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Entry version 153 (13 Nov 2019)
Sequence version 2 (01 Nov 1997)
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Responsible, at least in part, for generating a meso-diaminopimelyl-3-a meso-diaminopimelyl-3 cross-link.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei528Sequence analysis1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG11253-MONOMER
ECOL316407:JW0908-MONOMER
MetaCyc:EG11253-MONOMER

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00219

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Probable L,D-transpeptidase YcbB (EC:2.-.-.-)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:ycbB
Ordered Locus Names:b0925, JW0908
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular_location_section">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei11 – 26HelicalSequence analysisAdd BLAST16

GO - Cellular componenti

Keywords - Cellular componenti

Membrane

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>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

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001687661 – 615Probable L,D-transpeptidase YcbBAdd BLAST615

Proteomic databases

Encyclopedia of Proteome Dynamics

More...
EPDi
P22525

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P22525

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P22525

PRoteomics IDEntifications database

More...
PRIDEi
P22525

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
4260015, 128 interactors

Database of interacting proteins

More...
DIPi
DIP-11474N

Protein interaction database and analysis system

More...
IntActi
P22525, 8 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b0925

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1615
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P22525

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the YkuD family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105DIT Bacteria
COG2989 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000118794

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P22525

KEGG Orthology (KO)

More...
KOi
K21470

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
2.40.440.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR005490 LD_TPept_cat_dom
IPR002477 Peptidoglycan-bd-like
IPR036365 PGBD-like_sf
IPR038063 Transpep_catalytic_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01471 PG_binding_1, 1 hit
PF03734 YkuD, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF141523 SSF141523, 1 hit
SSF47090 SSF47090, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00092 N6_MTASE, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iCB16D78CFFD70C57
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti39 – 40DS → ER in CAA40777 (PubMed:1989883).Curated2

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC74011.1
AP009048 Genomic DNA Translation: BAA35671.1
X57550 Genomic DNA Translation: CAA40777.1

Protein sequence database of the Protein Information Resource

More...
PIRi
D64832

NCBI Reference Sequences

More...
RefSeqi
NP_415445.1, NC_000913.3
WP_000925969.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC74011; AAC74011; b0925
BAA35671; BAA35671; BAA35671

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
945541

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW0908
eco:b0925

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|511145.12.peg.956

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
6NTWX-ray2.76A31-615[»]
SMRiP22525
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4260015, 128 interactors
DIPiDIP-11474N
IntActiP22525, 8 interactors
STRINGi511145.b0925

Proteomic databases

EPDiP22525
jPOSTiP22525
PaxDbiP22525
PRIDEiP22525

Genome annotation databases

EnsemblBacteriaiAAC74011; AAC74011; b0925
BAA35671; BAA35671; BAA35671
GeneIDi945541
KEGGiecj:JW0908
eco:b0925
PATRICifig|511145.12.peg.956

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB1233

Phylogenomic databases

eggNOGiENOG4105DIT Bacteria
COG2989 LUCA
HOGENOMiHOG000118794
InParanoidiP22525
KOiK21470

Enzyme and pathway databases

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

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P22525

Family and domain databases

Gene3Di2.40.440.10, 1 hit
InterProiView protein in InterPro
IPR005490 LD_TPept_cat_dom
IPR002477 Peptidoglycan-bd-like
IPR036365 PGBD-like_sf
IPR038063 Transpep_catalytic_dom
PfamiView protein in Pfam
PF01471 PG_binding_1, 1 hit
PF03734 YkuD, 1 hit
SUPFAMiSSF141523 SSF141523, 1 hit
SSF47090 SSF47090, 1 hit
PROSITEiView protein in PROSITE
PS00092 N6_MTASE, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiYCBB_ECOLI
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P22525
Secondary accession number(s): P75847
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: November 1, 1997
Last modified: November 13, 2019
This is version 153 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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