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PGLYRP4 peptidoglycan recognition protein 4 [ Homo sapiens (human) ]

Gene ID: 57115, updated on 5-Mar-2024

Summary

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Official Symbol
PGLYRP4provided by HGNC
Official Full Name
peptidoglycan recognition protein 4provided by HGNC
Primary source
HGNC:HGNC:30015
See related
Ensembl:ENSG00000163218 MIM:608198; AllianceGenome:HGNC:30015
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PGRPIB; SBBI67; PGRP-Ibeta; PGLYRPIbeta
Summary
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]
Expression
Biased expression in skin (RPKM 2.9) and esophagus (RPKM 1.0) See more
Orthologs
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Genomic context

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Location:
1q21.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (153330120..153348841, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (152467338..152486071, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (153302596..153321317, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1338 Neighboring gene loricrin cornified envelope precursor protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1740 Neighboring gene peptidoglycan recognition protein 3 Neighboring gene RNA, U6 small nuclear 160, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1340 Neighboring gene S100 calcium binding protein A9 Neighboring gene S100 calcium binding protein A12

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota. Dabrowski AN, et al. Front Immunol, 2019. PMID 31616404, Free PMC Article
  2. Peptidoglycan recognition protein genes and risk of Parkinson's disease. Goldman SM, et al. Mov Disord, 2014 Aug. PMID 24838182, Free PMC Article
  3. Peptidoglycan recognition proteins Pglyrp3 and Pglyrp4 are encoded from the epidermal differentiation complex and are candidate genes for the Psors4 locus on chromosome 1q21. Sun C, et al. Hum Genet, 2006 Mar. PMID 16362825
  4. A Novel Innate Response of Human Corneal Epithelium to Heat-killed Candida albicans by Producing Peptidoglycan Recognition Proteins. Hua X, et al. PLoS One, 2015. PMID 26039076, Free PMC Article
  5. Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins. Cho S, et al. Proc Natl Acad Sci U S A, 2007 May 22. PMID 17502600, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota.
    Title: Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota.
  2. 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.
    Title: A Novel Innate Response of Human Corneal Epithelium to Heat-killed Candida albicans by Producing Peptidoglycan Recognition Proteins.
  3. This study demonistrated that PGLYRP4 single-nucleotide polymorphisms is risk of Parkinson's disease.
    Title: Peptidoglycan recognition protein genes and risk of Parkinson's disease.
  4. Results describe the function of mammalian antimicrobial peptidoglycan recognition proteins 3 and 4, and show that they are a new class of bactericidal and bacteriostatic proteins.
    Title: Peptidoglycan recognition proteins are a new class of human bactericidal proteins.
  5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: New genetic associations detected in a host response study to hepatitis B vaccine.
  7. Data are consistent with previous reports of association of psoriasis with genes on 1q21, and suggest a role for Pglyrp4 in skin biology.
    Title: Peptidoglycan recognition proteins Pglyrp3 and Pglyrp4 are encoded from the epidermal differentiation complex and are candidate genes for the Psors4 locus on chromosome 1q21.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120-treated vaginal epithelial cells show upregulation of peptidoglycan recognition protein 4 (PGLYRP4) expression as compared to untreated control PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables N-acetylmuramoyl-L-alanine amidase activity IEA
Inferred from Electronic Annotation
more info
  
enables peptidoglycan binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables peptidoglycan immune receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in antimicrobial humoral immune response mediated by antimicrobial peptide IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in defense response to Gram-positive bacterium IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in detection of bacterium IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in innate immune response NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in killing of cells of another organism IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in peptidoglycan catabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
peptidoglycan recognition protein 4
Names
PGRP-I-beta
peptidoglycan recognition protein I-beta
peptidoglycan recognition protein intermediate beta

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_020393.4 → NP_065126.2  peptidoglycan recognition protein 4 precursor

    See identical proteins and their annotated locations for NP_065126.2

    Status: REVIEWED

    Source sequence(s)
    AF242518, AK292203, BC142636
    Consensus CDS
    CCDS30871.1
    UniProtKB/Swiss-Prot
    A8K838, Q3B822, Q3B823, Q5SY63, Q5SY64, Q96LB8, Q9HD75
    Related
    ENSP00000352672.5, ENST00000359650.10
    Conserved Domains (1) summary
    smart00701
    Location:211 → 351
    PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    153330120..153348841 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509791.3 → XP_011508093.1  peptidoglycan recognition protein 4 isoform X2

    UniProtKB/Swiss-Prot
    Q96LB8
    Related
    ENSP00000357728.3, ENST00000368739.3
    Conserved Domains (1) summary
    smart00701
    Location:207 → 347
    PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

  2. XM_011509792.1 → XP_011508094.1  peptidoglycan recognition protein 4 isoform X3

    Conserved Domains (1) summary
    smart00701
    Location:53 → 194
    PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

  3. XM_011509789.3 → XP_011508091.1  peptidoglycan recognition protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011508091.1

    UniProtKB/Swiss-Prot
    A8K838, Q3B822, Q3B823, Q5SY63, Q5SY64, Q96LB8, Q9HD75
    Conserved Domains (1) summary
    smart00701
    Location:211 → 351
    PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

  4. XM_011509793.2 → XP_011508095.1  peptidoglycan recognition protein 4 isoform X4

    Conserved Domains (1) summary
    smart00701
    Location:43 → 183
    PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

  5. XM_011509790.1 → XP_011508092.1  peptidoglycan recognition protein 4 isoform X1

    See identical proteins and their annotated locations for XP_011508092.1

    UniProtKB/Swiss-Prot
    A8K838, Q3B822, Q3B823, Q5SY63, Q5SY64, Q96LB8, Q9HD75
    Conserved Domains (1) summary
    smart00701
    Location:211 → 351
    PGRP; Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme

RNA

  1. XR_921897.3 RNA Sequence

  2. XR_007062001.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    152467338..152486071 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337789.1 → XP_054193764.1  peptidoglycan recognition protein 4 isoform X2

  2. XM_054337790.1 → XP_054193765.1  peptidoglycan recognition protein 4 isoform X3

  3. XM_054337787.1 → XP_054193762.1  peptidoglycan recognition protein 4 isoform X1

  4. XM_054337791.1 → XP_054193766.1  peptidoglycan recognition protein 4 isoform X4

  5. XM_054337788.1 → XP_054193763.1  peptidoglycan recognition protein 4 isoform X1

RNA

  1. XR_008486116.1 RNA Sequence

  2. XR_008486115.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96LB8.2 GenPept UniProtKB/Swiss-Prot:Q96LB8

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