Summary: This gene encodes a peptidoglycan recognition protein, which belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. These proteins are part of the innate immune system and recognize peptidoglycan, a ubiquitous component of bacterial cell walls. This antimicrobial protein binds to murein peptidoglycans of Gram-positive bacteria. [provided by RefSeq, Oct 2014] See more...

Aliases for PGLYRP4 Gene

Aliases for PGLYRP4 Gene

  • Peptidoglycan Recognition Protein 4 2 3 4 5
  • Peptidoglycan Recognition Protein Intermediate Beta 3 4
  • Peptidoglycan Recognition Protein I-Beta 3 4
  • PGLYRPIbeta 3 4
  • PGRP-I-Beta 3 4
  • PGRPIB 3 4
  • Peptidoglycan Recognition Protein I Beta Precursor 2
  • PGRP-Ibeta 3
  • SBBI67 3

External Ids for PGLYRP4 Gene

Previous GeneCards Identifiers for PGLYRP4 Gene

  • GC01M150521
  • GC01M150116
  • GC01M151570
  • GC01M153302
  • GC01M124666

Summaries for PGLYRP4 Gene

Entrez Gene Summary for PGLYRP4 Gene

  • Summary: This gene encodes a peptidoglycan recognition protein, which belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. These proteins are part of the innate immune system and recognize peptidoglycan, a ubiquitous component of bacterial cell walls. This antimicrobial protein binds to murein peptidoglycans of Gram-positive bacteria. [provided by RefSeq, Oct 2014]

GeneCards Summary for PGLYRP4 Gene

PGLYRP4 (Peptidoglycan Recognition Protein 4) is a Protein Coding gene. Among its related pathways are Innate Immune System and Defensins. Gene Ontology (GO) annotations related to this gene include peptidoglycan binding and N-acetylmuramoyl-L-alanine amidase activity. An important paralog of this gene is PGLYRP3.

UniProtKB/Swiss-Prot Summary for PGLYRP4 Gene

  • Pattern receptor that binds to murein peptidoglycans (PGN) of Gram-positive bacteria. Has bactericidal activity towards Gram-positive bacteria. May kill Gram-positive bacteria by interfering with peptidoglycan biosynthesis. Binds also to Gram-negative bacteria, and has bacteriostatic activity towards Gram-negative bacteria. Plays a role in innate immunity.

Additional gene information for PGLYRP4 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PGLYRP4 Gene

Genomics for PGLYRP4 Gene

GeneHancer (GH) Regulatory Elements for PGLYRP4 Gene

Promoters and enhancers for PGLYRP4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J153343 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 550.5 +2.1 2140 9 NRF1 PHB2 ZIC2 ZBTB11 AFF1 TARDBP DNMT1 HES1 NR3C1 TOE1 PGLYRP4 lnc-S100A12-3 S100A6 PGLYRP3 RF00026-073 RNU6-160P
GH01J153561 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.4 -216.7 -216720 8.8 ZNF217 CTCF TCF12 NRF1 POLR2G JUND FOS ZFX ZNF639 ZNF10 S100A3 S100A2 HSALNG0007314 S100A6 S100A5 ENSG00000238279 S100A16 S100A13 S100A14 SNAPIN
GH01J153306 Enhancer 0.4 Ensembl 34.7 +41.9 41940 1 SPI1 CEBPB SUZ12 HLF PGLYRP4 PGLYRP3 piR-53227
GH01J153373 Promoter/Enhancer 1.1 EPDnew ENCODE dbSUPER 10.9 -26.9 -26948 1.9 EP300 SMARCC1 SMARCC2 FOS FOSL2 CEBPB JUN GATA3 GABPA STAT3 S100A12 PGLYRP4 RNU6-160P PGLYRP3 lnc-S100A12-1
GH01J153489 Enhancer 1 ENCODE dbSUPER 11.2 -142.0 -141986 2.1 ZSCAN5C JUND FOS ZNF10 ZIC2 ZNF623 TRIM28 EP300 ZEB1 ATF2 PGLYRP4 S100A9 RNU6-160P S100A1 CHTOP S100A13 PGLYRP3 RN7SL44P S100A3 RF00017-350
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PGLYRP4 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PGLYRP4

Top Transcription factor binding sites by QIAGEN in the PGLYRP4 gene promoter:
  • AML1a
  • AP-1
  • ATF-2
  • c-Fos
  • c-Jun
  • CP2
  • HTF

Genomic Locations for PGLYRP4 Gene

Genomic Locations for PGLYRP4 Gene
chr1:153,327,380-153,348,841
(GRCh38/hg38)
Size:
21,462 bases
Orientation:
Minus strand
chr1:153,302,596-153,321,316
(GRCh37/hg19)
Size:
18,721 bases
Orientation:
Minus strand

Genomic View for PGLYRP4 Gene

Genes around PGLYRP4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PGLYRP4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PGLYRP4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PGLYRP4 Gene

Proteins for PGLYRP4 Gene

  • Protein details for PGLYRP4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96LB8-PGRP4_HUMAN
    Recommended name:
    Peptidoglycan recognition protein 4
    Protein Accession:
    Q96LB8
    Secondary Accessions:
    • A8K838
    • Q3B822
    • Q3B823
    • Q5SY63
    • Q5SY64
    • Q9HD75

    Protein attributes for PGLYRP4 Gene

    Size:
    373 amino acids
    Molecular mass:
    40620 Da
    Quaternary structure:
    • Homodimer; disulfide-linked. Heterodimer with PGLYRP3; disulfide-linked.
    SequenceCaution:
    • Sequence=AAF99599.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PGLYRP4 Gene

    Alternative splice isoforms for PGLYRP4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PGLYRP4 Gene

Post-translational modifications for PGLYRP4 Gene

Other Protein References for PGLYRP4 Gene

No data available for DME Specific Peptides for PGLYRP4 Gene

Domains & Families for PGLYRP4 Gene

Gene Families for PGLYRP4 Gene

Protein Domains for PGLYRP4 Gene

Blocks:
  • N-acetylmuramoyl-L-alanine amidase, family 2
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PGLYRP4 Gene

GenScript: Design optimal peptide antigens:
  • Peptidoglycan recognition protein intermediate beta (PGRP4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96LB8

UniProtKB/Swiss-Prot:

PGRP4_HUMAN :
  • Belongs to the N-acetylmuramoyl-L-alanine amidase 2 family.
Family:
  • Belongs to the N-acetylmuramoyl-L-alanine amidase 2 family.
genes like me logo Genes that share domains with PGLYRP4: view

Function for PGLYRP4 Gene

Molecular function for PGLYRP4 Gene

UniProtKB/Swiss-Prot Function:
Pattern receptor that binds to murein peptidoglycans (PGN) of Gram-positive bacteria. Has bactericidal activity towards Gram-positive bacteria. May kill Gram-positive bacteria by interfering with peptidoglycan biosynthesis. Binds also to Gram-negative bacteria, and has bacteriostatic activity towards Gram-negative bacteria. Plays a role in innate immunity.
UniProtKB/Swiss-Prot Induction:
Up-regulated by exposure to Gram-positive and Gram-negative bacteria.

Phenotypes From GWAS Catalog for PGLYRP4 Gene

Gene Ontology (GO) - Molecular Function for PGLYRP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008270 zinc ion binding IEA --
GO:0008745 N-acetylmuramoyl-L-alanine amidase activity IBA 21873635
GO:0016019 peptidoglycan receptor activity IDA,IBA 11461926
GO:0042834 peptidoglycan binding IDA,IBA 11461926
GO:0046982 protein heterodimerization activity IPI 16354652
genes like me logo Genes that share ontologies with PGLYRP4: view
genes like me logo Genes that share phenotypes with PGLYRP4: view

Animal Models for PGLYRP4 Gene

MGI Knock Outs for PGLYRP4:

Animal Model Products

  • Taconic Biosciences Mouse Models for PGLYRP4

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for PGLYRP4 Gene

Localization for PGLYRP4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PGLYRP4 Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PGLYRP4 gene
Compartment Confidence
extracellular 4
plasma membrane 1
cytoskeleton 1
nucleus 1
cytosol 1
mitochondrion 0
peroxisome 0
lysosome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
  • Vesicles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PGLYRP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IBA 21873635
GO:0016020 membrane NAS 11461926
GO:0032991 protein-containing complex IDA 16354652
genes like me logo Genes that share ontologies with PGLYRP4: view

Pathways & Interactions for PGLYRP4 Gene

PathCards logo

SuperPathways for PGLYRP4 Gene

genes like me logo Genes that share pathways with PGLYRP4: view

Pathways by source for PGLYRP4 Gene

3 Reactome pathways for PGLYRP4 Gene

Interacting Proteins for PGLYRP4 Gene

;

Gene Ontology (GO) - Biological Process for PGLYRP4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002221 pattern recognition receptor signaling pathway IEA --
GO:0002376 immune system process IEA --
GO:0009253 peptidoglycan catabolic process IEA --
GO:0016045 detection of bacterium IDA,IBA 11461926
GO:0019730 antimicrobial humoral response IBA 21873635
genes like me logo Genes that share ontologies with PGLYRP4: view

No data available for SIGNOR curated interactions for PGLYRP4 Gene

Drugs & Compounds for PGLYRP4 Gene

(3) Drugs for PGLYRP4 Gene - From: PharmGKB and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Tumor necrosis factor alpha (TNF-alpha) inhibitors Pharma 0
L-Alanine Nutra Full agonist, Agonist Glycine receptor agonist 187

(2) Additional Compounds for PGLYRP4 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
N-Acetylmuramate
  • N-Acetyl-D-muramoate
  • N-Acetylmuramic acid
  • N-Acetyl-D-muramoic acid
  • N-Acetylisomuramic acid
  • Acetylmuramic acid
N-Acetylmuramoyl-Ala
  • N-Acetyl-D-muramoyl-L-alanine
genes like me logo Genes that share compounds with PGLYRP4: view

Transcripts for PGLYRP4 Gene

mRNA/cDNA for PGLYRP4 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PGLYRP4 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b
SP1: -
SP2:
SP3:

Relevant External Links for PGLYRP4 Gene

GeneLoc Exon Structure for
PGLYRP4

Expression for PGLYRP4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PGLYRP4 Gene

mRNA differential expression in normal tissues according to GTEx for PGLYRP4 Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x12.3), Skin - Sun Exposed (Lower leg) (x11.3), Cervix - Ectocervix (x9.0), Vagina (x9.0), and Esophagus - Mucosa (x8.5).

Protein differential expression in normal tissues from HIPED for PGLYRP4 Gene

This gene is overexpressed in Fetal Liver (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PGLYRP4 Gene



Protein tissue co-expression partners for PGLYRP4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PGLYRP4

SOURCE GeneReport for Unigene cluster for PGLYRP4 Gene:

Hs.58356

mRNA Expression by UniProt/SwissProt for PGLYRP4 Gene:

Q96LB8-PGRP4_HUMAN
Tissue specificity: Detected in skin epidermis, eccrine sweat glands and ducts, mucous cells in the submandibular salivary gland, mucous cells in the throat, ciliary body epithelial cells of the eye, small intestine, colon, stomach and in mature epithelial cells of the tongue (at protein level). High expression in skin and esophagus. Expressed also to a much lesser extent in the tonsils and thymus.
genes like me logo Genes that share expression patterns with PGLYRP4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PGLYRP4 Gene

Orthologs for PGLYRP4 Gene

This gene was present in the common ancestor of animals.

Orthologs for PGLYRP4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PGLYRP4 31 30
  • 99.11 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PGLYRP4 30
  • 81 (n)
mouse
(Mus musculus)
Mammalia Pglyrp4 17 31 30
  • 79.03 (n)
rat
(Rattus norvegicus)
Mammalia Pglyrp4 30
  • 78.23 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 62 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 46 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia pglyrp1 30
  • 51.39 (n)
zebrafish
(Danio rerio)
Actinopterygii pglyrp5 31
  • 26 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta PGRPS2 30
  • 57.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta PGRP-SC2 31 30
  • 51.25 (n)
ManyToMany
PGRP-SB1 31
  • 39 (a)
ManyToMany
PGRP-SC1b 31
  • 33 (a)
ManyToMany
PGRP-SC1a 31
  • 33 (a)
ManyToMany
PGRP-SA 31
  • 33 (a)
ManyToMany
PGRP-SD 31
  • 32 (a)
ManyToMany
PGRP-SB2 31
  • 29 (a)
ManyToMany
PGRP-LB 31
  • 28 (a)
ManyToMany
PGRP-LC 31
  • 6 (a)
ManyToMany
Species where no ortholog for PGLYRP4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PGLYRP4 Gene

ENSEMBL:
Gene Tree for PGLYRP4 (if available)
TreeFam:
Gene Tree for PGLYRP4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PGLYRP4: view image

Paralogs for PGLYRP4 Gene

Paralogs for PGLYRP4 Gene

(2) SIMAP similar genes for PGLYRP4 Gene using alignment to 1 proteins:

  • PGRP4_HUMAN
genes like me logo Genes that share paralogs with PGLYRP4: view

Variants for PGLYRP4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PGLYRP4 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs12063091 - p.Val213Ile
rs12096209 - p.Pro3Leu
rs3006448 - p.Gly192Val
rs3006453 - p.Gln92Arg
rs3006458 - p.Ile13Leu

Additional dbSNP identifiers (rs#s) for PGLYRP4 Gene

Structural Variations from Database of Genomic Variants (DGV) for PGLYRP4 Gene

Variant ID Type Subtype PubMed ID
esv6733 CNV loss 19470904
nsv1002705 CNV gain 25217958
nsv525937 CNV gain 19592680
nsv7184 OTHER inversion 18451855
nsv999024 CNV loss 25217958

Variation tolerance for PGLYRP4 Gene

Residual Variation Intolerance Score: 83.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.06; 60.71% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PGLYRP4 Gene

Human Gene Mutation Database (HGMD)
PGLYRP4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGLYRP4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PGLYRP4 Gene

Disorders for PGLYRP4 Gene

Additional Disease Information for PGLYRP4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PGLYRP4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PGLYRP4 Gene

Publications for PGLYRP4 Gene

  1. Peptidoglycan recognition proteins: a novel family of four human innate immunity pattern recognition molecules. (PMID: 11461926) Liu C … Dziarski R (The Journal of biological chemistry 2001) 2 3 4 54
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  3. Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins. (PMID: 17502600) Cho S … Mariuzza RA (Proceedings of the National Academy of Sciences of the United States of America 2007) 3 4 54
  4. Peptidoglycan recognition proteins are a new class of human bactericidal proteins. (PMID: 16354652) Lu X … Dziarski R (The Journal of biological chemistry 2006) 3 4 54
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54

Products for PGLYRP4 Gene

Sources for PGLYRP4 Gene