Q96LB8 (PGRP4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	373 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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. Hetrodimer 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 process	Immunity Innate immunity
Cellular component	Secreted
Coding sequence diversity	Alternative splicing Polymorphism
Domain	Signal
Molecular function	Antibiotic Antimicrobial
PTM	Disulfide bond Glycoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	defense 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: Compara innate immune response Non-traceable author statement Ref.1. Source: UniProtKB negative regulation of interferon-gamma production Inferred from electronic annotation. Source: Compara negative regulation of natural killer cell differentiation involved in immune response Inferred from electronic annotation. Source: Compara peptidoglycan catabolic process Inferred from electronic annotation. Source: InterPro
Cellular_component	extracellular 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_function	N-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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 17

17

Potential

Chain

18 – 373

356

Peptidoglycan recognition protein 4

PRO_0000023924

Regions

Region

293 – 302

10

Interaction with murein

Region

353 – 354

2

Interaction with murein

Sites

Binding site

263

1

Murein

Binding site

274

1

Murein

Amino acid modifications

Glycosylation

22

1

N-linked (GlcNAc...) Potential

Glycosylation

39

1

N-linked (GlcNAc...) Potential

Glycosylation

109

1

N-linked (GlcNAc...) Potential

Glycosylation

145

1

N-linked (GlcNAc...) Potential

Glycosylation

247

1

N-linked (GlcNAc...) Potential

Disulfide bond

210 ↔ 332

Ref.7

Disulfide bond

226 ↔ 270

Ref.7

Disulfide bond

246 ↔ 252

Ref.7

Natural variations

Alternative sequence

47 – 50

4

Missing in isoform 2.

VSP_024388

Natural variant

3

1

P → L. Ref.2 Ref.5
Corresponds to variant rs12096209 [ dbSNP | Ensembl ].

VAR_050503

Natural variant

13

1

I → L. Ref.1 Ref.3 Ref.5
Corresponds to variant rs3006458 [ dbSNP | Ensembl ].

VAR_033283

Natural variant

92

1

Q → R.
Corresponds to variant rs3006453 [ dbSNP | Ensembl ].

VAR_031586

Natural variant

192

1

G → V. Ref.1 Ref.3 Ref.5
Corresponds to variant rs3006448 [ dbSNP | Ensembl ].

VAR_031587

Natural variant

213

1

V → I. Ref.2 Ref.5
Corresponds to variant rs12063091 [ dbSNP | Ensembl ].

VAR_031588

Natural variant

301

1

D → N.
Corresponds to variant rs35347202 [ dbSNP | Ensembl ].

VAR_031589

Secondary structure

1

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373

Helix Strand Turn

Details...

Beta strand

212 – 214

3

Helix

216 – 219

4

Beta strand

231 – 240

10

Helix

249 – 265

17

Beta strand

275 – 278

4

Beta strand

284 – 288

5

Beta strand

290 – 292

3

Turn

298 – 300

3

Helix

301 – 303

3

Beta strand

304 – 311

8

Beta strand

314 – 316

3

Helix

320 – 335

16

Beta strand

338 – 347

10

Helix

348 – 351

4

Beta strand

352 – 354

3

Helix

359 – 365

7

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified April 3, 2007. Version 2. Checksum: 8E882E1FF608F6F3	FASTA	373	40,620
	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
	Isoform 2 [UniParc]. Checksum: 1D03920B70BDE735	FASTA	369	40,252
	10 20 30 40 50 60 MLPWLLVFSA LGIQAWGDSS WNKTQAKQVS EGLQYLFENI SQLTEKDVST TVSRKAWGAE 70 80 90 100 110 120 AVGCSIQLTT PVNVLVIHHV PGLECHDQTV CSQRLRELQA HHVHNNSGCD VAYNFLVGDD 130 140 150 160 170 180 GRVYEGVGWN IQGVHTQGYN NISLGFAFFG TKKGHSPSPA ALSAMENLIT YAVQKGHLSS 190 200 210 220 230 240 SYVQPLLGKG ENCLAPRQKT SLKKACPGVV PRSVWGARET HCPRMTLPAK YGIIIHTAGR 250 260 270 280 290 300 TCNISDECRL LVRDIQSFYI DRLKSCDIGY NFLVGQDGAI YEGVGWNVQG SSTPGYDDIA 310 320 330 340 350 360 LGITFMGTFT GIPPNAAALE AAQDLIQCAM VKGYLTPNYL LVGHSDVART LSPGQALYNI ISTWPHFKH

References

	« Hide 'large scale' referencesShow '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. , 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. , 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.

IPI

IPI00307125.
IPI00479339.

RefSeq

NP_065126.2. NM_020393.2.

UniGene

Hs.58356.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2EAV	X-ray	2.20	A/B	209-373	[»]
2EAX	X-ray	2.10	A/B/C	210-373	[»]

ProteinModelPortal

Q96LB8.

ModBase

Search...

Protein-protein interaction databases

STRING

9606.ENSP00000352672.

PTM databases

PhosphoSite

Q96LB8.

Polymorphism databases

DMDM

143811439.

Proteomic databases

PaxDb

Q96LB8.

PRIDE

Q96LB8.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000359650; ENSP00000352672; ENSG00000163218.
ENST00000368739; ENSP00000357728; ENSG00000163218.

GeneID

57115.

KEGG

hsa:57115.

UCSC

uc001fbo.3. human.
uc001fbp.3. human.

Organism-specific databases

CTD

57115.

GeneCards

GC01M153302.

H-InvDB

HIX0028539.

HGNC

HGNC:30015. PGLYRP4.

HPA

CAB025879.

MIM

608198. gene.

neXtProt

NX_Q96LB8.

PharmGKB

PA134902492.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG241935.

HOVERGEN

HBG053579.

InParanoid

Q96LB8.

KO

K01446.

OMA

RETHCPR.

PhylomeDB

Q96LB8.

Gene expression databases

Bgee

Q96LB8.

CleanEx

HS_PGLYRP4.

Genevestigator

Q96LB8.

GermOnline

ENSG00000163218. Homo sapiens.

Family and domain databases

Gene3D

3.40.80.10. 2 hits.

InterPro

IPR002502. Amidase_domain.
IPR015510. PGRP.
IPR006619. PGRP_domain_met/bac.
[Graphical view]

PANTHER

PTHR11022. PTHR11022. 1 hit.

Pfam

PF01510. Amidase_2. 2 hits.
[Graphical view]

SMART

SM00644. Ami_2. 2 hits.
SM00701. PGRP. 2 hits.
[Graphical view]

SUPFAM

SSF55846. Amidase_2. 2 hits.

ProtoNet

Search...

Other

EvolutionaryTrace

Q96LB8.

GenomeRNAi

57115.

NextBio

62975.

SOURCE

Search...

Entry information

Entry name

PGRP4_HUMAN

Accession

Primary (citable) accession number: Q96LB8
Secondary accession number(s): A8K838 , Q3B822, Q3B823, Q5SY63, Q5SY64, Q9HD75

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 28, 2003
Last sequence update:	April 3, 2007
Last modified:	May 1, 2013
This is version 99 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.