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Protein

Probable L,D-transpeptidase YbiS

Gene

ybiS

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei210 – 2101Sequence analysis

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
Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Hydrolase, Transferase

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Enzyme and pathway databases

BioCyciEcoCyc:G6422-MONOMER.
ECOL316407:JW0803-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13324. ybiS.

Subcellular locationi

GO - Cellular componenti

  • periplasmic space Source: EcoCyc
Complete GO annotation...

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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi210 – 2101C → A: Protein is unable to form sulfenic acid adducts. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 24241 PublicationAdd
BLAST
Chaini25 – 306282Probable L,D-transpeptidase YbiSPRO_0000013813Add
BLAST

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. 11 interactions.
DIPiDIP-48069N.
IntActiP0AAX8. 3 interactions.
STRINGi511145.b0819.

Structurei

3D structure databases

ProteinModelPortaliP0AAX8.
SMRiP0AAX8. Positions 23-306.
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

InterProiIPR005490. LD_TPept_cat_dom.
[Graphical view]
PfamiPF03734. YkuD. 1 hit.
[Graphical view]

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.
PATRICi32116841. VBIEscCol129921_0846.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliP0AAX8.
SMRiP0AAX8. Positions 23-306.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261201. 11 interactions.
DIPiDIP-48069N.
IntActiP0AAX8. 3 interactions.
STRINGi511145.b0819.

Protein family/group databases

MEROPSiC82.A04.

Proteomic databases

EPDiP0AAX8.
PaxDbiP0AAX8.
PRIDEiP0AAX8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73906; AAC73906; b0819.
BAA35500; BAA35500; BAA35500.
GeneIDi945441.
KEGGiecj:JW0803.
eco:b0819.
PATRICi32116841. VBIEscCol129921_0846.

Organism-specific databases

EchoBASEiEB3108.
EcoGeneiEG13324. ybiS.

Phylogenomic databases

eggNOGiENOG4107N1Q. Bacteria.
COG1376. LUCA.
HOGENOMiHOG000274378.
InParanoidiP0AAX8.
KOiK19235.
OMAiQNRSGMP.
PhylomeDBiP0AAX8.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciEcoCyc:G6422-MONOMER.
ECOL316407:JW0803-MONOMER.

Miscellaneous databases

PROiP0AAX8.

Family and domain databases

InterProiIPR005490. LD_TPept_cat_dom.
[Graphical view]
PfamiPF03734. YkuD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYBIS_ECOLI
AccessioniPrimary (citable) accession number: P0AAX8
Secondary accession number(s): P75789
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2005
Last sequence update: October 11, 2005
Last modified: September 7, 2016
This is version 80 of the entry and version 1 of the sequence. [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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.