YBIS_ECOLI
ID YBIS_ECOLI Reviewed; 306 AA.
AC P0AAX8; P75789;
DT 11-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2005, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=Probable L,D-transpeptidase YbiS;
DE EC=2.-.-.-;
DE Flags: Precursor;
GN Name=ybiS; OrderedLocusNames=b0819, JW0803;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PROTEIN SEQUENCE OF 25-36.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=B / BL21;
RX PubMed=10493123;
RX DOI=10.1002/(sici)1522-2683(19990801)20:11<2181::aid-elps2181>3.0.co;2-q;
RA Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B.;
RT "Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite
RT chromatography.";
RL Electrophoresis 20:2181-2195(1999).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=18456808; DOI=10.1128/jb.00025-08;
RA Magnet S., Dubost L., Marie A., Arthur M., Gutmann L.;
RT "Identification of the L,D-transpeptidases for peptidoglycan cross-linking
RT in Escherichia coli.";
RL J. Bacteriol. 190:4782-4785(2008).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, MUTAGENESIS OF CYS-210, AND
RP INTERACTION WITH DSBG.
RC STRAIN=K12 / MC1000 / ATCC 39531;
RX PubMed=19965429; DOI=10.1126/science.1179557;
RA Depuydt M., Leonard S.E., Vertommen D., Denoncin K., Morsomme P., Wahni K.,
RA Messens J., Carroll K.S., Collet J.F.;
RT "A periplasmic reducing system protects single cysteine residues from
RT oxidation.";
RL Science 326:1109-1111(2009).
CC -!- FUNCTION: Responsible, at least in part, for anchoring of the major
CC outer membrane lipoprotein (Lpp, also known as the Braun lipoprotein)
CC to the peptidoglycan via a meso-diaminopimelyl-L-Lys- bond on the
CC terminal residue of Lpp. Can be oxidized in vivo, its reduction depends
CC preferentially on DsbG, although DsbC is able to partially replace
CC DsbG. {ECO:0000269|PubMed:18456808}.
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC -!- SUBUNIT: Interacts with DsbG. {ECO:0000269|PubMed:19965429}.
CC -!- SUBCELLULAR LOCATION: Periplasm.
CC -!- PTM: In vivo a sulfenic acid can be formed on Cys-210, which probably
CC inactivates the protein. This disulfide is subsequently reduced by DsbG
CC and DsbC.
CC -!- DISRUPTION PHENOTYPE: Simultaneous disruption of erfK, ybiS, ycfS and
CC ynhG leads to loss of covalent anchoring of the major outer membrane
CC lipoprotein (Lpp) to the peptidoglycan. Complementation with ybiS
CC restores most of this anchoring. {ECO:0000269|PubMed:18456808}.
CC -!- SIMILARITY: Belongs to the YkuD family. {ECO:0000305}.
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DR EMBL; U00096; AAC73906.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35500.1; -; Genomic_DNA.
DR PIR; C64819; C64819.
DR RefSeq; NP_415340.1; NC_000913.3.
DR RefSeq; WP_001056384.1; NZ_STEB01000019.1.
DR AlphaFoldDB; P0AAX8; -.
DR SMR; P0AAX8; -.
DR BioGRID; 4261201; 15.
DR BioGRID; 849815; 1.
DR DIP; DIP-48069N; -.
DR IntAct; P0AAX8; 4.
DR STRING; 511145.b0819; -.
DR MEROPS; C82.A04; -.
DR jPOST; P0AAX8; -.
DR PaxDb; P0AAX8; -.
DR PRIDE; P0AAX8; -.
DR EnsemblBacteria; AAC73906; AAC73906; b0819.
DR EnsemblBacteria; BAA35500; BAA35500; BAA35500.
DR GeneID; 66670908; -.
DR GeneID; 945441; -.
DR KEGG; ecj:JW0803; -.
DR KEGG; eco:b0819; -.
DR PATRIC; fig|511145.12.peg.846; -.
DR EchoBASE; EB3108; -.
DR eggNOG; COG1376; Bacteria.
DR HOGENOM; CLU_046834_0_1_6; -.
DR InParanoid; P0AAX8; -.
DR OMA; QNRSGMP; -.
DR PhylomeDB; P0AAX8; -.
DR BioCyc; EcoCyc:G6422-MON; -.
DR BioCyc; MetaCyc:G6422-MON; -.
DR UniPathway; UPA00219; -.
DR PRO; PR:P0AAX8; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0030288; C:outer membrane-bounded periplasmic space; IDA:EcoCyc.
DR GO; GO:0016757; F:glycosyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0071972; F:peptidoglycan L,D-transpeptidase activity; IDA:EcoCyc.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0018104; P:peptidoglycan-protein cross-linking; IDA:EcoCyc.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR CDD; cd16913; YkuD_like; 1.
DR Gene3D; 2.40.440.10; -; 1.
DR InterPro; IPR005490; LD_TPept_cat_dom.
DR InterPro; IPR041597; Ldt_C.
DR InterPro; IPR038063; Transpep_catalytic_dom.
DR Pfam; PF17969; Ldt_C; 1.
DR Pfam; PF03734; YkuD; 1.
DR SUPFAM; SSF141523; SSF141523; 1.
PE 1: Evidence at protein level;
KW Cell shape; Cell wall biogenesis/degradation; Direct protein sequencing;
KW Glycosyltransferase; Hydrolase; Peptidoglycan synthesis; Periplasm;
KW Reference proteome; Signal; Transferase.
FT SIGNAL 1..24
FT /evidence="ECO:0000269|PubMed:9298646"
FT CHAIN 25..306
FT /note="Probable L,D-transpeptidase YbiS"
FT /id="PRO_0000013813"
FT ACT_SITE 210
FT /evidence="ECO:0000255"
FT MUTAGEN 210
FT /note="C->A: Protein is unable to form sulfenic acid
FT adducts."
FT /evidence="ECO:0000269|PubMed:19965429"
SQ SEQUENCE 306 AA; 33325 MW; 4D9DDED8B0ACD69F CRC64;
MNMKLKTLFA AAFAVVGFCS TASAVTYPLP TDGSRLVGQN QVITIPEGNT QPLEYFAAEY
QMGLSNMMEA NPGVDTFLPK GGTVLNIPQQ LILPDTVHEG IVINSAEMRL YYYPKGTNTV
IVLPIGIGQL GKDTPINWTT KVERKKAGPT WTPTAKMHAE YRAAGEPLPA VVPAGPDNPM
GLYALYIGRL YAIHGTNANF GIGLRVSHGC VRLRNEDIKF LFEKVPVGTR VQFIDEPVKA
TTEPDGSRYI EVHNPLSTTE AQFEGQEIVP ITLTKSVQTV TGQPDVDQVV LDEAIKNRSG
MPVRLN
