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Protein

Probable L,D-transpeptidase YcbB

Gene

ycbB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

Responsible, at least in part, for generating a meso-diaminopimelyl-3-a meso-diaminopimelyl-3 cross-link.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 sitei528 – 5281Sequence 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

  • cellular response to DNA damage stimulus Source: EcoliWiki
  • cell wall macromolecule metabolic process Source: EcoCyc
  • cell wall organization Source: UniProtKB-KW
  • Gram-negative-bacterium-type cell wall biogenesis Source: EcoCyc
  • peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
  • 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:EG11253-MONOMER.
ECOL316407:JW0908-MONOMER.
MetaCyc:EG11253-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable L,D-transpeptidase YcbB (EC:2.-.-.-)
Gene namesi
Name:ycbB
Ordered Locus Names:b0925, JW0908
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11253. ycbB.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei11 – 2616HelicalSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Disruption phenotypei

Simultaneous disruption of erfK, ybiS, ycfS and ynhG leads to loss of a significant proportion of muropeptides, including those with meso-DAP-3-meso-DAP-3 cross-links and with covalently anchored major outer membrane lipoprotein (Lpp) to the peptidoglycan. Overexpression of ycbB in this background increases meso-diaminopimelyl-3-a meso-diaminopimelyl-3 cross-links but does not restore Lpp anchoring.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 615615Probable L,D-transpeptidase YcbBPRO_0000168766Add
BLAST

Proteomic databases

EPDiP22525.
PaxDbiP22525.
PRIDEiP22525.

Interactioni

Protein-protein interaction databases

BioGridi4260015. 123 interactions.
DIPiDIP-11474N.
IntActiP22525. 8 interactions.
MINTiMINT-1263904.
STRINGi511145.b0925.

Structurei

3D structure databases

ProteinModelPortaliP22525.
SMRiP22525. Positions 322-370.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the YkuD family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105DIT. Bacteria.
COG2989. LUCA.
HOGENOMiHOG000118794.
InParanoidiP22525.
OMAiHNLFQRD.

Family and domain databases

Gene3Di1.10.101.10. 2 hits.
InterProiIPR005490. LD_TPept_cat_dom.
IPR002477. Peptidoglycan-bd-like.
[Graphical view]
PfamiPF01471. PG_binding_1. 1 hit.
PF03734. YkuD. 1 hit.
[Graphical view]
SUPFAMiSSF47090. SSF47090. 1 hit.
PROSITEiPS00092. N6_MTASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P22525-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLLNMMCGRQ LSAISLCLAV TFAPLFNAQA DEPEVIPGDS PVAVSEQGEA
60 70 80 90 100
LPQAQATAIM AGIQPLPEGA AEKARTQIES QLPAGYKPVY LNQLQLLYAA
110 120 130 140 150
RDMQPMWENR DAVKAFQQQL AEVAIAGFQP QFNKWVELLT DPGVNGMARD
160 170 180 190 200
VVLSDAMMGY LHFIANIPVK GTRWLYSSKP YALATPPLSV INQWQLALDK
210 220 230 240 250
GQLPTFVAGL APQHPQYAAM HESLLALLCD TKPWPQLTGK ATLRPGQWSN
260 270 280 290 300
DVPALREILQ RTGMLDGGPK ITLPGDDTPT DAVVSPSAVT VETAETKPMD
310 320 330 340 350
KQTTSRSKPA PAVRAAYDNE LVEAVKRFQA WQGLGADGAI GPATRDWLNV
360 370 380 390 400
TPAQRAGVLA LNIQRLRLLP TELSTGIMVN IPAYSLVYYQ NGNQVLDSRV
410 420 430 440 450
IVGRPDRKTP MMSSALNNVV VNPPWNVPPT LARKDILPKV RNDPGYLESH
460 470 480 490 500
GYTVMRGWNS REAIDPWQVD WSTITASNLP FRFQQAPGPR NSLGRYKFNM
510 520 530 540 550
PSSEAIYLHD TPNHNLFKRD TRALSSGCVR VNKASDLANM LLQDAGWNDK
560 570 580 590 600
RISDALKQGD TRYVNIRQSI PVNLYYLTAF VGADGRTQYR TDIYNYDLPA
610
RSSSQIVSKA EQLIR
Length:615
Mass (Da):67,812
Last modified:November 1, 1997 - v2
Checksum:iCB16D78CFFD70C57
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti39 – 402DS → ER in CAA40777 (PubMed:1989883).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74011.1.
AP009048 Genomic DNA. Translation: BAA35671.1.
X57550 Genomic DNA. Translation: CAA40777.1.
PIRiD64832.
RefSeqiNP_415445.1. NC_000913.3.
WP_000925969.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74011; AAC74011; b0925.
BAA35671; BAA35671; BAA35671.
GeneIDi945541.
KEGGiecj:JW0908.
eco:b0925.
PATRICi32117063. VBIEscCol129921_0956.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74011.1.
AP009048 Genomic DNA. Translation: BAA35671.1.
X57550 Genomic DNA. Translation: CAA40777.1.
PIRiD64832.
RefSeqiNP_415445.1. NC_000913.3.
WP_000925969.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP22525.
SMRiP22525. Positions 322-370.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260015. 123 interactions.
DIPiDIP-11474N.
IntActiP22525. 8 interactions.
MINTiMINT-1263904.
STRINGi511145.b0925.

Proteomic databases

EPDiP22525.
PaxDbiP22525.
PRIDEiP22525.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74011; AAC74011; b0925.
BAA35671; BAA35671; BAA35671.
GeneIDi945541.
KEGGiecj:JW0908.
eco:b0925.
PATRICi32117063. VBIEscCol129921_0956.

Organism-specific databases

EchoBASEiEB1233.
EcoGeneiEG11253. ycbB.

Phylogenomic databases

eggNOGiENOG4105DIT. Bacteria.
COG2989. LUCA.
HOGENOMiHOG000118794.
InParanoidiP22525.
OMAiHNLFQRD.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciEcoCyc:EG11253-MONOMER.
ECOL316407:JW0908-MONOMER.
MetaCyc:EG11253-MONOMER.

Miscellaneous databases

PROiP22525.

Family and domain databases

Gene3Di1.10.101.10. 2 hits.
InterProiIPR005490. LD_TPept_cat_dom.
IPR002477. Peptidoglycan-bd-like.
[Graphical view]
PfamiPF01471. PG_binding_1. 1 hit.
PF03734. YkuD. 1 hit.
[Graphical view]
SUPFAMiSSF47090. SSF47090. 1 hit.
PROSITEiPS00092. N6_MTASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYCBB_ECOLI
AccessioniPrimary (citable) accession number: P22525
Secondary accession number(s): P75847
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: November 1, 1997
Last modified: September 7, 2016
This is version 131 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, 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.