Escherichia coli K-12 substr. MG1655 Enzyme: L,D-carboxypeptidase A

Gene: ldcA Accession Numbers: G6621 (EcoCyc), b1192, ECK1180

Synonyms: ycgQ

Regulation Summary Diagram: ?

Regulation summary diagram for ldcA

LdcA is an L,D-carboxypeptidase that has an essential function in murein (peptidoglycan) recycling/turnover [Templin99]. LdcA is a cytoplasmic enzyme which accepts monomeric muropeptides, free tetrapeptide and UDP-activated murein precursors, but not crosslinked muropeptides or murein as substrates [Templin99].

An ldcA deletion mutant exhibits defects in murein recycling, including decreased peptidoglycan cross-linking. The mutation causes cell lysis at stationary phase [Templin99]. The mutant has decreased levels of UDP-MurNAc-pentapeptide and increased levels of UDP-MurNAc-tetrapeptide (a side product of Mpl activity) and the tetrapeptide L-Ala-γ-D-Glu-meso-A2pm-D-Ala [Herve07].

A dithiazoline inhibitor of LdcA has been identified [Baum05].

ldcA is one of a network of 93 genes believed to play a role in promoting the stress-induced mutagenesis (SIM) response of E. coli K-12 [Al12].

LdcA: "L,D-carboxypeptidase A" [Templin99].

Review: [Park08]

Citations: [Metz86, Metz86a, Beck76, Beck77]

Locations: cytosol

Map Position: [1,241,389 <- 1,242,303] (26.76 centisomes, 96°)
Length: 915 bp / 304 aa

Molecular Weight of Polypeptide: 33.567 kD (from nucleotide sequence), 32 kD (experimental) [Ursinus92 ]

pI: 5.5 [Ursinus92]

Unification Links: ASAP:ABE-0004002 , DIP:DIP-10085N , EchoBASE:EB3657 , EcoGene:EG13898 , EcoliWiki:b1192 , OU-Microarray:b1192 , PortEco:ldcA , PR:PRO_000023074 , Protein Model Portal:P76008 , RefSeq:NP_415710 , RegulonDB:G6621 , SMR:P76008 , String:511145.b1192 , UniProt:P76008

Relationship Links: EcoO157Cyc:Homolog:Z1955 , EcoO157Cyc:Homolog:Z1955-MONOMER , InterPro:IN-FAMILY:IPR003507 , InterPro:IN-FAMILY:IPR027461 , InterPro:IN-FAMILY:IPR027478 , InterPro:IN-FAMILY:IPR029062 , Pfam:IN-FAMILY:PF02016

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0009050 - glycopeptide catabolic process Inferred from experiment [Templin99]
GO:0009254 - peptidoglycan turnover Inferred from experiment Inferred by computational analysis [UniProtGOA12, Templin99]
GO:0006508 - proteolysis Inferred by computational analysis [UniProtGOA11a]
GO:0008360 - regulation of cell shape Inferred by computational analysis [UniProtGOA11a]
GO:0009252 - peptidoglycan biosynthetic process Inferred by computational analysis [UniProtGOA11a]
GO:0071555 - cell wall organization Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004180 - carboxypeptidase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Ursinus92]
GO:0008233 - peptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0008236 - serine-type peptidase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Templin99]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: cell structure murein
metabolism central intermediary metabolism murein turnover, recycling
metabolism degradation of macromolecules proteins/peptides/glycopeptides

Essentiality data for ldcA 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]

Last-Curated ? 07-Nov-2012 by Keseler I , SRI International

Enzymatic reaction of: L,D-carboxypeptidase

EC Number:

L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanine + H2O <=> L-alanyl-γ-D-glutamyl-meso-diaminopimelate + D-alanine

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: muropeptide degradation , anhydromuropeptides recycling

Enzymatic reaction of: L,D-carboxypeptidase

UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanine + H2O <=> D-alanine + UDP-N-acetyl-α-D-muramoyl-L-alanyl-γ-D-glutamyl-meso-2,6-diaminopimelate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Inhibitors (Competitive): nocardicin A (Kic = 50µM) [Ursinus92, Templin99]

Kinetic Parameters:

Km (μM)

pH(opt): 8.4 [Ursinus92]

Sequence Features

Protein sequence of L,D-carboxypeptidase A with features indicated

Feature Class Location Citations Comment
Active-Site 106
UniProt: Nucleophile; Non-Experimental Qualifier: by similarity;
Active-Site 200
UniProt: Charge relay system; Non-Experimental Qualifier: by similarity;
Active-Site 270
UniProt: Charge relay system; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Al12: Al Mamun AA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM (2012). "Identity and function of a large gene network underlying mutagenic repair of DNA breaks." Science 338(6112);1344-8. PMID: 23224554

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

Baum05: Baum EZ, Crespo-Carbone SM, Foleno B, Peng S, Hilliard JJ, Abbanat D, Goldschmidt R, Bush K (2005). "Identification of a dithiazoline inhibitor of Escherichia coli L,D-carboxypeptidase A." Antimicrob Agents Chemother 49(11);4500-7. PMID: 16251288

Beck76: Beck BD, Park JT (1976). "Activity of three murein hydrolases during the cell division cycle of Escherichia coli K-12 as measured in toluene-treated cells." J Bacteriol 126(3);1250-60. PMID: 780345

Beck77: Beck BD, Park JT (1977). "Basis for the observed fluctuation of carboxypeptidase II activity during the cell cycle in BUG 6, a temperature-sensitive division mutant of Escherichia coli." J Bacteriol 130(3);1292-302. PMID: 405375

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

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

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

Herve07: Herve M, Boniface A, Gobec S, Blanot D, Mengin-Lecreulx D (2007). "Biochemical characterization and physiological properties of Escherichia coli UDP-N-acetylmuramate:L-alanyl-{gamma}-D-glutamyl-meso-diaminopimelate ligase (Mpl)." J Bacteriol 189(11):3987-95. PMID: 17384195

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Leguina94: Leguina JI, Quintela JC, de Pedro MA (1994). "Substrate specificity of Escherichia coli LD-carboxypeptidase on biosynthetically modified muropeptides." FEBS Lett 339(3);249-52. PMID: 8112463

Metz86: Metz R, Henning S, Hammes WP (1986). "LD-carboxypeptidase activity in Escherichia coli. I. The LD-carboxypeptidase activity in ether treated cells." Arch Microbiol 144(2);175-80. PMID: 3521529

Metz86a: Metz R, Henning S, Hammes WP (1986). "LD-carboxypeptidase activity in Escherichia coli. II. Isolation, purification and characterization of the enzyme from E. coli K 12." Arch Microbiol 144(2);181-6. PMID: 3521530

Park08: Park JT, Uehara T (2008). "How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan)." Microbiol Mol Biol Rev 72(2);211-27, table of contents. PMID: 18535144

Templin99: Templin MF, Ursinus A, Holtje JV (1999). "A defect in cell wall recycling triggers autolysis during the stationary growth phase of Escherichia coli." EMBO J 18(15);4108-17. PMID: 10428950

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 the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

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

Ursinus92: Ursinus A, Steinhaus H, Holtje JV (1992). "Purification of a nocardicin A-sensitive LD-carboxypeptidase from Escherichia coli by affinity chromatography." J Bacteriol 174(2);441-6. PMID: 1729236

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Fri Oct 9, 2015, biocyc12.