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Protein

Probable L,D-transpeptidase YbiS

Gene

ybiS

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Responsible, at least in part, for anchoring of the major outer membrane lipoprotein (Lpp, also known as the Braun lipoprotein) to the peptidoglycan via a meso-diaminopimelyl-L-Lys- bond on the terminal residue of Lpp. Can be oxidized in vivo, its reduction depends preferentially on DsbG, although DsbC is able to partially replace DsbG.1 Publication

Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei210Sequence analysis1

GO - Molecular functioni

  • cysteine-type carboxypeptidase activity Source: EcoCyc
  • peptidoglycan L,D-transpeptidase activity Source: EcoCyc
  • transferase activity, transferring amino-acyl groups Source: EcoCyc
  • transferase activity, transferring glycosyl groups Source: UniProtKB-KW

GO - Biological processi

  • cell wall organization Source: UniProtKB-KW
  • Gram-negative-bacterium-type cell wall biogenesis Source: EcoCyc
  • peptidoglycan-protein cross-linking Source: EcoCyc
  • regulation of cell shape Source: UniProtKB-KW

Keywordsi

Molecular functionGlycosyltransferase, Hydrolase, Transferase
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Enzyme and pathway databases

BioCyciEcoCyc:G6422-MONOMER
MetaCyc:G6422-MONOMER
UniPathwayiUPA00219

Protein family/group databases

MEROPSiC82.A04

Names & Taxonomyi

Protein namesi
Recommended name:
Probable L,D-transpeptidase YbiS (EC:2.-.-.-)
Gene namesi
Name:ybiS
Ordered Locus Names:b0819, JW0803
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13324 ybiS

Subcellular locationi

GO - Cellular componenti

  • periplasmic space Source: EcoCyc

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Disruption phenotypei

Simultaneous disruption of erfK, ybiS, ycfS and ynhG leads to loss of covalent anchoring of the major outer membrane lipoprotein (Lpp) to the peptidoglycan. Complementation with ybiS restores most of this anchoring.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi210C → A: Protein is unable to form sulfenic acid adducts. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 241 PublicationAdd BLAST24
ChainiPRO_000001381325 – 306Probable L,D-transpeptidase YbiSAdd BLAST282

Post-translational modificationi

In vivo a sulfenic acid can be formed on Cys-210, which probably inactivates the protein. This disulfide is subsequently reduced by DsbG and DsbC.

Proteomic databases

EPDiP0AAX8
PaxDbiP0AAX8
PRIDEiP0AAX8

Interactioni

Subunit structurei

Interacts with DsbG.1 Publication

Protein-protein interaction databases

BioGridi4261201, 15 interactors
DIPiDIP-48069N
IntActiP0AAX8, 4 interactors
STRINGi316385.ECDH10B_0888

Structurei

3D structure databases

ProteinModelPortaliP0AAX8
SMRiP0AAX8
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the YkuD family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4107N1Q Bacteria
COG1376 LUCA
HOGENOMiHOG000274378
InParanoidiP0AAX8
KOiK19235
OMAiQNRSGMP
PhylomeDBiP0AAX8

Family and domain databases

Gene3Di2.40.440.10, 1 hit
InterProiView protein in InterPro
IPR005490 LD_TPept_cat_dom
IPR038063 Transpep_catalytic_dom
PfamiView protein in Pfam
PF03734 YkuD, 1 hit
SUPFAMiSSF141523 SSF141523, 2 hits

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0AAX8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNMKLKTLFA AAFAVVGFCS TASAVTYPLP TDGSRLVGQN QVITIPEGNT
60 70 80 90 100
QPLEYFAAEY QMGLSNMMEA NPGVDTFLPK GGTVLNIPQQ LILPDTVHEG
110 120 130 140 150
IVINSAEMRL YYYPKGTNTV IVLPIGIGQL GKDTPINWTT KVERKKAGPT
160 170 180 190 200
WTPTAKMHAE YRAAGEPLPA VVPAGPDNPM GLYALYIGRL YAIHGTNANF
210 220 230 240 250
GIGLRVSHGC VRLRNEDIKF LFEKVPVGTR VQFIDEPVKA TTEPDGSRYI
260 270 280 290 300
EVHNPLSTTE AQFEGQEIVP ITLTKSVQTV TGQPDVDQVV LDEAIKNRSG

MPVRLN
Length:306
Mass (Da):33,325
Last modified:October 11, 2005 - v1
Checksum:i4D9DDED8B0ACD69F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC73906.1
AP009048 Genomic DNA Translation: BAA35500.1
PIRiC64819
RefSeqiNP_415340.1, NC_000913.3
WP_001056384.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC73906; AAC73906; b0819
BAA35500; BAA35500; BAA35500
GeneIDi945441
KEGGiecj:JW0803
eco:b0819
PATRICifig|511145.12.peg.846

Similar proteinsi

Entry informationi

Entry nameiYBIS_ECOLI
AccessioniPrimary (citable) accession number: P0AAX8
Secondary accession number(s): P75789
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 11, 2005
Last sequence update: October 11, 2005
Last modified: March 28, 2018
This is version 91 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

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