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14  structures 1883  species 0  interactions 20131  sequences 2229  architectures

Family: Kelch_4 (PF13418)

Summary: Galactose oxidase, central domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Kelch motif". More...

Kelch motif Edit Wikipedia article

Kelch motif
PDB 1gof EBI.jpg
Structure of Galactose oxidase containing kelch repeats.[1]
Identifiers
SymbolKelch_1
PfamPF01344
InterProIPR006652
SMARTKelch
SCOPe1gof / SUPFAM
OPM superfamily319
OPM protein3ii7
Kelch motif
Identifiers
SymbolKelch_2
PfamPF07646
Pfam clanCL0186
InterProIPR011498
SCOPe1gof / SUPFAM
Galactose oxidase, central domain
Identifiers
SymbolKelch_3
PfamPF13415
Pfam clanCL0186
Galactose oxidase, central domain
Identifiers
SymbolKelch_4
PfamPF13418
Pfam clanCL0186
Kelch motif
Identifiers
SymbolKelch_5
PfamPF13854
Pfam clanCL0186
Kelch motif
Identifiers
SymbolKelch_6
PfamPF13964
Pfam clanCL0186

The Kelch motif is a region of protein sequence found widely in proteins from bacteria and eukaryotes.[2] This sequence motif is composed of about 50 amino acid residues which form a structure of a four stranded beta-sheet "blade". This sequence motif is found in between five and eight tandem copies per protein which fold together to form a larger circular solenoid structure called a beta-propeller domain.

Proteins containing Kelch motifs

The Kelch motif is widely found in eukaryotic and bacterial species. Notably the human genome contains around 100 proteins containing the Kelch motif. Within individual proteins the motif occurs multiple times. For example, the motif appears 6 times in Drosophila egg-chamber regulatory protein. The motif is also found in mouse protein MIPP[3] and in a number of poxviruses. In addition, kelch repeats have been recognised in alpha- and beta-scruin,[4][5] in galactose oxidase from the fungus Dactylium dendroides[6][7] and in the Escherichia coli NanM protein, that is a sialic acid mutarotase.[8]

Structure

The structure of galactose oxidase reveals that the repeated Kelch sequence motif corresponds to a 4-stranded anti-parallel beta-sheet motif that forms the repeat unit in a super-barrel structural fold commonly known as a beta propeller.[9]

Function

The known functions of kelch-containing proteins are diverse:

  • scruin is an actin cross-linking protein;
  • galactose oxidase catalyses the oxidation of the hydroxyl group at the C6 position in D-galactose;
  • neuraminidase hydrolyses sialic acid residues from glycoproteins;
  • NanM is a sialic acid mutarotase, involved in efficient utilisation of sialic acid by bacteria;
  • kelch may have a cytoskeletal function, as it is localised to the actin-rich ring canals that connect the 15 nurse cells to the developing oocyte in Drosophila.[4]

See also

References

  1. ^ Ito N, Phillips SE, Stevens C, et al. (March 1991). "Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase". Nature. 350 (6313): 87–90. doi:10.1038/350087a0. PMID 2002850.
  2. ^ Adams J, Kelso R, Cooley L (January 2000). "The kelch repeat superfamily of proteins: propellers of cell function". Trends Cell Biol. 10 (1): 17–24. doi:10.1016/S0962-8924(99)01673-6. PMID 10603472.
  3. ^ Xue F, Cooley L (1993). "kelch encodes a component of intercellular bridges in Drosophila egg chambers". Cell. 72 (5): 681–693. doi:10.1016/0092-8674(93)90397-9. PMID 8453663.
  4. ^ a b Way M, Sanders M, Matsudaira P, Chafel M, Knight A, Tu YH (1995). "beta-Scruin, a homologue of the actin crosslinking protein scruin, is localized to the acrosomal vesicle of Limulus sperm". J. Cell Sci. 108: 3155–3162. PMID 7593276.
  5. ^ Way M, Sakai J, Sanders M, Garcia C, Matsudaira P (1995). "Sequence and domain organization of scruin, an actin-cross-linking protein in the acrosomal process of Limulus sperm". J. Cell Biol. 128 (1): 51–60. doi:10.1083/jcb.128.1.51. PMC 2120335. PMID 7822422.
  6. ^ Doolittle RF, Bork P (1994). "Drosophila kelch motif is derived from a common enzyme fold". J. Mol. Biol. 236 (5): 1277–1282. doi:10.1016/0022-2836(94)90056-6. PMID 8126718.
  7. ^ Keen JN, Ito N, Phillips SE, Stevens C, Ogel ZB, McPherson MJ, Yadav KD, Knowles PF (1991). "Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase". Nature. 350 (6313): 87–90. doi:10.1038/350087a0. PMID 2002850.
  8. ^ Severi E, Müller A, Potts JR, Leech A, Williamson D, Wilson KS, Thomas GH (2008). "Sialic acid mutarotation is catalyzed by the Escherichia coli beta-propeller protein YjhT". J. Biol. Chem. 283 (8): 4841–4849. doi:10.1074/jbc.m707822200. PMID 18063573.
  9. ^ Ito N, Phillips SE, Yadav KD, Knowles PF (1994). "Crystal structure of a free radical enzyme, galactose oxidase". J. Mol. Biol. 238 (5): 794–814. doi:10.1006/jmbi.1994.1335. PMID 8182749.

External links

This article incorporates text from the public domain Pfam and InterPro: IPR006652
This article incorporates text from the public domain Pfam and InterPro: IPR011498

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Galactose oxidase, central domain Provide feedback

No Pfam abstract.

Internal database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Beta_propeller (CL0186), which has the following description:

This large clan contains proteins that contain beta propellers. These are composed of between 6 and 8 repeats. The individual repeats are composed of a four stranded sheet. The clan includes families such as WD40 Pfam:PF00400 where the individual repeats are modeled. The clan also includes families where the entire propeller is modeled such as Pfam:PF02239 usually because the individual repeats are not discernible. These proteins carry out a very wide diversity of functions including catalysis.

The clan contains the following 88 members:

ANAPC4_WD40 APMAP_N Arylesterase Arylsulfotran_2 Arylsulfotrans B_lectin BBS2_Mid Beta_propel Coatomer_WDAD CPSF_A CyRPA Cytochrom_D1 Dpp_8_9_N DPPIV_N DPPIV_rep DUF1513 DUF1668 DUF2415 DUF3748 DUF4221 DUF4933 DUF4934 DUF5046 DUF5050 DUF5122 DUF5128 DUF5711 DUF839 eIF2A FG-GAP FG-GAP_2 FG-GAP_3 Frtz Ge1_WD40 Glu_cyclase_2 Gmad1 GSDH Hyd_WA IKI3 Itfg2 Kelch_1 Kelch_2 Kelch_3 Kelch_4 Kelch_5 Kelch_6 Lactonase Ldl_recept_b LGFP Lgl_C LVIVD Me-amine-dh_H MgpC MRJP Nbas_N Neisseria_PilC NHL nos_propeller nos_propeller_2 Nucleoporin_N Nup160 PALB2_WD40 PD40 Pectate_lyase22 Peptidase_S9_N PHTB1_N Phytase-like PQQ PQQ_2 PQQ_3 RAG2 RCC1 RCC1_2 Reg_prop SBBP SBP56 SdiA-regulated SGL Str_synth TcdB_toxin_midN Tectonin TolB_like VID27 WD40 WD40_2 WD40_3 WD40_4 WD40_like

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(51)
Full
(20131)
Representative proteomes UniProt
(42359)
RP15
(4750)
RP35
(10100)
RP55
(16993)
RP75
(22587)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

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  Seed
(51)
Full
(20131)
Representative proteomes UniProt
(42359)
RP15
(4750)
RP35
(10100)
RP55
(16993)
RP75
(22587)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(51)
Full
(20131)
Representative proteomes UniProt
(42359)
RP15
(4750)
RP35
(10100)
RP55
(16993)
RP75
(22587)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:B0SIN9
Previous IDs: none
Type: Repeat
Sequence Ontology: SO:0001068
Author: Coggill P
Number in seed: 51
Number in full: 20131
Average length of the domain: 50.90 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 9.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 19.9
Trusted cut-off 21.6 19.9
Noise cut-off 21.5 19.8
Model length: 49
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Structures

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 Kelch_4 domain has been found. There are 14 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.

Protein Predicted structure External Information
A0A0G2KAE3 View 3D Structure Click here
A0A0R0E973 View 3D Structure Click here
A0A0R0G990 View 3D Structure Click here
A0A0R0G990 View 3D Structure Click here
A0A0R0H385 View 3D Structure Click here
A0A0R0H3J2 View 3D Structure Click here
A0A0R0HHJ5 View 3D Structure Click here
A0A0R0IU53 View 3D Structure Click here
A0A0R4IHX2 View 3D Structure Click here
A0A1D6E7V3 View 3D Structure Click here
A0A1D6E802 View 3D Structure Click here
A0A1D6F6I1 View 3D Structure Click here
A0A1D6GDQ0 View 3D Structure Click here
A0A1D6GLG2 View 3D Structure Click here
A0A1D6GSB0 View 3D Structure Click here
A0A1D6GUE9 View 3D Structure Click here
A0A1D6H122 View 3D Structure Click here
A0A1D6H122 View 3D Structure Click here
A0A1D6HW85 View 3D Structure Click here
A0A1D6ICZ6 View 3D Structure Click here
A0A1D6IWK2 View 3D Structure Click here
A0A1D6IWK2 View 3D Structure Click here
A0A1D6IWK2 View 3D Structure Click here
A0A1D6IYY6 View 3D Structure Click here
A0A1D6IYY6 View 3D Structure Click here
A0A1D6KJ51 View 3D Structure Click here
A0A1D6LAM6 View 3D Structure Click here
A0A1D6LP15 View 3D Structure Click here
A0A1D6LYG2 View 3D Structure Click here
A0A1D6M667 View 3D Structure Click here
A0A1D6P2L3 View 3D Structure Click here
A0A1D6PPA8 View 3D Structure Click here
A0A1D6PPA8 View 3D Structure Click here
A0A1D6PWM4 View 3D Structure Click here
A0A1D6PWM4 View 3D Structure Click here
A0A1D8PMG6 View 3D Structure Click here
A0A1X7YHM0 View 3D Structure Click here
A0A6V7QYH4 View 3D Structure Click here
A1ZB86 View 3D Structure Click here
A4HWG2 View 3D Structure Click here
A4HWQ7 View 3D Structure Click here
A4HYL2 View 3D Structure Click here
A4I0N8 View 3D Structure Click here
A4I0T9 View 3D Structure Click here
A8WHX0 View 3D Structure Click here
B5DFI4 View 3D Structure Click here
B9MST0 View 3D Structure Click here
C0P665 View 3D Structure Click here
C0PGG9 View 3D Structure Click here
C0PLU8 View 3D Structure Click here
C0PLU8 View 3D Structure Click here
C0PLU8 View 3D Structure Click here
C4IZJ4 View 3D Structure Click here
C4IZJ4 View 3D Structure Click here
E7F538 View 3D Structure Click here
E7F6C7 View 3D Structure Click here
E7FFD1 View 3D Structure Click here
E7FFD1 View 3D Structure Click here
F1M3T8 View 3D Structure Click here
F1R533 View 3D Structure Click here
F1R533 View 3D Structure Click here
F4HTV1 View 3D Structure Click here
F4HTV1 View 3D Structure Click here
F4IMW3 View 3D Structure Click here
G5EC23 View 3D Structure Click here
G5EC23 View 3D Structure Click here
I1JFE9 View 3D Structure Click here
I1JR48 View 3D Structure Click here
I1JR48 View 3D Structure Click here
I1JWM9 View 3D Structure Click here
I1JWM9 View 3D Structure Click here
I1JWM9 View 3D Structure Click here
I1JWM9 View 3D Structure Click here
I1JXG3 View 3D Structure Click here
I1JXG3 View 3D Structure Click here
I1JZH1 View 3D Structure Click here
I1JZH1 View 3D Structure Click here
I1K5J7 View 3D Structure Click here
I1KD29 View 3D Structure Click here
I1KD29 View 3D Structure Click here
I1KGQ0 View 3D Structure Click here
I1KGQ0 View 3D Structure Click here
I1KN21 View 3D Structure Click here
I1KN21 View 3D Structure Click here
I1KNC8 View 3D Structure Click here
I1KNC8 View 3D Structure Click here
I1KQC3 View 3D Structure Click here
I1KU18 View 3D Structure Click here
I1KVQ2 View 3D Structure Click here
I1L1A1 View 3D Structure Click here
I1MGY9 View 3D Structure Click here
I1MLM5 View 3D Structure Click here
I1MRF7 View 3D Structure Click here
I1MRF7 View 3D Structure Click here
I1MRF7 View 3D Structure Click here
I1MSP6 View 3D Structure Click here
I1N7L8 View 3D Structure Click here
I1NBY7 View 3D Structure Click here
I1NJ06 View 3D Structure Click here
K7KGN3 View 3D Structure Click here
K7KVK9 View 3D Structure Click here
K7KVK9 View 3D Structure Click here
K7LGZ4 View 3D Structure Click here
K7LJG5 View 3D Structure Click here
K7M123 View 3D Structure Click here
K7M123 View 3D Structure Click here
K7MKJ2 View 3D Structure Click here
K7MKJ2 View 3D Structure Click here
K7N4D2 View 3D Structure Click here
O04316 View 3D Structure Click here
O49326 View 3D Structure Click here
P38853 View 3D Structure Click here
P39371 View 3D Structure Click here
P50090 View 3D Structure Click here
P50090 View 3D Structure Click here
Q0JC97 View 3D Structure Click here
Q0JC97 View 3D Structure Click here
Q0WWX4 View 3D Structure Click here
Q0WWX4 View 3D Structure Click here
Q10AZ7 View 3D Structure Click here
Q10AZ7 View 3D Structure Click here
Q10AZ7 View 3D Structure Click here
Q2QP85 View 3D Structure Click here
Q2QP85 View 3D Structure Click here
Q2R2W1 View 3D Structure Click here
Q32PP0 View 3D Structure Click here
Q3KRE6 View 3D Structure Click here
Q3KRE6 View 3D Structure Click here
Q4CSQ5 View 3D Structure Click here
Q4CSQ5 View 3D Structure Click here
Q4D2Y1 View 3D Structure Click here
Q4D7G9 View 3D Structure Click here
Q4DA29 View 3D Structure Click here
Q4DA29 View 3D Structure Click here
Q4DD21 View 3D Structure Click here
Q4DEW3 View 3D Structure Click here
Q4DEW3 View 3D Structure Click here
Q4DEW3 View 3D Structure Click here
Q4DI12 View 3D Structure Click here
Q4DI16 View 3D Structure Click here
Q4DIG9 View 3D Structure Click here
Q4DU84 View 3D Structure Click here
Q4DWR0 View 3D Structure Click here
Q4DY96 View 3D Structure Click here
Q4DY96 View 3D Structure Click here
Q4DY96 View 3D Structure Click here
Q4G5Y1 View 3D Structure Click here
Q4G5Y1 View 3D Structure Click here
Q54CD2 View 3D Structure Click here
Q54CD2 View 3D Structure Click here
Q54DR2 View 3D Structure Click here
Q54JW7 View 3D Structure Click here
Q54S48 View 3D Structure Click here
Q54TZ4 View 3D Structure Click here
Q54U90 View 3D Structure Click here
Q54U90 View 3D Structure Click here
Q54UX1 View 3D Structure Click here
Q54UX1 View 3D Structure Click here
Q54V91 View 3D Structure Click here
Q552M8 View 3D Structure Click here
Q552S8 View 3D Structure Click here
Q55A02 View 3D Structure Click here
Q55F00 View 3D Structure Click here
Q55F00 View 3D Structure Click here
Q55FH8 View 3D Structure Click here
Q5A931 View 3D Structure Click here
Q5U3Y0 View 3D Structure Click here
Q5VV63 View 3D Structure Click here
Q5Z8K3 View 3D Structure Click here
Q67UX0 View 3D Structure Click here
Q6A051 View 3D Structure Click here
Q6AYI2 View 3D Structure Click here
Q6GQN7 View 3D Structure Click here
Q6NUZ4 View 3D Structure Click here
Q6PAR0 View 3D Structure Click here
Q6PID8 View 3D Structure Click here
Q6Z1R8 View 3D Structure Click here
Q6Z1R8 View 3D Structure Click here
Q6ZK44 View 3D Structure Click here
Q6ZK44 View 3D Structure Click here
Q6ZXK6 View 3D Structure Click here
Q75LJ4 View 3D Structure Click here
Q7XSB4 View 3D Structure Click here
Q7ZUL3 View 3D Structure Click here
Q80YG3 View 3D Structure Click here
Q80YG3 View 3D Structure Click here
Q84VX7 View 3D Structure Click here
Q86AD8 View 3D Structure Click here
Q86J11 View 3D Structure Click here
Q86L99 View 3D Structure Click here
Q86L99 View 3D Structure Click here
Q8H4D4 View 3D Structure Click here
Q8I5Z1 View 3D Structure Click here
Q8IIA6 View 3D Structure Click here
Q8IIA6 View 3D Structure Click here
Q8IIA6 View 3D Structure Click here
Q8IIA7 View 3D Structure Click here
Q8IJH9 View 3D Structure Click here
Q8IJH9 View 3D Structure Click here
Q8IJL6 View 3D Structure Click here
Q8IKF6 View 3D Structure Click here
Q8IKH5 View 3D Structure Click here
Q8N653 View 3D Structure Click here
Q8N7A1 View 3D Structure Click here
Q8N7A1 View 3D Structure Click here
Q8T2A6 View 3D Structure Click here
Q8TBB5 View 3D Structure Click here
Q8VEM9 View 3D Structure Click here
Q8W420 View 3D Structure Click here
Q8W4K1 View 3D Structure Click here
Q8W4K1 View 3D Structure Click here
Q921I2 View 3D Structure Click here
Q945N1 View 3D Structure Click here
Q945N1 View 3D Structure Click here
Q94BT6 View 3D Structure Click here
Q94BT6 View 3D Structure Click here
Q94BT6 View 3D Structure Click here
Q94D04 View 3D Structure Click here
Q94D04 View 3D Structure Click here
Q9BQ90 View 3D Structure Click here
Q9C8K7 View 3D Structure Click here
Q9C8K7 View 3D Structure Click here
Q9C8K7 View 3D Structure Click here
Q9C9W9 View 3D Structure Click here
Q9CQ33 View 3D Structure Click here
Q9FZ82 View 3D Structure Click here
Q9FZ82 View 3D Structure Click here
Q9LK31 View 3D Structure Click here
Q9LR78 View 3D Structure Click here
Q9LZ83 View 3D Structure Click here
Q9LZ83 View 3D Structure Click here
Q9S7W4 View 3D Structure Click here
Q9SHS7 View 3D Structure Click here
Q9SJF0 View 3D Structure Click here
Q9VTZ7 View 3D Structure Click here
Q9VTZ7 View 3D Structure Click here
Q9VTZ7 View 3D Structure Click here
Q9Y2U9 View 3D Structure Click here
Q9Y2U9 View 3D Structure Click here