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Peptidoglycan-recognition protein LB (EC 3.5.1.28)

 PGPLB_DROME             Reviewed;         232 AA.
Q8INK6; Q9VGN3;
10-MAY-2005, integrated into UniProtKB/Swiss-Prot.
01-MAR-2003, sequence version 1.
25-OCT-2017, entry version 123.
RecName: Full=Peptidoglycan-recognition protein LB;
EC=3.5.1.28;
Flags: Precursor;
Name=PGRP-LB; ORFNames=CG14704;
Drosophila melanogaster (Fruit fly).
Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta;
Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha;
Ephydroidea; Drosophilidae; Drosophila; Sophophora.
NCBI_TaxID=7227;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A), TISSUE SPECIFICITY,
DEVELOPMENTAL STAGE, AND INDUCTION.
PubMed=11106397; DOI=10.1073/pnas.97.25.13772;
Werner T., Liu G., Kang D., Ekengren S., Steiner H., Hultmark D.;
"A family of peptidoglycan recognition proteins in the fruit fly
Drosophila melanogaster.";
Proc. Natl. Acad. Sci. U.S.A. 97:13772-13777(2000).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Berkeley;
PubMed=10731132; DOI=10.1126/science.287.5461.2185;
Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X.,
Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D.,
Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G.,
Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D.,
Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M.,
Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S.,
Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P.,
Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I.,
Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P.,
de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M.,
Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P.,
Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W.,
Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K.,
Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J.,
Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C.,
Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A.,
Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z.,
Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X.,
Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D.,
Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A.,
Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L.,
Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M.,
Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G.,
Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H.,
Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
Spier E., Spradling A.C., Stapleton M., Strong R., Sun E.,
Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X.,
Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J.,
Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A.,
Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L.,
Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X.,
Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.;
"The genome sequence of Drosophila melanogaster.";
Science 287:2185-2195(2000).
[3]
GENOME REANNOTATION, AND ALTERNATIVE SPLICING.
STRAIN=Berkeley;
PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q.,
Stapleton M., Yamada C., Ashburner M., Gelbart W.M., Rubin G.M.,
Lewis S.E.;
"Annotation of the Drosophila melanogaster euchromatic genome: a
systematic review.";
Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM A).
STRAIN=Berkeley; TISSUE=Embryo;
PubMed=12537569; DOI=10.1186/gb-2002-3-12-research0080;
Stapleton M., Carlson J.W., Brokstein P., Yu C., Champe M.,
George R.A., Guarin H., Kronmiller B., Pacleb J.M., Park S., Wan K.H.,
Rubin G.M., Celniker S.E.;
"A Drosophila full-length cDNA resource.";
Genome Biol. 3:RESEARCH0080.1-RESEARCH0080.8(2002).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM C).
STRAIN=Berkeley; TISSUE=Embryo;
Stapleton M., Carlson J.W., Chavez C., Frise E., George R.A.,
Pacleb J.M., Park S., Wan K.H., Yu C., Rubin G.M., Celniker S.E.;
Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases.
[6]
INDUCTION.
PubMed=12032070; DOI=10.1093/emboj/21.11.2568;
De Gregorio E., Spellman P.T., Tzou P., Rubin G.M., Lemaitre B.;
"The Toll and Imd pathways are the major regulators of the immune
response in Drosophila.";
EMBO J. 21:2568-2579(2002).
[7]
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-215 (ISOFORM A) IN COMPLEX
WITH ZINC, FUNCTION, SUBUNIT, DISULFIDE BOND, AND MUTAGENESIS OF
THR-175.
PubMed=12845326; DOI=10.1038/ni952;
Kim M.-S., Byun M., Oh B.-H.;
"Crystal structure of peptidoglycan recognition protein LB from
Drosophila melanogaster.";
Nat. Immunol. 4:787-793(2003).
-!- FUNCTION: N-acetylmuramyl-L-alanine amidase involved in innate
immunity by degrading bacterial peptidoglycans (PGN). Probably
plays a scavenger role by digesting biologically active PGN into
biologically inactive fragments. Has no direct bacteriolytic
activity. {ECO:0000269|PubMed:12845326}.
-!- CATALYTIC ACTIVITY: Hydrolyzes the link between N-acetylmuramoyl
residues and L-amino acid residues in certain cell-wall
glycopeptides.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000269|PubMed:12845326};
Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:12845326};
-!- SUBUNIT: Monomer. {ECO:0000269|PubMed:12845326}.
-!- SUBCELLULAR LOCATION: Isoform C: Secreted {ECO:0000305}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=C;
IsoId=Q8INK6-1; Sequence=Displayed;
Note=No experimental confirmation available.;
Name=A; Synonyms=B;
IsoId=Q8INK6-2; Sequence=VSP_013593;
Note=Does not contain a signal sequence.;
-!- TISSUE SPECIFICITY: Widely expressed.
{ECO:0000269|PubMed:11106397}.
-!- DEVELOPMENTAL STAGE: Expressed from old embryos. Expressed in
larvae and adults. {ECO:0000269|PubMed:11106397}.
-!- INDUCTION: Strongly up-regulated by PGN from B.subtilis. Regulated
by the imd/Relish pathway. {ECO:0000269|PubMed:11106397,
ECO:0000269|PubMed:12032070}.
-!- SIMILARITY: Belongs to the N-acetylmuramoyl-L-alanine amidase 2
family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AF207537; AAG23731.1; -; mRNA.
EMBL; AF207538; AAG23732.1; -; mRNA.
EMBL; AE014297; AAF54643.1; -; Genomic_DNA.
EMBL; AE014297; AAN13505.1; -; Genomic_DNA.
EMBL; AY060759; AAL28307.1; -; mRNA.
EMBL; BT011455; AAR99113.1; -; mRNA.
RefSeq; NP_001247053.1; NM_001260124.2. [Q8INK6-2]
RefSeq; NP_001247054.1; NM_001260125.2. [Q8INK6-2]
RefSeq; NP_650079.1; NM_141822.3. [Q8INK6-2]
RefSeq; NP_731575.1; NM_169392.2. [Q8INK6-1]
RefSeq; NP_731576.1; NM_169393.3. [Q8INK6-2]
UniGene; Dm.3374; -.
PDB; 1OHT; X-ray; 2.00 A; A=18-232.
PDBsum; 1OHT; -.
ProteinModelPortal; Q8INK6; -.
SMR; Q8INK6; -.
BioGrid; 66511; 4.
IntAct; Q8INK6; 1.
MINT; MINT-1594493; -.
STRING; 7227.FBpp0297234; -.
PaxDb; Q8INK6; -.
PRIDE; Q8INK6; -.
EnsemblMetazoa; FBtr0082396; FBpp0081872; FBgn0037906. [Q8INK6-1]
EnsemblMetazoa; FBtr0082397; FBpp0081873; FBgn0037906. [Q8INK6-2]
EnsemblMetazoa; FBtr0082398; FBpp0081874; FBgn0037906. [Q8INK6-2]
EnsemblMetazoa; FBtr0306098; FBpp0297235; FBgn0037906. [Q8INK6-2]
EnsemblMetazoa; FBtr0306099; FBpp0297236; FBgn0037906. [Q8INK6-2]
GeneID; 41379; -.
KEGG; dme:Dmel_CG14704; -.
CTD; 41379; -.
FlyBase; FBgn0037906; PGRP-LB.
eggNOG; ENOG410IIH1; Eukaryota.
eggNOG; ENOG4111PAY; LUCA.
GeneTree; ENSGT00390000016833; -.
InParanoid; Q8INK6; -.
KO; K01446; -.
OrthoDB; EOG091G0O6Z; -.
PhylomeDB; Q8INK6; -.
Reactome; R-DME-6803157; Antimicrobial peptides.
EvolutionaryTrace; Q8INK6; -.
GenomeRNAi; 41379; -.
PRO; PR:Q8INK6; -.
Proteomes; UP000000803; Chromosome 3R.
Bgee; FBgn0037906; -.
ExpressionAtlas; Q8INK6; differential.
Genevisible; Q8INK6; DM.
GO; GO:0005576; C:extracellular region; IDA:UniProtKB.
GO; GO:0004040; F:amidase activity; NAS:FlyBase.
GO; GO:0008745; F:N-acetylmuramoyl-L-alanine amidase activity; IDA:FlyBase.
GO; GO:0042834; F:peptidoglycan binding; ISS:FlyBase.
GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
GO; GO:0050830; P:defense response to Gram-positive bacterium; IDA:UniProtKB.
GO; GO:0006955; P:immune response; ISS:FlyBase.
GO; GO:0045087; P:innate immune response; NAS:UniProtKB.
GO; GO:0061060; P:negative regulation of peptidoglycan recognition protein signaling pathway; IDA:FlyBase.
GO; GO:0009253; P:peptidoglycan catabolic process; ISS:FlyBase.
GO; GO:0000270; P:peptidoglycan metabolic process; NAS:FlyBase.
CDD; cd06583; PGRP; 1.
Gene3D; 3.40.80.10; -; 1.
InterPro; IPR002502; Amidase_domain.
InterPro; IPR036505; Amidase_sf.
InterPro; IPR017331; Peptidoglycan_recognition.
InterPro; IPR015510; PGRP.
InterPro; IPR006619; PGRP_domain_met/bac.
PANTHER; PTHR11022; PTHR11022; 1.
Pfam; PF01510; Amidase_2; 1.
PIRSF; PIRSF037945; PGRPs; 1.
SMART; SM00644; Ami_2; 1.
SMART; SM00701; PGRP; 1.
SUPFAM; SSF55846; SSF55846; 1.
1: Evidence at protein level;
3D-structure; Alternative splicing; Complete proteome; Disulfide bond;
Glycoprotein; Hydrolase; Immunity; Innate immunity; Metal-binding;
Reference proteome; Secreted; Signal; Zinc.
SIGNAL 1 15 {ECO:0000255}.
CHAIN 16 232 Peptidoglycan-recognition protein LB.
/FTId=PRO_0000023905.
METAL 59 59 Zinc; via pros nitrogen.
{ECO:0000244|PDB:1OHT,
ECO:0000269|PubMed:12845326}.
METAL 169 169 Zinc; via pros nitrogen.
{ECO:0000244|PDB:1OHT,
ECO:0000269|PubMed:12845326}.
METAL 177 177 Zinc. {ECO:0000244|PDB:1OHT,
ECO:0000269|PubMed:12845326}.
SITE 95 95 Essential for zinc hydrate coordination.
{ECO:0000303|PubMed:12845326}.
CARBOHYD 196 196 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
DISULFID 67 73 {ECO:0000269|PubMed:12845326}.
VAR_SEQ 1 17 Missing (in isoform A).
{ECO:0000303|PubMed:11106397,
ECO:0000303|PubMed:12537569}.
/FTId=VSP_013593.
MUTAGEN 175 175 T->K: Loss of function.
{ECO:0000269|PubMed:12845326}.
HELIX 36 38 {ECO:0000244|PDB:1OHT}.
STRAND 51 60 {ECO:0000244|PDB:1OHT}.
STRAND 62 64 {ECO:0000244|PDB:1OHT}.
HELIX 70 86 {ECO:0000244|PDB:1OHT}.
STRAND 94 99 {ECO:0000244|PDB:1OHT}.
STRAND 105 109 {ECO:0000244|PDB:1OHT}.
STRAND 116 118 {ECO:0000244|PDB:1OHT}.
TURN 119 123 {ECO:0000244|PDB:1OHT}.
STRAND 124 132 {ECO:0000244|PDB:1OHT}.
STRAND 135 137 {ECO:0000244|PDB:1OHT}.
HELIX 141 156 {ECO:0000244|PDB:1OHT}.
STRAND 159 168 {ECO:0000244|PDB:1OHT}.
HELIX 169 171 {ECO:0000244|PDB:1OHT}.
STRAND 173 175 {ECO:0000244|PDB:1OHT}.
HELIX 180 186 {ECO:0000244|PDB:1OHT}.
HELIX 195 197 {ECO:0000244|PDB:1OHT}.
SEQUENCE 232 AA; 25436 MW; 7BD18D4EC41F021E CRC64;
MTALGLVLLS MMGYSQHMQQ ANLGDGVATA RLLSRSDWGA RLPKSVEHFQ GPAPYVIIHH
SYMPAVCYST PDCMKSMRDM QDFHQLERGW NDIGYSFGIG GDGMIYTGRG FNVIGAHAPK
YNDKSVGIVL IGDWRTELPP KQMLDAAKNL IAFGVFKGYI DPAYKLLGHR QVRDTECPGG
RLFAEISSWP HFTHINDTEG VSSTTAPVVP HVHPQAAAPQ KPHQSPPAAP KV


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