Escherichia coli K-12 substr. MG1655 Enzyme: L,D-transpeptidase LdtD

Gene: ldtD Accession Numbers: EG11253 (EcoCyc), b0925, ECK0916

Synonyms: ycbB

Regulation Summary Diagram: ?

Regulation summary diagram for ldtD

LdtD (formerly YcbB) is an L,D-transpeptidase responsible for the removal of the D-alanine residue of an acyl donor peptidoglycan tetrapeptide stem and attachment of the meso-diaminopimelyl (DAP) residue to the meso-DAP residue of a second, acyl acceptor peptidoglycan tetrapeptide.

An erfK ycfS ybiS ynhG ycbB quintuple mutant did not form attachments of peptidogycan to Braun lipoprotein, did not form meso-DAP - meso-DAP peptidoglycan cross-links, did not form tripeptide stems, and did not form tetrapeptide stems with Gly as the fourth aminoacid [Magnet08]. Expression of ycbB restored meso-DAP - meso-DAP peptidoglycan cross-links, tripeptide stems, and tetrapeptide stems with Gly as the fourth aminoacid [Magnet08].

Expression of ycbB increased in response to shift to acidic pH [Kannan08]. Constitutive activation of the Cpx two component pathway results in upregulation of ldtD and a resultant increase in the level of DAP-DAP crosslinks; ldtD is a member of the CpxR regulon [BernalCabas14]

Locations: membrane

Map Position: [980,270 -> 982,117] (21.13 centisomes, 76°)
Length: 1848 bp / 615 aa

Molecular Weight of Polypeptide: 67.812 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003142 , DIP:DIP-11474N , EchoBASE:EB1233 , EcoGene:EG11253 , EcoliWiki:b0925 , Mint:MINT-1263904 , ModBase:P22525 , OU-Microarray:b0925 , PortEco:ycbB , Pride:P22525 , Protein Model Portal:P22525 , RefSeq:NP_415445 , RegulonDB:EG11253 , SMR:P22525 , String:511145.b0925 , UniProt:P22525

Relationship Links: InterPro:IN-FAMILY:IPR002477 , InterPro:IN-FAMILY:IPR005490 , Pfam:IN-FAMILY:PF01471 , Pfam:IN-FAMILY:PF03734 , Prosite:IN-FAMILY:PS00092

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006508 - proteolysis Inferred from experiment [Magnet08]
GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0043164 - Gram-negative-bacterium-type cell wall biogenesis Inferred from experiment [Magnet08]
GO:0044036 - cell wall macromolecule metabolic process Inferred from experiment [Magnet08]
GO:0008360 - regulation of cell shape Inferred by computational analysis [UniProtGOA11a]
GO:0009252 - peptidoglycan biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11a]
GO:0071555 - cell wall organization Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0016755 - transferase activity, transferring amino-acyl groups Inferred from experiment [Magnet08]
GO:0016807 - cysteine-type carboxypeptidase activity Inferred from experiment [Magnet08]
GO:0071972 - peptidoglycan L,D-transpeptidase activity Inferred from experiment [Magnet08]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016757 - transferase activity, transferring glycosyl groups Inferred by computational analysis [UniProtGOA11a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

MultiFun Terms: metabolism biosynthesis of macromolecules (cellular constituents) murein (peptidoglycan)

Essentiality data for ldtD 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]

Curated 12-Oct-2006 by Keseler I , SRI International
Last-Curated ? 09-Jul-2008 by Johnson A , JCVI

Enzymatic reaction of: L,D-transpeptidase

peptidoglycan tetrapeptide, glycan chain 2 + peptidoglycan tetrapeptide, glycan chain 1 <=> peptidoglycan DAP-DAP crosslink + D-alanine + H+

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.

Sequence Features

Protein sequence of L,D-transpeptidase LdtD with features indicated

Feature Class Location Citations Comment
Transmembrane-Region 11 -> 26
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 39 -> 40
[Niki91, UniProt10]
UniProt: (in Ref. 4; CAA40777);
Active-Site 528
UniProt: Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b0925 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11253; 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

BernalCabas14: Bernal-Cabas M, Ayala JA, Raivio T (2014). "The Cpx envelope stress response modifies peptidoglycan cross-linking via the L,D-transpeptidase LdtD and the novel protein YgaU." J Bacteriol. PMID: 25422305

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Kannan08: Kannan G, Wilks JC, Fitzgerald DM, Jones BD, Bondurant SS, Slonczewski JL (2008). "Rapid acid treatment of Escherichia coli: transcriptomic response and recovery." BMC Microbiol 8;37. PMID: 18302792

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Magnet08: Magnet S, Dubost L, Marie A, Arthur M, Gutmann L (2008). "Identification of the L,D-transpeptidases for peptidoglycan cross-linking in Escherichia coli." J Bacteriol 190(13);4782-5. PMID: 18456808

Niki91: Niki H, Jaffe A, Imamura R, Ogura T, Hiraga S (1991). "The new gene mukB codes for a 177 kd protein with coiled-coil domains involved in chromosome partitioning of E. coli." EMBO J 10(1);183-93. PMID: 1989883

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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 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."

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

Raivio13: Raivio TL, Leblanc SK, Price NL (2013). "The Escherichia coli Cpx envelope stress response regulates genes of diverse function that impact antibiotic resistance and membrane integrity." J Bacteriol 195(12);2755-67. PMID: 23564175

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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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