EBI Databases InterPro	Search Open in usermanual InterPro:
Jump to: InterProScan Databases Documentation FTP site Help Click on the icon for context sensitive help from the user manual. Advanced search

InterPro: IPR000601 PKD

Protein matches Help

UniProtKB

Matches:

2307 proteins

Overview:	sorted by AC,	sorted by name,	of known structure,	proteins with splice variants
Detailed:	sorted by AC,	sorted by name,	of known structure	proteins with splice variants
Table:	For all matching proteins,	of known structure
Architectures
Accession List
Matches in BioMart

Accession

IPR000601 PKD

Type

Domain

Signatures Help

Database	ID	Name	Proteins
Pfam	PF00801	PKD	1559
PROSITE profile	PS50093	PKD	1443
SMART	SM00089	PKD	2118
SuperFamily	SSF49299	PKD	1471
Signatures in BioMart

InterPro Relationships Help

Found in

IPR006228 Polycystin cation channel
IPR017323 Lysyl endopeptidase

InterPro annotation

Entry Details in BioMart

Abstract

The PKD domain was first identified in the Polycystic kidney disease protein, polycystin-1 (PDK1 gene), and contains an Ig-like fold consisting of a beta-sandwich of seven strands in two sheets with a Greek key topology, although some members have additional strands [1]. Polycystin-1 is a large cell-surface glycoprotein involved in adhesive protein-protein and protein-carbohydrate interactions; however it is not clear if the PKD domain mediates any of these interactions.

PKD domains are also found in other proteins, usually in the extracellular parts of proteins involved in interactions with other proteins. For example, domains with a PKD-type fold are found in archaeal surface layer proteins that protect the cell from extreme environments [2], and in the human VPS10 domain-containing receptor SorCS2 [3].

Structural links Help

PDB - click here

SCOP: b.1.18.2 , b.1.3.1 , c.1.8.5

CATH: 2.60.40.10 , 2.60.40.670 , 3.20.20.80

Database links Help

PROSITE doc: PDOC50093

PANDIT: PF00801

Blocks: IPB000601

Pfam Clan: CL0159.12

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR000601

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

O08852 Polycystin-1

O10363 Probable endochitinase

P07254 Chitinase A

P98161 Polycystin-1

Q06154 Melanocyte protein Pmel 17

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR013781	Glycoside hydrolase, subgroup, catalytic core
IPR013783	Immunoglobulin-like fold
IPR013122	Polycystin cation channel, PKD1/PKD2
IPR014756	Immunoglobulin E-set
IPR000483	Cysteine-rich flanking region, C-terminal domain
IPR001579	Glycoside hydrolase, chitinase active site
IPR000203	GPS domain
IPR001024	Lipoxygenase, LH2
IPR002889	Carbohydrate-binding WSC
IPR014010	Egg jelly receptor, REJ-like
IPR001304	C-type lectin
IPR008976	Lipase/lipooxygenase, PLAT/LH2
IPR001611	Leucine-rich repeat
IPR013540	Chitinase A N-terminal
IPR017853	Glycoside hydrolase, catalytic core
IPR013994	Carbohydrate-binding WSC, subgroup
IPR001223	Glycoside hydrolase, family 18, catalytic domain
IPR006228	Polycystin cation channel
IPR003591	Leucine-rich repeat, typical subtype
IPR016187	C-type lectin fold
IPR016186	C-type lectin-like
IPR000372	Leucine-rich repeat-containing N-terminal domain
IPR000434	Polycystic kidney disease type 1 protein
IPR011583	Chitinase II
IPR002859	PKD/REJ-like protein
IPR000601	PKD
	ModBase
	SWISS-MODEL
	PDB Chain
	CATH Domain
	SCOP Domain

Publications Open in usermanual
1.	Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C. The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease. EMBO J. 18 297-305 1999 [PubMed: 9889186] http://dx.doi.org/10.1093/emboj/18.2.297
2.	Jing H, Takagi J, Liu JH, Lindgren S, Zhang RG, Joachimiak A, Wang JH, Springer TA. Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins. Structure 10 1453-64 2002 [PubMed: 12377130] http://dx.doi.org/10.1016/S0969-2126(02)00840-7
3.	Hampe W, Rezgaoui M, Hermans-Borgmeyer I, Schaller HC. The genes for the human VPS10 domain-containing receptors are large and contain many small exons. Hum. Genet. 108 529-36 2001 [PubMed: 11499680] http://dx.doi.org/10.1007/s004390100504

Additional Reading Open in usermanual
	Aronson NN Jr, Halloran BA, Alexeyev MF, Zhou XE, Wang Y, Meehan EJ, Chen L. Mutation of a conserved tryptophan in the chitin-binding cleft of Serratia marcescens chitinase A enhances transglycosylation. Biosci. Biotechnol. Biochem. 70 2006 243-51 [PubMed: 16428843] http://dx.doi.org/10.1271/bbb.70.243
	Callebaut I, Gilges D, Vigon I, Mornon JP. HYR, an extracellular module involved in cellular adhesion and related to the immunoglobulin-like fold. Protein Sci. 9 2000 1382-90 [PubMed: 10933504] http://www.pubmedcentral.nih.gov/picrender.fcgi?tool=EBI&pubmedid=10933504&action=stream&blobtype=pdf
	Polycystic kidney disease: the complete structure of the PKD1 gene and its protein. The International Polycystic Kidney Disease Consortium. Cell 81 1995 289-98 [PubMed: 7736581]
	Hughes J, Ward CJ, Peral B, Aspinwall R, Clark K, San Millan JL, Gamble V, Harris PC. The polycystic kidney disease 1 (PKD1) gene encodes a novel protein with multiple cell recognition domains. Nat. Genet. 10 1995 151-60 [PubMed: 7663510]
	Papanikolau Y, Prag G, Tavlas G, Vorgias CE, Oppenheim AB, Petratos K. High resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis. Biochemistry 40 2001 11338-43 [PubMed: 11560481] http://dx.doi.org/10.1021/bi010505h
	Papanikolau Y, Tavlas G, Vorgias CE, Petratos K. De novo purification scheme and crystallization conditions yield high-resolution structures of chitinase A and its complex with the inhibitor allosamidin. Acta Crystallogr. D Biol. Crystallogr. 59 2003 400-3 [PubMed: 12554965] http://dx.doi.org/10.1107/S0907444902021923
	Aronson NN Jr, Halloran BA, Alexyev MF, Amable L, Madura JD, Pasupulati L, Worth C, Van Roey P. Family 18 chitinase-oligosaccharide substrate interaction: subsite preference and anomer selectivity of Serratia marcescens chitinase A. Biochem. J. 376 2003 87-95 [PubMed: 12932195] http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=12932195

InterPro 23.1