PGLYRP2

gene
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Also known as PGRP-LPGLYRPLTAGL-liketagLtagL-alphatagl-betaPGRPL

Summary

PGLYRP2 (peptidoglycan recognition protein 2, HGNC:30013) is a protein-coding gene on chromosome 19p13.12, encoding N-acetylmuramoyl-L-alanine amidase (Q96PD5). May play a scavenger role by digesting biologically active peptidoglycan (PGN) into biologically inactive fragments.

This gene encodes a peptidoglycan recognition protein, which belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. This protein hydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in bacterial cell wall glycopeptides, and thus may play a scavenger role by digesting biologically active peptidoglycan into biologically inactive fragments.

Source: NCBI Gene 114770 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 75 total
  • MANE Select transcript: NM_052890

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30013
Approved symbolPGLYRP2
Namepeptidoglycan recognition protein 2
Location19p13.12
Locus typegene with protein product
StatusApproved
AliasesPGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL
Ensembl geneENSG00000161031
Ensembl biotypeprotein_coding
OMIM608199
Entrez114770

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 14 protein_coding

ENST00000292609, ENST00000340880, ENST00000594637, ENST00000601792, ENST00000851089, ENST00000851090, ENST00000851091, ENST00000851092, ENST00000851093, ENST00000851094, ENST00000851095, ENST00000851096, ENST00000851097, ENST00000969569

RefSeq mRNA: 2 — MANE Select: NM_052890 NM_001363546, NM_052890

CCDS: CCDS12330, CCDS86718

Canonical transcript exons

ENST00000340880 — 5 exons

ExonStartEnd
ENSE000010560421547553815476608
ENSE000010560451547189015472100
ENSE000013676761546864515468752
ENSE000013686121546963215469929
ENSE000030982551547931115479501

Expression profiles

Bgee: expression breadth broad, 46 present calls, max score 95.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7899 / max 348.6537, expressed in 42 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1797550.416616
1797580.251820
1797560.085110
1797570.03658

Top tissues by expression

220 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111495.98gold quality
liverUBERON:000210795.25gold quality
pancreatic ductal cellCL:000207971.12silver quality
left testisUBERON:000453369.36gold quality
right testisUBERON:000453468.75gold quality
testisUBERON:000047367.48gold quality
tibialis anteriorUBERON:000138563.96silver quality
secondary oocyteCL:000065560.96gold quality
ileal mucosaUBERON:000033159.99silver quality
granulocyteCL:000009458.44gold quality
buccal mucosa cellCL:000233656.82gold quality
deltoidUBERON:000147656.09silver quality
epithelial cell of pancreasCL:000008356.00gold quality
adult organismUBERON:000702355.77silver quality
bone marrow cellCL:000209254.76gold quality
cardiac muscle of right atriumUBERON:000337954.34gold quality
monocyteCL:000057654.33gold quality
leukocyteCL:000073854.27gold quality
left ventricle myocardiumUBERON:000656654.23gold quality
kidney epitheliumUBERON:000481953.93gold quality
upper arm skinUBERON:000426353.52gold quality
middle temporal gyrusUBERON:000277150.64gold quality
colonic epitheliumUBERON:000039750.43gold quality
myocardiumUBERON:000234950.25gold quality
bloodUBERON:000017850.11gold quality
quadriceps femorisUBERON:000137748.37gold quality
upper leg skinUBERON:000426247.26silver quality
nasal cavity epitheliumUBERON:000538447.03gold quality
skin of hipUBERON:000155446.74silver quality
vastus lateralisUBERON:000137946.61gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-GEOD-100618no77.55
E-ANND-3no2.12

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ATF2, NFKB1, NFKB, SP1

Literature-anchored findings (GeneRIF, showing 12)

  • Various types of human blood cells were tested for expression of the Tag7/PGRP-SA and TagL/PGRP-L proteins, which belong to the family of proteins possessing the lysozyme-like peptidoglycan recognition protein (PGRP) domain (PMID:12669421)
  • Serum N-acetylmuramoyl-l-alanine amidaseand liver PGLYRP2 are the same protein encoded by the pglyrp2 gene. (PMID:16054449)
  • PGLYRP2 may function in the skin and the eyes as an inducible scavenger of proinflammatory peptidoglycan. (PMID:16239516)
  • pglyrp2 expression in skin and liver is important for systemic and local innate immune responses to bacterial infections (PMID:16714290)
  • This study demonistrated that PGLYRP2 single-nucleotide polymorphisms is risk of Parkinson’s disease. (PMID:24838182)
  • a significant induction of three PGLYRPs 2-4 in primary human corneal epithelial cells (HCECs) exposed to live or heat-killed Candida albicans, is reported. (PMID:26039076)
  • The expression of IL-36gamma by oral epithelial cells in response to P. gingivalis might enable the subsequent autocrine stimulation of PGLYRP2 expression. Our data identify how IL-36gamma may promote oral mucosal homeostasis by regulating PGLYRP2 expression. (PMID:29914927)
  • Tumor-Derived Peptidoglycan Recognition Protein 2 Predicts Survival and Antitumor Immune Responses in Hepatocellular Carcinoma. (PMID:31479523)
  • Serum sCD14, PGLYRP2 and FGA as potential biomarkers for multidrug-resistant tuberculosis based on data-independent acquisition and targeted proteomics. (PMID:32967043)
  • Antibody to peptidoglycan recognition protein (PGLYRP)-2 as a novel biomarker in rheumatoid arthritis. (PMID:33427621)
  • PGLYRP2 as a novel biomarker for the activity and lipid metabolism of systemic lupus erythematosus. (PMID:34461924)
  • Association of PGLYRP2 gene polymorphism and sporadic Parkinson’s disease in northern Chinese Han population. (PMID:35218888)

Cross-species orthologs

14 orthologs

OrganismSymbolGene ID
danio_reriopglyrp2ENSDARG00000062998
danio_reriopglyrp6ENSDARG00000103642
mus_musculusPglyrp2ENSMUSG00000079563
rattus_norvegicusPglyrp2ENSRNOG00000042318
drosophila_melanogasterPGRP-SAFBGN0030310
drosophila_melanogasterPGRP-LEFBGN0030695
drosophila_melanogasterPGRP-SC1bFBGN0033327
drosophila_melanogasterPGRP-SDFBGN0035806
drosophila_melanogasterPGRP-LFFBGN0035977
drosophila_melanogasterPGRP-SC2FBGN0043575
drosophila_melanogasterPGRP-SC1aFBGN0043576
drosophila_melanogasterPGRP-SB2FBGN0043577
drosophila_melanogasterPGRP-SB1FBGN0043578
drosophila_melanogasterPGRP-LDFBGN0260458

Paralogs (3): PGLYRP1 (ENSG00000008438), PGLYRP3 (ENSG00000159527), PGLYRP4 (ENSG00000163218)

Protein

Protein identifiers

N-acetylmuramoyl-L-alanine amidaseQ96PD5 (reviewed: Q96PD5)

Alternative names: Peptidoglycan recognition protein 2, Peptidoglycan recognition protein long

All UniProt accessions (3): Q96PD5, M0QYW3, M0R2W8

UniProt curated annotations — full annotation on UniProt →

Function. May play a scavenger role by digesting biologically active peptidoglycan (PGN) into biologically inactive fragments. Has no direct bacteriolytic activity.

Subcellular location. Secreted. Membrane.

Tissue specificity. Strongly expressed in liver and fetal liver, and secreted into serum. Expressed to a much lesser extent in transverse colon, lymph nodes, heart, thymus, pancreas, descending colon, stomach and testis. Isoform 2 is not detected in the liver or serum.

Miscellaneous. Major isoform. May be due to an intron retention.

Similarity. Belongs to the N-acetylmuramoyl-L-alanine amidase 2 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q96PD5-11yes
Q96PD5-22

RefSeq proteins (2): NP_001350475, NP_443122* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002502Amidase_domainDomain
IPR006619PGRP_domain_met/bacDomain
IPR015510PGRPFamily
IPR036505Amidase/PGRP_sfHomologous_superfamily

Pfam: PF01510

Enzyme classification (BRENDA):

  • EC 3.5.1.28 — N-acetylmuramoyl-L-alanine amidase (BRENDA: 55 organisms, 158 substrates, 76 inhibitors, 18 Km, 6 kcat entries)

Substrate kinetics (BRENDA)

14 substrates with measured Km, best-characterized 14. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
GLCNAC-MURNAC-L-ALA-D-ISOGLUTAMINYL-MESO-DIAMINO8–172
1,6-ANHYDRO-MURNAC-L-ALA-GAMMA-D-GLU-M-DAP0.361
1,6-ANHYDRO-MURNAC-L-ALA-GAMMA-D-GLU-M-DAP-D-ALA0.51
4-O-BETA-D-GLCNAC-1,6-ANHYDRO-MURNAC-L-ALA-GAMMA1.761
7-METHOXYCOUMARIN-4-YL-ACETYL-ALA-D-ISOGLN-LYS(20.28491
7-METHOXYCOUMARIN-4-YL-ACETYL-ALA-D-ISOGLU-LYS(20.36011
BETA-N-ACETYLGLUCOSAMINYL-(1-4)-N,6-O-DIACETYLMU41
BETA-N-ACETYLGLUCOSAMINYL-(1-4)-N,6-O-DIACETYLMU1.81
BETA-N-ACETYLGLUCOSAMINYL-(1-4)-N-ACETYLMURAMOYL2.51
BETA-N-ACETYLGLUCOSAMINYL-(1-4)-N-ACETYLMURAMOYL41
BETA-N-ACETYLGLUCOSAMINYL-(1-4)-N-ACETYLMURAMOYL21
GLCNAC-MURNAC-L-ALA-D-ISOGIN-MESO-DIAMINOPIMELYL2.51
N-ACETYLMURAMOYL-L-ALANYL-D-GAMMA-GLUTAMINYL-MES0.041
N-ACETYLMURAMOYL-L-ALANYL-GAMMA-D-GLUTAMINYL-MES0.51

UniProt features (31 total): sequence variant 6, mutagenesis site 6, modified residue 3, glycosylation site 3, sequence conflict 3, binding site 3, signal peptide 1, chain 1, disulfide bond 1, splice variant 1, domain 1, region of interest 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96PD5-F179.200.58

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 447 (important for catalytic activity; essential for amidase activity and zinc hydrate coordination)

Ligand- & substrate-binding residues (3): 410; 522; 530

Post-translational modifications (3): 322, 239, 274

Disulfide bonds (1): 419–425

Glycosylation sites (3): 77, 367, 485

Mutagenesis-validated functional residues (6):

PositionPhenotype
411no effect on amidase activity.
419abolishes amidase activity.
436no effect on amidase activity.
442reduced amidase activity.
447abolishes amidase activity.
530abolishes amidase activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6803157Antimicrobial peptides

MSigDB gene sets: 169 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_NEGATIVE_REGULATION_OF_CELL_DEVELOPMENT, GOBP_NATURAL_KILLER_CELL_DIFFERENTIATION, REACTOME_INNATE_IMMUNE_SYSTEM, MODULE_255, GOBP_INFLAMMATORY_RESPONSE, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, MODULE_317, GOBP_DETECTION_OF_OTHER_ORGANISM, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_PEPTIDE_METABOLIC_PROCESS, GOBP_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION, GOBP_REGULATION_OF_IMMUNE_RESPONSE

GO Biological Process (12): peptide amidation (GO:0001519), immune response (GO:0006955), peptidoglycan catabolic process (GO:0009253), detection of bacterium (GO:0016045), negative regulation of type II interferon production (GO:0032689), obsolete negative regulation of natural killer cell differentiation involved in immune response (GO:0032827), defense response to bacterium (GO:0042742), innate immune response (GO:0045087), regulation of inflammatory response (GO:0050727), defense response to Gram-positive bacterium (GO:0050830), biological process involved in interaction with host (GO:0051701), immune system process (GO:0002376)

GO Molecular Function (8): zinc ion binding (GO:0008270), N-acetylmuramoyl-L-alanine amidase activity (GO:0008745), peptidoglycan immune receptor activity (GO:0016019), peptidoglycan binding (GO:0042834), molecular condensate scaffold activity (GO:0140693), protein binding (GO:0005515), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (3): extracellular region (GO:0005576), membrane (GO:0016020), extracellular exosome (GO:0070062)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Innate Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
response to bacterium2
cellular anatomical structure2
peptide modification1
immune system process1
response to stimulus1
peptidoglycan metabolic process1
glycosaminoglycan catabolic process1
detection of other organism1
negative regulation of cytokine production1
type II interferon production1
regulation of type II interferon production1
defense response1
immune response1
defense response to symbiont1
inflammatory response1
regulation of defense response1
regulation of response to external stimulus1
defense response to bacterium1
biological process involved in symbiotic interaction1
biological_process1
transition metal ion binding1
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides1
peptidoglycan muralytic activity1
pattern recognition receptor activity1
peptidoglycan binding1
glycosaminoglycan binding1
protein-macromolecule adaptor activity1
binding1
catalytic activity1
cation binding1
extracellular vesicle1

Protein interactions and networks

STRING

578 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PGLYRP2SERPIND1P05546513
PGLYRP2AFMP43652508
PGLYRP2AZGP1P25311479
PGLYRP2CFIP05156472
PGLYRP2PGLYRP4Q96LB8452
PGLYRP2TECRQ9NZ01433
PGLYRP2SUSD4Q5VX71422
PGLYRP2CCDC3Q9BQI4406
PGLYRP2PNLIPP16233397
PGLYRP2GCSAMQ8N6F7389
PGLYRP2PGLYRP3Q96LB9388
PGLYRP2CPN2P22792381
PGLYRP2LIPCP11150370
PGLYRP2SCINQ9Y6U3362
PGLYRP2MGLLQ99685357

IntAct

3 interactions, top by confidence:

ABTypeScore
ORF60PGLYRP2psi-mi:“MI:0914”(association)0.350
recNPGLYRP2psi-mi:“MI:0915”(physical association)0.000

BioGRID (2): PGLYRP2 (Affinity Capture-MS), PGLYRP2 (Two-hybrid)

ESM2 similar proteins: A0A1B0GTW7, A0A1D5NSK0, A0A1L8HYT7, A0A286YEC0, D3ZT86, D3ZWJ9, D4A929, F8W3R9, G7PWZ3, I6M4H4, O08852, O43157, O43278, O75074, O88204, P17813, P49000, P59383, Q04912, Q17R55, Q499Z3, Q4R3B7, Q4TUC0, Q5ND34, Q62190, Q63961, Q6AXX1, Q76MJ5, Q7TN88, Q7TQH7, Q7Z442, Q7Z4F1, Q80W87, Q80YN4, Q866Y3, Q86VZ4, Q8BHW9, Q8BMN4, Q8BYI8, Q8BZT7

Diamond homologs: A1A547, B5T255, C0HK98, C0HK99, D1L2U8, O75594, O76537, O88593, P00806, P20331, Q0VB07, Q3ZFI3, Q70PR8, Q70PU1, Q70PU2, Q70PW6, Q70PY2, Q765P2, Q765P3, Q765P4, Q866Y3, Q8INK6, Q8SPP7, Q8VCS0, Q96LB8, Q96LB9, Q96PD5, Q9GK12, Q9GNK5, Q9JLN4, Q9V4X2, Q9VS97, Q9VV96, Q9VXN9, Q9VYX7, Q9XTN0, Q8SXQ7, Q95T64, O05071, Q9GN97

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

75 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance66
Likely benign6
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

736 predictions. Top by Δscore:

VariantEffectΔscore
19:15469925:CGAAA:Cacceptor_gain1.0000
19:15469930:C:CCacceptor_gain1.0000
19:15471884:TCCTA:Tdonor_loss1.0000
19:15471885:CCTA:Cdonor_loss1.0000
19:15471886:CTA:Cdonor_loss1.0000
19:15471887:TA:Tdonor_loss1.0000
19:15471888:A:ACdonor_gain1.0000
19:15471888:ACC:Adonor_loss1.0000
19:15471889:C:CCdonor_gain1.0000
19:15472096:GCATC:Gacceptor_gain1.0000
19:15472097:CATC:Cacceptor_gain1.0000
19:15472097:CATCC:Cacceptor_gain1.0000
19:15472098:ATC:Aacceptor_gain1.0000
19:15472098:ATCCT:Aacceptor_loss1.0000
19:15472099:TC:Tacceptor_gain1.0000
19:15472099:TCCT:Tacceptor_loss1.0000
19:15472100:CC:Cacceptor_gain1.0000
19:15472100:CCTAC:Cacceptor_loss1.0000
19:15472101:C:CAacceptor_loss1.0000
19:15472101:C:CCacceptor_gain1.0000
19:15472102:T:Cacceptor_loss1.0000
19:15472108:C:CTacceptor_gain1.0000
19:15472109:A:Tacceptor_gain1.0000
19:15475466:C:Adonor_gain1.0000
19:15475531:T:TAdonor_gain1.0000
19:15475558:T:TAdonor_gain1.0000
19:15476604:GGAGG:Gacceptor_gain1.0000
19:15476605:GAGG:Gacceptor_gain1.0000
19:15476606:AGG:Aacceptor_gain1.0000
19:15476607:GG:Gacceptor_gain1.0000

AlphaMissense

3662 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:15472069:C:AW388C0.995
19:15472069:C:GW388C0.995
19:15475923:C:AW249C0.988
19:15475923:C:GW249C0.988
19:15472071:A:GW388R0.986
19:15472071:A:TW388R0.986
19:15469638:G:CF545L0.982
19:15469638:G:TF545L0.982
19:15469640:A:GF545L0.982
19:15475837:T:AD278V0.978
19:15469926:G:CF449L0.977
19:15469926:G:TF449L0.977
19:15469928:A:GF449L0.977
19:15475838:C:GD278H0.977
19:15475896:A:CF258L0.975
19:15475896:A:TF258L0.975
19:15475898:A:GF258L0.975
19:15471907:C:AW442C0.970
19:15471907:C:GW442C0.970
19:15475555:A:GF372S0.969
19:15469822:C:AG484V0.968
19:15469884:C:AW463C0.967
19:15469884:C:GW463C0.967
19:15471934:C:AQ433H0.966
19:15471934:C:GQ433H0.966
19:15475925:A:GW249R0.966
19:15475925:A:TW249R0.966
19:15469927:A:CF449C0.965
19:15472005:G:CH410D0.965
19:15475722:G:CS316R0.965

dbSNP variants (sampled 300 via entrez): RS1000072285 (19:15480558 G>A), RS1000114048 (19:15470890 C>T), RS1000226092 (19:15476851 C>T), RS1000615247 (19:15472044 G>A,C), RS1001066133 (19:15469623 A>G), RS1001446665 (19:15472342 C>A), RS1001549170 (19:15471281 T>A,C), RS1001706017 (19:15473858 A>G), RS1001897410 (19:15468844 G>A), RS1002017215 (19:15478895 T>A), RS1002046122 (19:15475201 T>C), RS1002096683 (19:15474797 A>G), RS1002117461 (19:15473428 T>C), RS1002123343 (19:15472451 A>C,G), RS1002393902 (19:15468504 G>A)

Disease associations

OMIM: gene MIM:608199 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST006585_2277Blood protein levels2.000000e-47
GCST90002388_45Lymphocyte count5.000000e-12

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004587lymphocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Aflatoxin B1affects expression, decreases expression, increases methylation3
Benzo(a)pyreneaffects methylation, decreases expression2
Estradioldecreases expression, increases expression2
Tetrachlorodibenzodioxinaffects cotreatment, decreases expression2
Zincaffects binding2
lasiocarpinedecreases expression1
methyleugenoldecreases expression1
sodium arsenitedecreases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2decreases methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment1
perfluorooctane sulfonic aciddecreases expression1
perfluoro-n-nonanoic aciddecreases expression1
abrineincreases expression1
Bosentanaffects expression1
Acetaminophendecreases expression1
Arsenicaffects methylation1
Chenodeoxycholic Acidaffects cotreatment, decreases expression1
Copperaffects binding1
Deoxycholic Acidaffects cotreatment, decreases expression1
Diazinonincreases methylation1
Endosulfanaffects cotreatment, decreases expression1
Glycochenodeoxycholic Acidaffects cotreatment, decreases expression1
Glycocholic Acidaffects cotreatment, decreases expression1
Glycodeoxycholic Acidaffects cotreatment, decreases expression1
Lipopolysaccharidesincreases expression, affects response to substance, affects cotreatment1
Methapyrileneincreases methylation1
Nickelaffects binding1
Triclosanaffects cotreatment, decreases expression1
Valproic Aciddecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.