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2  structures 120  species 0  interactions 236  sequences 1  architecture

Family: Engrail_1_C_sig (PF10525)

Summary: Engrailed homeobox C-terminal signature domain

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This is the Wikipedia entry entitled "Engrailed homeobox protein". More...

Engrailed homeobox protein Edit Wikipedia article

Engrailed homeobox C-terminal signature domain
Identifiers
Symbol Engrail_1_C_sig
Pfam PF10525
InterPro IPR019549

In molecular biology, the engrailed homeobox proteins are a family of homeobox proteins which are characterised by the presence of a region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain. This region forms a signature pattern for this subfamily of proteins.[1]

References[edit]

  1. ^ Scott MP, Tamkun JW, Hartzell GW (July 1989). "The structure and function of the homeodomain". Biochim. Biophys. Acta 989 (1): 25–48. PMID 2568852. 

This article incorporates text from the public domain Pfam and InterPro IPR019549

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.

Engrailed homeobox C-terminal signature domain Provide feedback

Engrailed homeobox proteins are characterised by the presence of a conserved region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain. This domain of approximately 20 residues forms a kind of a signature pattern for this subfamily of proteins [1].

Literature references

  1. Scott MP, Tamkun JW, Hartzell GW 3rd; , Biochim Biophys Acta. 1989;989:25-48.: The structure and function of the homeodomain. PUBMED:2568852 EPMC:2568852


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019549

Homeodomain proteins are transcription factors that share a related DNA-binding homeodomain [PUBMED:10377888]. The homeodomain was initially identified in Drosophila melanogaster (Fruit fly) homeotic and segmentation proteins, but is well conserved throughout metazoans [PUBMED:2568852, PUBMED:1357790]. The homeodomain binds DNA through a helix-turn-helix (HTH) structure, consisting of approximately 20 residues [PUBMED:1970866]. The HTH motif is comprised of two alpha-helices that make intimate contacts with the DNA; the second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions. These interactions occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA. The first helix helps to stabilise the structure and is joined to the second through a short turn.

Most proteins which contain a homeobox domain can be classified [PUBMED:2568852, PUBMED:2884726], on the basis of their sequence characteristics, into three subfamilies, engrailed, antennapedia and paired. A number of different proteins contain homeodomains, including Drosophila engrailed, yeast mating type proteins, hepatocyte nuclear factor 1a and Hox proteins. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies [PUBMED:12445403]. The homeodomain motif is very similar in sequence identity and structure to domains in other DNA-binding proteins, including recombinases, GARP response regulators, human telomeric protein, AraC type transcriptional activator and tetracycline repressor [PUBMED:12215502, PUBMED:9739097, PUBMED:7707374].

This entry represents a conserved region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain and forms a kind of a signature pattern for this subfamily of proteins [PUBMED:2568852].

Domain organisation

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Alignments

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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.

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(23)
Full
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Representative proteomes NCBI
(226)
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RP35
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RP55
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RP75
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  Seed
(23)
Full
(236)
Representative proteomes NCBI
(226)
Meta
(0)
RP15
(27)
RP35
(36)
RP55
(68)
RP75
(106)
Alignment:
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  Seed
(23)
Full
(236)
Representative proteomes NCBI
(226)
Meta
(0)
RP15
(27)
RP35
(36)
RP55
(68)
RP75
(106)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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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.

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Curation and family details

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Curation View help on the curation process

Seed source: PROSITE_PS00033, Pfam-B_11539 (release 22.0)
Previous IDs: none
Type: Domain
Author: Finn R, Coggill P
Number in seed: 23
Number in full: 236
Average length of the domain: 30.00 aa
Average identity of full alignment: 64 %
Average coverage of the sequence by the domain: 10.64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.7 21.7
Trusted cut-off 22.5 21.7
Noise cut-off 19.9 21.6
Model length: 32
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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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 Engrail_1_C_sig domain has been found. There are 2 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 seqence.

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