006). "Identification of a new chromophoric substrate in the library of amino acid p-nitroanilides for continuous assay of VanX, a D,D-dipeptidase essential for vancomycin resistance." Anal Biochem 354(1);104-10. PMID: 16701071

Josephine06: Josephine HR, Charlier P, Davies C, Nicholas RA, Pratt RF (2006). "Reactivity of penicillin-binding proteins with peptidoglycan-mimetic beta-lactams: what's wrong with these enzymes?." Biochemistry 45(51);15873-83. PMID: 17176110

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Meberg04: Meberg BM, Paulson AL, Priyadarshini R, Young KD (2004). "Endopeptidase penicillin-binding proteins 4 and 7 play auxiliary roles in determining uniform morphology of Escherichia coli." J Bacteriol 186(24);8326-36. PMID: 15576782

Nelson01: Nelson DE, Young KD (2001). "Contributions of PBP 5 and DD-carboxypeptidase penicillin binding proteins to maintenance of cell shape in Escherichia coli." J Bacteriol 183(10);3055-64. PMID: 11325933

Nelson02: Nelson DE, Ghosh AS, Paulson AL, Young KD (2002). "Contribution of membrane-binding and enzymatic domains of penicillin binding protein 5 to maintenance of uniform cellular morphology of Escherichia coli." J Bacteriol 184(13);3630-9. PMID: 12057958

Priyadarshini06: 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. PMID: 16855223

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Scheffers05: Scheffers DJ, Pinho MG (2005). "Bacterial cell wall synthesis: new insights from localization studies." Microbiol Mol Biol Rev 69(4);585-607. PMID: 16339737

Stefanova02: Stefanova ME, Davies C, Nicholas RA, Gutheil WG (2002). "pH, inhibitor, and substrate specificity studies on Escherichia coli penicillin-binding protein 5." Biochim Biophys Acta 1597(2);292-300. PMID: 12044907

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Varma04: 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. PMID: 15466028

Other References Related to Gene Regulation

Baquero95: Baquero MR, Bouzon M, Varea J, Moreno F (1995). "sbmC, a stationary-phase induced SOS Escherichia coli gene, whose product protects cells from the DNA replication inhibitor microcin B17." Mol Microbiol 1995;18(2);301-11. PMID: 8709849

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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