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1299  structures 1103  species 23  interactions 43284  sequences 621  architectures

Family: Arm (PF00514)

Summary: Armadillo/beta-catenin-like repeat

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 "Armadillo repeat". More...

Armadillo repeat Edit Wikipedia article

Armadillo repeat domain
PDB 3bct EBI.jpg
Structure of the 5armadillo domain of beta-catenin.[1]
Identifiers
Symbol Arm
Pfam PF00514
Pfam clan CL0020
InterPro IPR000225
SMART SM00185
PROSITE PS50176
SCOP 3bct
SUPERFAMILY 3bct
CDD cd00020

An armadillo repeat is the name of a characteristic, repetitive amino acid sequence of about 40 residues in length that is found in many proteins. Proteins that contain armadillo repeats typically contain several tandemly repeated copies.[2][3] Each armadillo repeat is composed of a pair of alpha helices that form a hairpin structure. Multiple copies of the repeat form what is known as an alpha solenoid structure.

Examples of proteins that contain armadillo repeats include β-catenin, α-importin,[4] plakoglobin,[5] adenomatous polyposis coli (APC),[6] and many others.

The term armadillo derives from the historical name of the β-catenin gene in the fruitfly Drosophila where the armadillo repeat was first discovered. Although β-catenin was previously believed to be a protein involved in linking cadherin cell adhesion proteins to the cytoskeleton, recent work indicates that β-catenin regulates the homodimerization of alpha-catenin, which in turn controls act branching and bundling [7]. But, the armadillo repeat is found in a wide range of proteins with other functions. This type of protein domain is important in transducing WNT signals during embryonic development.

Structure

The 3-dimensional fold of an armadillo repeat was first observed in the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit.[1] The cylindrical structure features a positively charged groove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.[8]

References

  1. ^ a b Huber AH, Nelson WJ, Weis WI (September 1997). "Three-dimensional structure of the armadillo repeat region of beta-catenin". Cell. 90 (5): 871–82. doi:10.1016/S0092-8674(00)80352-9. PMID 9298899. 
  2. ^ Peifer M, Berg S, Reynolds AB (1994). "A repeating amino acid motif shared by proteins with diverse cellular roles". Cell. 76 (5): 789–91. doi:10.1016/0092-8674(94)90353-0. PMID 7907279. 
  3. ^ Groves MR, Barford D (1999). "Topological characteristics of helical repeat proteins". Current Opinion in Structural Biology. 9 (3): 383–9. doi:10.1016/S0959-440X(99)80052-9. PMID 10361086. 
  4. ^ Herold A, Truant R, Wiegand H, Cullen BR (October 1998). "Determination of the functional domain organization of the importin alpha nuclear import factor". J. Cell Biol. 143 (2): 309–18. doi:10.1083/jcb.143.2.309. PMC 2132842Freely accessible. PMID 9786944. 
  5. ^ McCrea PD, Turck CW, Gumbiner B (November 1991). "A homolog of the armadillo protein in Drosophila (plakoglobin) associated with E-cadherin". Science. 254 (5036): 1359–61. doi:10.1126/science.1962194. PMID 1962194. 
  6. ^ Hirschl D, Bayer P, Müller O (March 1996). "Secondary structure of an armadillo single repeat from the APC protein". FEBS Lett. 383 (1-2): 31–6. doi:10.1016/0014-5793(96)00215-3. PMID 8612785. 
  7. ^ Nusse, Roel, and Hans Clevers. “Wnt/β-Catenin Signaling, Disease, and Emerging Therapeutic Modalities.” Cell, vol. 169, no. 6, 1 June 2017, pp. 985–999., doi:10.1016/j.cell.2017.05.016.
  8. ^ "Armadillo (IPR000225)". InterPro. EMBL-EBI. 

External links


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

This is the Wikipedia entry entitled "Armadillo repeats". More...

Armadillo repeats Edit Wikipedia article

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Armadillo/beta-catenin-like repeat Provide feedback

Approx. 40 amino acid repeat. Tandem repeats form super-helix of helices that is proposed to mediate interaction of beta-catenin with its ligands. CAUTION: This family does not contain all known armadillo repeats.

Literature references

  1. Huber AH, Nelson WJ, Weis WI; , Cell 1997;90:871-882.: Three-dimensional structure of the armadillo repeat region of beta-catenin. PUBMED:9298899 EPMC:9298899

  2. Gumbiner BM; , Curr Opin Cell Biol 1995;7:634-640.: Signal transduction of beta-catenin. PUBMED:8573337 EPMC:8573337

  3. Cavallo R, Rubenstein D, Peifer M; , Curr Opin Genet Dev 1997;7:459-466.: Armadillo and dTCF: a marriage made in the nucleus. PUBMED:9309175 EPMC:9309175

  4. Su LK, Vogelstein B, Kinzler KW; , Science 1993;262:1734-1737.: Association of the APC tumor suppressor protein with catenins. PUBMED:8259519 EPMC:8259519

  5. Rubinfeld B, Souza B, Albert I, Muller O, Chamberlain SH, Masiarz FR, Munemitsu S, Polakis P; , Science 1993;262:1731-1734.: Association of the APC gene product with beta-catenin. PUBMED:8259518 EPMC:8259518

  6. Peifer M, Wieschaus E; , Cell 1990;63:1167-1176.: The segment polarity gene armadillo encodes a functionally modular protein that is the Drosophila homolog of human plakoglobin. PUBMED:2261639 EPMC:2261639


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000225

The armadillo (Arm) repeat is an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila melanogaster segment polarity gene armadillo involved in signal transduction through wingless. Animal Arm-repeat proteins function in various processes, including intracellular signalling and cytoskeletal regulation, and include such proteins as beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumour suppressor protein, and the nuclear transport factor importin-alpha, amongst others [PUBMED:9770300]. A subset of these proteins is conserved across eukaryotic kingdoms. In higher plants, some Arm-repeat proteins function in intracellular signalling like their mammalian counterparts, while others have novel functions [PUBMED:12946625].

The 3-dimensional fold of an armadillo repeat is known from the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit [PUBMED:9298899]. The cylindrical structure features a positively charged grove, which presumably interacts with the acidic surfaces of the known interaction partners of beta-catenin.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 TPR (CL0020), which has the following description:

Tetratricopeptide-like repeats are found in a numerous and diverse proteins involved in such functions as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.

The clan contains the following 149 members:

Adaptin_N Alkyl_sulf_dimr ANAPC3 ANAPC5 ANAPC8 API5 Arm Arm_2 Arm_3 Atx10homo_assoc B56 BAF250_C BTAD CAS_CSE1 ChAPs CHIP_TPR_N CLASP_N Clathrin Clathrin-link Clathrin_H_link Clathrin_propel Cnd1 Cnd3 Coatomer_E Cohesin_HEAT Cohesin_load ComR_TPR COPI_C CPL CRM1_C Cse1 DHR-2 DNA_alkylation Drf_FH3 Drf_GBD DUF1822 DUF2019 DUF2225 DUF3385 DUF3458_C DUF3808 DUF3856 DUF4042 DUF924 EST1 EST1_DNA_bind FAT Fis1_TPR_C Fis1_TPR_N Foie-gras_1 GUN4_N HAT HEAT HEAT_2 HEAT_EZ HEAT_PBS HemY_N HrpB1_HrpK IBB IBN_N IFRD KAP Leuk-A4-hydro_C LRV LRV_FeS MA3 MIF4G MIF4G_like MIF4G_like_2 MMS19_C Mo25 MRP-S27 NARP1 Neurochondrin Nipped-B_C Nro1 NSF Paf67 ParcG PC_rep PHAT PI3Ka PknG_TPR PPP5 PPR PPR_1 PPR_2 PPR_3 PPR_long PPTA Proteasom_PSMB PUF Rab5-bind Rapsyn_N RIX1 RPM2 RPN7 Sel1 SHNi-TPR SNAP SPO22 SRP_TPR_like ST7 Suf SusD-like SusD-like_2 SusD-like_3 SusD_RagB SYCP2_ARLD TAF6_C TAL_effector TAtT Tcf25 TIP120 TOM20_plant TPR_1 TPR_10 TPR_11 TPR_12 TPR_14 TPR_15 TPR_16 TPR_17 TPR_18 TPR_19 TPR_2 TPR_20 TPR_21 TPR_3 TPR_4 TPR_5 TPR_6 TPR_7 TPR_8 TPR_9 TPR_MalT UNC45-central Upf2 V-ATPase_H_C V-ATPase_H_N Vac14_Fab1_bd Vitellogenin_N Vps39_1 W2 Wzy_C_2 Xpo1 YcaO_C YfiO Zmiz1_N

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(197)
Full
(43284)
Representative proteomes UniProt
(63821)
NCBI
(103021)
Meta
(312)
RP15
(9783)
RP35
(21469)
RP55
(33035)
RP75
(39498)
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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.

Format an alignment

  Seed
(197)
Full
(43284)
Representative proteomes UniProt
(63821)
NCBI
(103021)
Meta
(312)
RP15
(9783)
RP35
(21469)
RP55
(33035)
RP75
(39498)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(197)
Full
(43284)
Representative proteomes UniProt
(63821)
NCBI
(103021)
Meta
(312)
RP15
(9783)
RP35
(21469)
RP55
(33035)
RP75
(39498)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: SMART
Previous IDs: Armadillo_seg;
Type: Repeat
Sequence Ontology: SO:0001068
Author: Bateman A , Ponting CP , Schultz J, Bork P
Number in seed: 197
Number in full: 43284
Average length of the domain: 40.70 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 18.14 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.3
Trusted cut-off 20.6 20.3
Noise cut-off 20.5 20.2
Model length: 41
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 23 interactions for this family. More...

Hormone_recep Parathyroid CTNNB1_binding Nucleoplasmin Snurportin1 Cadherin_C IBB IBB BCL9 MHC_I ICAT zf-C4 NUP50 Ku_C Ig_3 APC_15aa Myc_N Cse1 Flu_PB2 Axin_b-cat_bind Nucleoplasmin APC_r Arm

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 Arm domain has been found. There are 1299 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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