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Entry version 123 (07 Oct 2020)
Sequence version 2 (16 Jun 2009)
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Protein

Peptidoglycan endopeptidase LytF

Gene

lytF

Organism
Bacillus subtilis (strain 168)
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

Cell wall hydrolase that cleaves gamma-D-glutamate-meso-diaminopimelate bonds in peptidoglycan. LytF is necessary and sufficient for vegetative daughter cell separation, and also seems to play a role in cell autolysis.3 Publications

Caution

In domesticated laboratory strains (168 and derivatives), lytF is not expressed in a majority of the growing cells. These cells form a subpopulation that grows in multicellular, nonmotile chains. Undomesticated strains (3610) express lytF in a majority of the population, that grows as separate individual motile cells (PubMed:19542270).1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Is inhibited in vitro by para-hydroxymercuribenzoate, a sulfydryl inhibitor.1 Publication

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>pH dependencei

Optimum pH is 8.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei400NucleophileBy similarity1
Active sitei449Proton acceptorBy similarity1

<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 functionHydrolase, Protease, Thiol protease
Biological processCell wall biogenesis/degradation

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
BSUB:BSU09370-MONOMER

Protein family/group databases

Carbohydrate-Active enZymes

More...
CAZyi
CBM50, Carbohydrate-Binding Module Family 50

MEROPS protease database

More...
MEROPSi
C40.002

<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%5Fand%5Ftaxonomy%5Fsection">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:
Peptidoglycan endopeptidase LytF (EC:3.4.-.-)
Alternative name(s):
Autolysin LytF
Cell wall-associated polypeptide CWBP49'
Gamma-D-glutamate-meso-diaminopimelate muropeptidase LytF
Peptidoglycan hydrolase LytF
Vegetative cell wall hydrolase LytF
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:lytF
Synonyms:cwlE, yhdD
Ordered Locus Names:BSU09370
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiBacillus subtilis (strain 168)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri224308 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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

<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

GO - Cellular componenti

Keywords - Cellular componenti

Cell wall, Secreted

<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

Cells from an undomesticated strain (3610) lacking this gene grow predominantly as chains, whereas wild-type cells grow as separate individuals. They do not show a reduction in the rate of swarming motility.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 denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 261 PublicationAdd BLAST26
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_000001975327 – 488Peptidoglycan endopeptidase LytFAdd BLAST462

Proteomic databases

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

More...
PaxDbi
O07532

PRoteomics IDEntifications database

More...
PRIDEi
O07532

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Expressed in the vegetative growth phase under exclusive control of sigma-D (SigD). Expression of lytF is heterogeneous in the exponentially growing cell population; it is ON in single cells and OFF in long chains. The same subpopulation of cells that express lytF also express flagellin.3 Publications

<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

STRING: functional protein association networks

More...
STRINGi
224308.BSU09370

<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

3D structure databases

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

More...
SMRi
O07532

Database of comparative protein structure models

More...
ModBasei
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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini27 – 70LysM 1PROSITE-ProRule annotationAdd BLAST44
Domaini92 – 135LysM 2PROSITE-ProRule annotationAdd BLAST44
Domaini174 – 217LysM 3PROSITE-ProRule annotationAdd BLAST44
Domaini240 – 283LysM 4PROSITE-ProRule annotationAdd BLAST44
Domaini307 – 350LysM 5PROSITE-ProRule annotationAdd BLAST44

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi73 – 370Ser-richAdd BLAST298

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The N-terminal domain contains LysM domains that are thought to be involved in peptidoglycan binding, while the C-terminal domain is endowed with the catalytic activity.1 Publication

<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 peptidase C40 family.Curated

Keywords - Domaini

Repeat, Signal

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG0791, Bacteria
COG1388, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
O07532

KEGG Orthology (KO)

More...
KOi
K19223

Identification of Orthologs from Complete Genome Data

More...
OMAi
TIYVNQV

Database for complete collections of gene phylogenies

More...
PhylomeDBi
O07532

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00118, LysM, 5 hits

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.10.350.10, 5 hits

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR018392, LysM_dom
IPR036779, LysM_dom_sf
IPR000064, NLP_P60_dom
IPR038765, Papain-like_cys_pep_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01476, LysM, 5 hits
PF00877, NLPC_P60, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00257, LysM, 5 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF54001, SSF54001, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51782, LYSM, 5 hits

<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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

O07532-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKKKLAAGLT ASAIVGTTLV VTPAEAATIK VKSGDSLWKL AQTYNTSVAA
60 70 80 90 100
LTSANHLSTT VLSIGQTLTI PGSKSSTSSS TSSSTTKKSG SSVYTVKSGD
110 120 130 140 150
SLWLIANEFK MTVQELKKLN GLSSDLIRAG QKLKVSGTVS SSSSSSKKSN
160 170 180 190 200
SNKSSSSSSK SSSNKSSSSS SSTGTYKVQL GDSLWKIANK VNMSIAELKV
210 220 230 240 250
LNNLKSDTIY VNQVLKTKSS GSDTSSKDNS SKSNQTSATT KYTVKSGDSL
260 270 280 290 300
WKIANNYNLT VQQIRNINNL KSDVLYVGQV LKLTGKASSG SSSSSSSSSN
310 320 330 340 350
ASSGTTTTYT VKSGDSLWVI AQKFNVTAQQ IREKNNLKTD VLQVGQKLVI
360 370 380 390 400
SGKASSSSSS GSSNTTSSTS AKINTMISAA KAQLGVPYRW GGTTPSGFDC
410 420 430 440 450
SGFIYYVLNK VTSVSRLTAA GYWNTMKSVS QPAVGDFVFF STYKAGPSHV
460 470 480
GIYLGNGEFI NANDSGVVIS NMNNSYWKQR YLGAKRYF
Length:488
Mass (Da):51,395
Last modified:June 16, 2009 - 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:i4C2191EF2E059CB4
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 conflicti87K → M in CAA74437 (PubMed:9579061).Curated1

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
Y14079 Genomic DNA Translation: CAA74437.1
AL009126 Genomic DNA Translation: CAB12776.2

Protein sequence database of the Protein Information Resource

More...
PIRi
B69825

NCBI Reference Sequences

More...
RefSeqi
NP_388818.2, NC_000964.3
WP_003244874.1, NZ_JNCM01000035.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB12776; CAB12776; BSU09370

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
939271

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU09370

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.1010

<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
Y14079 Genomic DNA Translation: CAA74437.1
AL009126 Genomic DNA Translation: CAB12776.2
PIRiB69825
RefSeqiNP_388818.2, NC_000964.3
WP_003244874.1, NZ_JNCM01000035.1

3D structure databases

SMRiO07532
ModBaseiSearch...

Protein-protein interaction databases

STRINGi224308.BSU09370

Protein family/group databases

CAZyiCBM50, Carbohydrate-Binding Module Family 50
MEROPSiC40.002

Proteomic databases

PaxDbiO07532
PRIDEiO07532

Genome annotation databases

EnsemblBacteriaiCAB12776; CAB12776; BSU09370
GeneIDi939271
KEGGibsu:BSU09370
PATRICifig|224308.179.peg.1010

Phylogenomic databases

eggNOGiCOG0791, Bacteria
COG1388, Bacteria
InParanoidiO07532
KOiK19223
OMAiTIYVNQV
PhylomeDBiO07532

Enzyme and pathway databases

BioCyciBSUB:BSU09370-MONOMER

Family and domain databases

CDDicd00118, LysM, 5 hits
Gene3Di3.10.350.10, 5 hits
InterProiView protein in InterPro
IPR018392, LysM_dom
IPR036779, LysM_dom_sf
IPR000064, NLP_P60_dom
IPR038765, Papain-like_cys_pep_sf
PfamiView protein in Pfam
PF01476, LysM, 5 hits
PF00877, NLPC_P60, 1 hit
SMARTiView protein in SMART
SM00257, LysM, 5 hits
SUPFAMiSSF54001, SSF54001, 1 hit
PROSITEiView protein in PROSITE
PS51782, LYSM, 5 hits

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 nameiLYTF_BACSU
<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: O07532
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 16, 2004
Last sequence update: June 16, 2009
Last modified: October 7, 2020
This is version 123 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

Direct protein sequencing, Reference proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  3. SIMILARITY comments
    Index of protein domains and families
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