Summary: PKD domain
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PKD domain Edit Wikipedia article
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PKD (Polycystic Kidney Disease) domain was first identified in the polycystic kidney disease protein, polycystin-1 (PKD1 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. 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, and in the human receptor SorCS2.
Human proteins containing this domain
- Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C (1999). "The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease". EMBO J. 18 (2): 297–305. PMC . PMID 9889186. doi:10.1093/emboj/18.2.297.
- Joachimiak A, Springer TA, Zhang RG, Wang JH, Liu JH, Jing H, Takagi J, Lindgren S (2002). "Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins". Structure. 10 (10): 1453–1464. PMID 12377130. doi:10.1016/S0969-2126(02)00840-7.
- Hermans-Borgmeyer I, Hampe W, Schaller HC, Rezgaoui M (2001). "The genes for the human VPS10 domain-containing receptors are large and contain many small exons". Hum. Genet. 108 (6): 529–36. PMID 11499680. doi:10.1007/s004390100504.
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PKD domain Provide feedback
This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold .
Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C; , EMBO J 1999;18:297-305.: The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease. PUBMED:9889186 EPMC:9889186
Internal database links
|SCOOP:||Big_9 DUF5011 Ig_7 InlK_D3 PKD_3 PKD_4 PKD_6 REJ Y_Y_Y|
|Similarity to PfamA using HHSearch:||PKD_3 PKD_4|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000601
The polycystic kidney disease (PKD) domain is an 80-90 amino acid module originally found in 16 copies in the extracellular segment of polycystin-1, a large cell surface glycoprotein. Polycystin-1 is encoded by the PKD1 gene, which is mutated in autosomal dominant polycystic kidney disease (ADPKD). Although its function is unknown, it may be involved in protein-protein and protein-carbohydrate interactions based on its predicted domain structure. One or more copies of the PKD domain are also found in several other extracellular proteins from higher organisms, eubacteria, and archaebacteria. Singles copies of the PKD domain are found in the melanocytes heavily glycosylated cell-surface proteins Pmel 17, MMP and Nmp. Some bacterial collagenases and proteases also contain a single PKD domain adjacent to their catalytic domains, whereas four copies are present in the heavily glycosylated surface layer protein of archaebacteria [ PUBMED:7663510 ]. The PKD modules are often observed, within a same protein sequence, in association with FnIII domains [ PUBMED:10933504 ].
The most conserved motif is the WDFGDGS sequence that is found in the central part of many PKD domains and could play a structural role [ PUBMED:7663510 , PUBMED:9889186 ]. Determination of the solution structure of the first PKD domain from human polycystin-1 has shown that the module is built from two beta-sheet, one of three strands and one of four strands, which are packed face-to-face [ PUBMED:9889186 ].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This clan includes a diverse range of domains that have an Ig-like fold and appear to be distantly related to each other. The clan includes: PKD domains, cadherins and several families of bacterial Ig-like domains as well as viral tail fibre proteins. it also includes several Fibronectin type III domain-containing families.
The clan contains the following 257 members:A2M A2M_BRD A2M_recep AA9 Adeno_GP19K AlcCBM31 Alpha-amylase_N Alpha_adaptinC2 Alpha_E2_glycop Anth_Ig aRib Arylsulfotran_N ASF1_hist_chap ATG19 BACON BACON_2 BatD BIg21 Big_1 Big_10 Big_11 Big_12 Big_13 Big_14 Big_15 Big_2 Big_3 Big_3_2 Big_3_3 Big_3_4 Big_3_5 Big_4 Big_5 Big_6 Big_7 Big_8 Big_9 Bile_Hydr_Trans BiPBP_C bMG1 bMG10 bMG3 bMG5 bMG6 BslA BsuPI Cadherin Cadherin-like Cadherin_2 Cadherin_3 Cadherin_4 Cadherin_5 Cadherin_pro CagX Calx-beta Candida_ALS_N CARDB CBM39 CBM_X2 CD45 CelD_N Ceramidse_alk_C CHB_HEX_C CHB_HEX_C_1 ChitinaseA_N ChiW_Ig_like Chlam_OMP6 CHU_C Coatamer_beta_C COP-gamma_platf CopC CshA_repeat Cyc-maltodext_N Cytomega_US3 DBB DsbC DUF11 DUF1410 DUF1425 DUF2271 DUF3244 DUF3458 DUF3501 DUF3823_C DUF3859 DUF4165 DUF4179 DUF4426 DUF4469 DUF4625 DUF4784_N DUF4879 DUF4959 DUF4982 DUF4998 DUF5001 DUF5008 DUF5011 DUF5060 DUF5065 DUF5103 DUF5115 DUF525 DUF5643 DUF6383 DUF6595 DUF916 EB_dh ECD Enterochelin_N EpoR_lig-bind ERAP1_C EstA_Ig_like Expansin_C Filamin FixG_C Flavi_glycop_C FlgD_ig fn3 Fn3-like fn3_2 fn3_4 fn3_5 fn3_6 FN3_7 Fn3_assoc fn3_PAP GBS_Bsp-like GlgE_dom_N_S Glucodextran_B Glyco_hydro2_C5 Glyco_hydro_2 Gmad2 GMP_PDE_delta GO-like_E_set GspA_SrpA_N Hanta_G1 He_PIG HECW_N HemeBinding_Shp Hemocyanin_C Herpes_BLLF1 HYR IalB IFNGR1 Ig_GlcNase Ig_mannosidase IL12p40_C Il13Ra_Ig IL17R_fnIII_D1 IL17R_fnIII_D2 IL2RB_N1 IL3Ra_N IL4Ra_N IL6Ra-bind Inhibitor_I42 Inhibitor_I71 InlK_D3 Integrin_alpha2 Interfer-bind Invasin_D3 IRK_C IrmA Iron_transport Kre9_KNH LacZ_4 LEA_2 Lep_receptor_Ig LIFR_D2 LIFR_N Lipase_bact_N LodA_N LPMO_10 LRR_adjacent LTD MALT1_Ig Mannosidase_ig MetallophosC MG1 MG2 MG3 MG4 Mo-co_dimer N_BRCA1_IG Na_K-ATPase NAR2 NDNF NDNF_C NEAT Neocarzinostat Neurexophilin NPCBM_assoc Omp28 PapD_C PBP-Tp47_c Peptidase_C25_C Phlebo_G2_C PhoD_N PKD PKD_2 PKD_3 PKD_4 PKD_5 PKD_6 Por_Secre_tail Pox_vIL-18BP Psg1 PTP_tm Pullulanase_N2 Pur_ac_phosph_N Qn_am_d_aIII Qn_am_d_aIV RabGGT_insert Reeler REJ RET_CLD1 RET_CLD3 RET_CLD4 RGI_lyase RHD_dimer Rho_GDI Rib RibLong SCAB-Ig SKICH SLAM SoxZ SprB SusE SVA SWM_repeat T2SS-T3SS_pil_N Tafi-CsgC TarS_C1 TcA_RBD TcfC TIG TIG_2 TIG_plexin TIG_SUH Tissue_fac Top6b_C TPPII TQ Transglut_C Transglut_N TRAP_beta TraQ_transposon UL16 Velvet WIF Wzt_C Y_Y_Y YBD YscW ZirS_C Zona_pellucida
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Number in seed:||42|
|Number in full:||8597|
|Average length of the domain:||71.80 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||11.69 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||23|
|Download:||download the raw HMM for this family|
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How the sunburst is generated
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PKD domain has been found. There are 7 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.