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

Gene: ldtB Accession Numbers: G6422 (EcoCyc), b0819, ECK0809

Synonyms: ybiS

Regulation Summary Diagram: ?

Regulation summary diagram for ldtB

YbiS is an L,D-transpeptidase responsible removal of the D-alanine residue of peptidoglycan tetrapeptide stems and attachment of the lysine residue of Braun lipoprotein to the meso-diaminopimelyl (DAP) residue of the resulting tripeptide. This activity results in covalent attachment of peptidoglycan to the outer membrane.

Sequence similarity suggested that YbiS may be an outer membrane β-barrel porin [Zhai02], but it was subsequently identified as a periplasmic protein [LopezCampistrou05].

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 ybiS in the quintuple background restores formation of tripeptide stems and tetrapeptide stems with Gly as the fourth aminoacid [Magnet08]. Expression of ybiS restores attachment of peptidoglycan to Braun lipoprotein by L,D-transpeptidase activity in an erfK ycfS ybiS ynhG quadruple mutant [Magnet07].

Transctription of ybiS is activated by Rob [Bennik00]. The ybiS gene is controlled by a CRP-binding site that represses transcription [Djordjevic03, Zheng04].

Review: [Han06]

Locations: periplasmic space

Map Position: [854,047 <- 854,967] (18.41 centisomes, 66°)
Length: 921 bp / 306 aa

Molecular Weight of Polypeptide: 33.325 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002797 , DIP:DIP-48069N , EchoBASE:EB3108 , EcoGene:EG13324 , EcoliWiki:b0819 , OU-Microarray:b0819 , PortEco:ybiS , Pride:P0AAX8 , Protein Model Portal:P0AAX8 , RefSeq:NP_415340 , RegulonDB:G6422 , SMR:P0AAX8 , String:511145.b0819 , UniProt:P0AAX8

Relationship Links: InterPro:IN-FAMILY:IPR005490 , Pfam:IN-FAMILY:PF03734

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for ldtB

GO Terms:

Biological Process: GO:0006508 - proteolysis Inferred from experiment [Magnet08, Magnet07]
GO:0018104 - peptidoglycan-protein cross-linking Inferred from experiment [Magnet07, Magnet08]
GO:0043164 - Gram-negative-bacterium-type cell wall biogenesis Inferred from experiment [Magnet07, Magnet08]
GO:0008360 - regulation of cell shape Inferred by computational analysis [UniProtGOA11]
GO:0009252 - peptidoglycan biosynthetic process Inferred by computational analysis [UniProtGOA12, UniProtGOA11]
GO:0071555 - cell wall organization Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0016755 - transferase activity, transferring amino-acyl groups Inferred from experiment [Magnet07, Magnet08]
GO:0016807 - cysteine-type carboxypeptidase activity Inferred from experiment [Magnet07, Magnet08]
GO:0071972 - peptidoglycan L,D-transpeptidase activity Inferred from experiment [Magnet07]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016757 - transferase activity, transferring glycosyl groups Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0042597 - periplasmic space Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, LopezCampistrou05]
GO:0030288 - outer membrane-bounded periplasmic space [LopezCampistrou05]

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

Essentiality data for ldtB 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]

Last-Curated ? 09-Jul-2008 by Johnson A , JCVI

Enzymatic reaction of: L,D-transpeptidase

peptidoglycan tetrapeptide, glycan chain 1[periplasmic space] + murein lipoprotein[periplasmic space] <=> D-alanine[periplasmic space] + peptidoglycan tripeptide-Lpp crosslink[periplasmic space]

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.

Alternative Substrates for murein lipoprotein: glycine [Magnet08 ]

Sequence Features

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

Feature Class Location Citations Comment
Signal-Sequence 1 -> 24
[Link97, UniProt11]
Chain 25 -> 306
UniProt: Uncharacterized protein ybiS;
Mutagenesis-Variant 210
[Depuydt09, UniProt11]
UniProt: Protein is unable to form sulfenic acid adducts.
Active-Site 210
UniProt: Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Bennik00: Bennik MH, Pomposiello PJ, Thorne DF, Demple B (2000). "Defining a rob regulon in Escherichia coli by using transposon mutagenesis." J Bacteriol 182(13);3794-801. PMID: 10850996

Depuydt09: Depuydt M, Leonard SE, Vertommen D, Denoncin K, Morsomme P, Wahni K, Messens J, Carroll KS, Collet JF (2009). "A periplasmic reducing system protects single cysteine residues from oxidation." Science 326(5956);1109-11. PMID: 19965429

Djordjevic03: Djordjevic M, Sengupta AM, Shraiman BI (2003). "A biophysical approach to transcription factor binding site discovery." Genome Res 13(11);2381-90. PMID: 14597652

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

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

Han06: Han MJ, Lee SY (2006). "The Escherichia coli proteome: past, present, and future prospects." Microbiol Mol Biol Rev 70(2);362-439. PMID: 16760308

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

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Magnet07: Magnet S, Bellais S, Dubost L, Fourgeaud M, Mainardi JL, Petit-Frere S, Marie A, Mengin-Lecreulx D, Arthur M, Gutmann L (2007). "Identification of the L,D-transpeptidases responsible for attachment of the Braun lipoprotein to Escherichia coli peptidoglycan." J Bacteriol 189(10);3927-31. PMID: 17369299

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

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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."

Zhai02: Zhai Y, Saier MH (2002). "The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes." Protein Sci 11(9);2196-207. PMID: 12192075

Zheng04: Zheng D, Constantinidou C, Hobman JL, Minchin SD (2004). "Identification of the CRP regulon using in vitro and in vivo transcriptional profiling." Nucleic Acids Res 32(19);5874-93. PMID: 15520470

Other References Related to Gene Regulation

Raghavan11: Raghavan R, Sage A, Ochman H (2011). "Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli." J Bacteriol 193(11);2871-4. PMID: 21460078

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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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