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Q96LB8 (PGRP4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 109. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Peptidoglycan recognition protein 4
Alternative name(s):
Peptidoglycan recognition protein I-beta
Short name=PGLYRPIbeta
Short name=PGRP-I-beta
Peptidoglycan recognition protein intermediate beta
Gene names
Name:PGLYRP4
Synonyms:PGRPIB
ORF Names:SBBI67
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length373 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.6

Subunit structure

Homodimer; disulfide-linked. Heterodimer with PGLYRP3; disulfide-linked. Ref.6 Ref.7

Subcellular location

Secreted Ref.6.

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. Ref.1 Ref.6

Induction

Up-regulated by exposure to Gram-positive and Gram-negative bacteria. Ref.6

Post-translational modification

N-glycosylated. Ref.6

Sequence similarities

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

Sequence caution

The sequence AAF99599.1 differs from that shown. Reason: Frameshift at positions 209, 224 and 227.

Ontologies

Keywords
   Biological processImmunity
Innate immunity
   Cellular componentSecreted
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainSignal
   Molecular functionAntibiotic
Antimicrobial
   PTMDisulfide bond
Glycoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processdefense response to Gram-positive bacterium

Inferred from direct assay Ref.1. Source: UniProtKB

detection of bacterium

Inferred from direct assay Ref.1. Source: UniProtKB

growth of symbiont in host

Inferred from electronic annotation. Source: Ensembl

innate immune response

Non-traceable author statement Ref.1. Source: UniProtKB

negative regulation of interferon-gamma production

Inferred from electronic annotation. Source: Ensembl

negative regulation of natural killer cell differentiation involved in immune response

Inferred from electronic annotation. Source: Ensembl

pattern recognition receptor signaling pathway

Inferred from direct assay Ref.1. Source: GOC

peptidoglycan catabolic process

Inferred from electronic annotation. Source: InterPro

   Cellular_componentextracellular region

Inferred from electronic annotation. Source: UniProtKB-SubCell

intracellular

Non-traceable author statement Ref.1. Source: UniProtKB

membrane

Non-traceable author statement Ref.1. Source: UniProtKB

   Molecular_functionN-acetylmuramoyl-L-alanine amidase activity

Inferred from electronic annotation. Source: InterPro

peptidoglycan binding

Inferred from direct assay Ref.1Ref.7. Source: UniProtKB

peptidoglycan receptor activity

Inferred from direct assay Ref.1. Source: UniProtKB

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q96LB8-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q96LB8-2)

The sequence of this isoform differs from the canonical sequence as follows:
     47-50: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1717 Potential
Chain18 – 373356Peptidoglycan recognition protein 4
PRO_0000023924

Regions

Region293 – 30210Interaction with murein
Region353 – 3542Interaction with murein

Sites

Binding site2631Murein
Binding site2741Murein

Amino acid modifications

Glycosylation221N-linked (GlcNAc...) Potential
Glycosylation391N-linked (GlcNAc...) Potential
Glycosylation1091N-linked (GlcNAc...) Potential
Glycosylation1451N-linked (GlcNAc...) Potential
Glycosylation2471N-linked (GlcNAc...) Potential
Disulfide bond210 ↔ 332 Ref.7
Disulfide bond226 ↔ 270 Ref.7
Disulfide bond246 ↔ 252 Ref.7

Natural variations

Alternative sequence47 – 504Missing in isoform 2.
VSP_024388
Natural variant31P → L. Ref.2 Ref.5
Corresponds to variant rs12096209 [ dbSNP | Ensembl ].
VAR_050503
Natural variant131I → L. Ref.1 Ref.3 Ref.5
Corresponds to variant rs3006458 [ dbSNP | Ensembl ].
VAR_033283
Natural variant921Q → R.
Corresponds to variant rs3006453 [ dbSNP | Ensembl ].
VAR_031586
Natural variant1921G → V. Ref.1 Ref.3 Ref.5
Corresponds to variant rs3006448 [ dbSNP | Ensembl ].
VAR_031587
Natural variant2131V → I. Ref.2 Ref.5
Corresponds to variant rs12063091 [ dbSNP | Ensembl ].
VAR_031588
Natural variant3011D → N.
Corresponds to variant rs35347202 [ dbSNP | Ensembl ].
VAR_031589

Secondary structure

........................... 373
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified April 3, 2007. Version 2.
Checksum: 8E882E1FF608F6F3

FASTA37340,620
        10         20         30         40         50         60 
MLPWLLVFSA LGIQAWGDSS WNKTQAKQVS EGLQYLFENI SQLTEKGLPT DVSTTVSRKA 

        70         80         90        100        110        120 
WGAEAVGCSI QLTTPVNVLV IHHVPGLECH DQTVCSQRLR ELQAHHVHNN SGCDVAYNFL 

       130        140        150        160        170        180 
VGDDGRVYEG VGWNIQGVHT QGYNNISLGF AFFGTKKGHS PSPAALSAME NLITYAVQKG 

       190        200        210        220        230        240 
HLSSSYVQPL LGKGENCLAP RQKTSLKKAC PGVVPRSVWG ARETHCPRMT LPAKYGIIIH 

       250        260        270        280        290        300 
TAGRTCNISD ECRLLVRDIQ SFYIDRLKSC DIGYNFLVGQ DGAIYEGVGW NVQGSSTPGY 

       310        320        330        340        350        360 
DDIALGITFM GTFTGIPPNA AALEAAQDLI QCAMVKGYLT PNYLLVGHSD VARTLSPGQA 

       370 
LYNIISTWPH FKH 

« Hide

Isoform 2 [UniParc].

Checksum: 1D03920B70BDE735
Show »

FASTA36940,252

References

« Hide 'large scale' references
[1]"Peptidoglycan recognition proteins: a novel family of four human innate immunity pattern recognition molecules."
Liu C., Xu Z., Gupta D., Dziarski R.
J. Biol. Chem. 276:34686-34694(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, VARIANTS LEU-13 AND VAL-192.
[2]Zhang W., Wan T., Cao X.
Submitted (MAR-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), VARIANTS LEU-3 AND ILE-213.
[3]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANTS LEU-13 AND VAL-192.
Tissue: Esophagus.
[4]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANTS LEU-3; LEU-13; VAL-192 AND ILE-213.
[6]"Peptidoglycan recognition proteins are a new class of human bactericidal proteins."
Lu X., Wang M., Qi J., Wang H., Li X., Gupta D., Dziarski R.
J. Biol. Chem. 281:5895-5907(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBUNIT, GLYCOSYLATION, INDUCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
[7]"Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins."
Cho S., Wang Q., Swaminathan C.P., Hesek D., Lee M., Boons G.-J., Mobashery S., Mariuzza R.A.
Proc. Natl. Acad. Sci. U.S.A. 104:8761-8766(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 210-373 IN COMPLEX WITH PEPTIDOGLYCAN-PEPTIDE, SUBUNIT, DISULFIDE BONDS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AY035377 mRNA. Translation: AAK72485.1.
AF242518 mRNA. Translation: AAF99599.1. Frameshift.
AK292203 mRNA. Translation: BAF84892.1.
AL591704 Genomic DNA. Translation: CAI19492.1.
AL591704 Genomic DNA. Translation: CAI19493.1.
BC142636 mRNA. Translation: AAI42637.1.
BC107157 mRNA. Translation: AAI07158.1.
BC107158 mRNA. Translation: AAI07159.1.
CCDSCCDS30871.1. [Q96LB8-1]
RefSeqNP_065126.2. NM_020393.2. [Q96LB8-1]
UniGeneHs.58356.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2EAVX-ray2.20A/B214-373[»]
2EAXX-ray2.10A/B/C214-373[»]
ProteinModelPortalQ96LB8.
SMRQ96LB8. Positions 56-187, 210-373.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING9606.ENSP00000352672.

PTM databases

PhosphoSiteQ96LB8.

Polymorphism databases

DMDM143811439.

Proteomic databases

PaxDbQ96LB8.
PRIDEQ96LB8.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000359650; ENSP00000352672; ENSG00000163218. [Q96LB8-1]
ENST00000368739; ENSP00000357728; ENSG00000163218. [Q96LB8-2]
GeneID57115.
KEGGhsa:57115.
UCSCuc001fbo.3. human. [Q96LB8-1]
uc001fbp.3. human. [Q96LB8-2]

Organism-specific databases

CTD57115.
GeneCardsGC01M153302.
H-InvDBHIX0028539.
HGNCHGNC:30015. PGLYRP4.
HPACAB025879.
MIM608198. gene.
neXtProtNX_Q96LB8.
PharmGKBPA134902492.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG241935.
HOVERGENHBG053579.
InParanoidQ96LB8.
KOK01446.
OMAHTAGRTC.
OrthoDBEOG757CZ5.
PhylomeDBQ96LB8.
TreeFamTF323898.

Gene expression databases

BgeeQ96LB8.
CleanExHS_PGLYRP4.
GenevestigatorQ96LB8.

Family and domain databases

Gene3D3.40.80.10. 2 hits.
InterProIPR002502. Amidase_domain.
IPR015510. PGRP.
IPR006619. PGRP_domain_met/bac.
[Graphical view]
PANTHERPTHR11022. PTHR11022. 1 hit.
PfamPF01510. Amidase_2. 2 hits.
[Graphical view]
SMARTSM00644. Ami_2. 2 hits.
SM00701. PGRP. 2 hits.
[Graphical view]
SUPFAMSSF55846. SSF55846. 2 hits.
ProtoNetSearch...

Other

EvolutionaryTraceQ96LB8.
GenomeRNAi57115.
NextBio62975.
PROQ96LB8.
SOURCESearch...

Entry information

Entry namePGRP4_HUMAN
AccessionPrimary (citable) accession number: Q96LB8
Secondary accession number(s): A8K838 expand/collapse secondary AC list , Q3B822, Q3B823, Q5SY63, Q5SY64, Q9HD75
Entry history
Integrated into UniProtKB/Swiss-Prot: November 28, 2003
Last sequence update: April 3, 2007
Last modified: July 9, 2014
This is version 109 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM