Q96LB9 (PGRP3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Peptidoglycan recognition protein 3

Alternative name(s):
Peptidoglycan recognition protein I-alpha
Short name=PGLYRPIalpha
Short name=PGRP-I-alpha
Peptidoglycan recognition protein intermediate alpha

Gene names

Name:	PGLYRP3
Synonyms:	PGRPIA

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	341 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.4
Subunit structure	Monomer. Homodimer; disulfide-linked. Heterodimer with PGLYRP4; disulfide-linked. Ref.4 Ref.5
Subcellular location	Secreted Ref.4.
Tissue specificity	Detected in skin epidermis, eccrine sweat glands and ducts, ciliary body epithelial cells of the eye, in small intestine, colon, stomach and in mature epithelial cells of the tongue (at protein level). Highly expressed in skin and esophagus, expressed also in tonsils and thymus and to a much lesser extent in the stomach, descending colon, rectum and brain. Ref.1 Ref.4
Induction	Up-regulated by exposure to Gram-positive and Gram-negative bacteria. Ref.4
Post-translational modification	N-glycosylated. Ref.4
Sequence similarities	Belongs to the N-acetylmuramoyl-L-alanine amidase 2 family.

Ontologies

Keywords
Biological process	Immunity Innate immunity
Cellular component	Secreted
Coding sequence diversity	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.1PubMed 17502600. 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...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 17

17

Potential

Chain

18 – 341

324

Peptidoglycan recognition protein 3

PRO_0000023923

Regions

Region

264 – 269

6

Interaction with murein

Sites

Binding site

231

1

Murein

Binding site

235

1

Murein

Binding site

242

1

Murein

Amino acid modifications

Glycosylation

113

1

N-linked (GlcNAc...) Potential

Disulfide bond

178 ↔ 300

Disulfide bond

194 ↔ 238

Disulfide bond

214 ↔ 220

Natural variations

Natural variant

35

1

A → T.
Corresponds to variant rs55991125 [ dbSNP | Ensembl ].

VAR_061515

Natural variant

126

1

G → S. Ref.3
Corresponds to variant rs843971 [ dbSNP | Ensembl ].

VAR_024561

Secondary structure

1

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341

Helix Strand Turn

Details...

Helix

184 – 187

4

Beta strand

199 – 208

10

Helix

217 – 233

17

Beta strand

243 – 246

4

Beta strand

252 – 256

5

Beta strand

258 – 260

3

Beta strand

263 – 265

3

Turn

269 – 271

3

Beta strand

272 – 279

8

Beta strand

282 – 284

3

Helix

288 – 303

16

Beta strand

306 – 315

10

Helix

316 – 318

3

Beta strand

320 – 322

3

Helix

328 – 333

6

Turn

337 – 340

4

Sequences

	Sequence		Length	Mass (Da)
	Q96LB9 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: 8ADD5AA97B632076	FASTA	341	37,611
	10 20 30 40 50 60 MGTLPWLLAF FILGLQAWDT PTIVSRKEWG ARPLACRALL TLPVAYIITD QLPGMQCQQQ 70 80 90 100 110 120 SVCSQMLRGL QSHSVYTIGW CDVAYNFLVG DDGRVYEGVG WNIQGLHTQG YNNISLGIAF 130 140 150 160 170 180 FGNKIGSSPS PAALSAAEGL ISYAIQKGHL SPRYIQPLLL KEETCLDPQH PVMPRKVCPN 190 200 210 220 230 240 IIKRSAWEAR ETHCPKMNLP AKYVIIIHTA GTSCTVSTDC QTVVRNIQSF HMDTRNFCDI 250 260 270 280 290 300 GYHFLVGQDG GVYEGVGWHI QGSHTYGFND IALGIAFIGY FVEKPPNAAA LEAAQDLIQC 310 320 330 340 AVVEGYLTPN YLLMGHSDVV NILSPGQALY NIISTWPHFK H

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], TISSUE SPECIFICITY.
[2]	"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].
[3]	"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], VARIANT SER-126.
[4]	"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, SUBCELLULAR LOCATION, INDUCTION, TISSUE SPECIFICITY.
[5]	"Crystal structure of the C-terminal peptidoglycan-binding domain of human peptidoglycan recognition protein Ialpha." Guan R., Malchiodi E.L., Wang Q., Schuck P., Mariuzza R.A. J. Biol. Chem. 279:31873-31882(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 177-341, SUBUNIT.
[6]	"Structural basis for peptidoglycan binding by peptidoglycan recognition proteins." Guan R., Roychowdhury A., Ember B., Kumar S., Boons G.-J., Mariuzza R.A. Proc. Natl. Acad. Sci. U.S.A. 101:17168-17173(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 177-341 IN COMPLEX WITH MUREIN FRAGMENT.
[7]	"Crystal structure of human peptidoglycan recognition protein I alpha bound to a muramyl pentapeptide from Gram-positive bacteria." Guan R., Brown P.H., Swaminathan C.P., Roychowdhury A., Boons G.-J., Mariuzza R.A. Protein Sci. 15:1199-1206(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 177-341 IN COMPLEX WITH MUREIN FRAGMENT.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY035376 mRNA. Translation: AAK72484.1.
AL591704, AL161636 Genomic DNA. Translation: CAI19491.1.
AL161636, AL591704 Genomic DNA. Translation: CAI19556.1.
BC069741 mRNA. Translation: AAH69741.1.
BC069798 mRNA. Translation: AAH69798.1.
BC069801 mRNA. Translation: AAH69801.1.
BC128114 mRNA. Translation: AAI28115.1.
BC128115 mRNA. Translation: AAI28116.1.

IPI

IPI00064969.

RefSeq

NP_443123.1. NM_052891.1.

UniGene

Hs.348266.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SK3	X-ray	2.80	A	177-341	[»]
1SK4	X-ray	1.65	A	179-341	[»]
1TWQ	X-ray	2.30	A	177-341	[»]
2APH	X-ray	2.10	A/B	177-341	[»]

ProteinModelPortal

Q96LB9.

ModBase

Search...

Protein-protein interaction databases

STRING

9606.ENSP00000290722.

PTM databases

PhosphoSite

Q96LB9.

Polymorphism databases

DMDM

38604974.

Proteomic databases

PaxDb

Q96LB9.

PRIDE

Q96LB9.

Protocols and materials databases

DNASU

114771.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000290722; ENSP00000290722; ENSG00000159527.

GeneID

114771.

KEGG

hsa:114771.

UCSC

uc001fbn.1. human.

Organism-specific databases

CTD

114771.

GeneCards

GC01M153270.

HGNC

HGNC:30014. PGLYRP3.

HPA

HPA030369.

MIM

608197. gene.

neXtProt

NX_Q96LB9.

PharmGKB

PA134861692.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG5479.

HOGENOM

HOG000267017.

HOVERGEN

HBG053579.

InParanoid

Q96LB9.

KO

K01446.

OMA

VEKPPNA.

OrthoDB

EOG4DFPPK.

PhylomeDB

Q96LB9.

Gene expression databases

Bgee

Q96LB9.

CleanEx

HS_PGLYRP3.

Genevestigator

Q96LB9.

GermOnline

ENSG00000159527. 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

Q96LB9.

GenomeRNAi

114771.

NextBio

79145.

SOURCE

Search...

Entry information

Entry name

PGRP3_HUMAN

Accession

Primary (citable) accession number: Q96LB9
Secondary accession number(s): A1A4U8, Q5SY65

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 28, 2003
Last sequence update:	December 1, 2001
Last modified:	May 1, 2013
This is version 97 of the entry and version 1 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.