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5  structures 728  species 0  interactions 5868  sequences 52  architectures

Family: AP2 (PF00847)

Summary: AP2 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 "Apetala 2". More...

Apetala 2 Edit Wikipedia article

AP2 domain
PDB 3gcc EBI.jpg
Structure of the GCC-box binding domain in complex with DNA.[1]
Identifiers
Symbol AP2
Pfam PF00847
Pfam clan CL0081
InterPro IPR001471
SMART SM00380
PROSITE PS51032
SCOP 3gcc
SUPERFAMILY 3gcc
Apetala 2
Identifiers
Symbol AP2
Entrez 829845
UniProt P47927

Apetala 2 (AP2) is a gene coding for a member of a large family of transcription factors, the AP2/EREBP family. In Arabidopsis thaliana which plays a role in the ABC model of flower development.[2] It was originally thought that this family of proteins was plant-specific, however recent studies have shown that apicomplexans, including the causative agent of malaria, Plasmodium falciparum encode a related set of transcription factors, called the ApiAP2 family.[3]

In the A. thaliana transcription factor RAV1 the N-terminal AP2 domain binds 5'-CAACA-3' sequence, while the C-terminal highly conserved B3 domain binds 5'-CACCTG-3' sequence.[4]

References[edit]

  1. ^ Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M (September 1998). "A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA". EMBO J. 17 (18): 5484–96. doi:10.1093/emboj/17.18.5484. PMC 1170874. PMID 9736626. 
  2. ^ Riechmann JL, Meyerowitz EM (1998). "The AP2/EREBP family of plant transcription factors". Biol. Chem. 379 (6): 633–46. doi:10.1515/bchm.1998.379.6.633. PMID 9687012. 
  3. ^ Balaji S, Babu MM, Iyer LM, Aravind L (2005). "Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains". Nucleic Acids Research 33 (13): 3994–4006. doi:10.1093/nar/gki709. PMC 1178005. PMID 16040597. 
  4. ^ Kagaya Y, Ohmiya K, Hattori T (1999). "RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants". Nucleic Acids Res. 27 (2): 470–8. doi:10.1093/nar/27.2.470. PMC 148202. PMID 9862967. 

External links[edit]

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 "Ethylene-responsive element binding protein". More...

Ethylene-responsive element binding protein Edit Wikipedia article

Ethylene-responsive element binding protein
1GCC.png
NMR structure of the GCC-BOX binding domain of EREBP (green) complexed with DNA (brown) based on the PDB 1GCC coordinates.
Identifiers
Symbol EREBP
Entrez 827464
UniProt O80337
AP2 domain
PDB 3gcc EBI.jpg
Structure of the GCC-box binding domain.[1]
Identifiers
Symbol AP2
Pfam PF00847
Pfam clan CL0081
InterPro IPR001471
SMART SM00380
PROSITE PS51032
SCOP 3gcc
SUPERFAMILY 3gcc

Ethylene-responsive element binding protein (EREBP) is a homeobox gene from Arabidopsis thaliana and other plants which encodes a transcription factor.[2] EREBP is responsible in part for mediating the response in plants to the plant hormone ethylene.[3][4]

References[edit]

  1. ^ Allen MD, Yamasaki K, Ohme-Takagi M, Tateno M, Suzuki M (September 1998). "A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA". EMBO J. 17 (18): 5484–96. doi:10.1093/emboj/17.18.5484. PMC 1170874. PMID 9736626. 
  2. ^ Riechmann JL, Meyerowitz EM (June 1998). "The AP2/EREBP family of plant transcription factors". Biol. Chem. 379 (6): 633–46. doi:10.1515/bchm.1998.379.6.633. PMID 9687012. 
  3. ^ Ohme-Takagi M, Shinshi H (February 1995). "Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element". Plant Cell 7 (2): 173–82. doi:10.1105/tpc.7.2.173. PMC 160773. PMID 7756828. 
  4. ^ Büttner M, Singh KB (May 1997). "Arabidopsis thaliana ethylene-responsive element binding protein (AtEBP), an ethylene-inducible, GCC box DNA-binding protein interacts with an ocs element binding protein". Proc. Natl. Acad. Sci. U.S.A. 94 (11): 5961–6. doi:10.1073/pnas.94.11.5961. PMC 20889. PMID 9159183. 

External links[edit]

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.

AP2 domain Provide feedback

This 60 amino acid residue domain can bind to DNA [2] and is found in transcription factor proteins.

Literature references

  1. Jofuku KD, den Boer BG, Van Montagu M, Okamuro JK; , Plant Cell. 1994;6:1211-1225.: Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. PUBMED:7919989 EPMC:7919989

  2. Ohme-takagi M, Shinshi H; , Plant Cell 1995;7:173-182.: Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. PUBMED:7756828 EPMC:7756828

  3. Weigel D; , Plant Cell 1995;7:388-389.: The APETALA2 domain is related to a novel type of DNA binding domain. PUBMED:7773013 EPMC:7773013

  4. Balaji S, Babu MM, Iyer LM, Aravind L; , Nucleic Acids Res. 2005;33:3994-4006.: Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. PUBMED:16040597 EPMC:16040597

  5. Okamuro JK, Caster B, Villarroel R, Van Montagu M, Jofuku KD; , Proc Natl Acad Sci U S A. 1997;94:7076-7081.: The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. PUBMED:9192694 EPMC:9192694


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001471

Ethylene is an endogenous plant hormone that influences many aspects of plant growth and development. Some defense related genes that are induced by ethylene contain a cis-regulatory element known as the Ethylene- Responsive Element (ERE) [PUBMED:2535512]. Sequence analysis on various ERE regions has identified a short motif rich in G/C nucleotides, the GCC-box, essential for the response to ethylene. This short motif is recognised by a family of transcrition factors, the ERE binding factors (ERF) [PUBMED:10715325].

ERF proteins contain a domain of around 60 amino acids which is also found in the APETALA2 (AP2) protein [PUBMED:7773013]. This AP2/ERF domain has been shown in various proteins to be necessary and sufficient to bind the GCC-box [PUBMED:9756931].

The structure of the AP2/ERF domain in complex with the target DNA has been solved [PUBMED:9736626]. The structure resembles that of bacteriophage integrases and the methyl-CpG-binding domain (MBD): a three-stranded beta-sheet and an alpha helix almost parallel to the beta-sheet. It contacts DNA via Arg and Trp residues located in the beta- sheet.

Some proteins known to contain an AP2/ERF domain include:

  • Arabidopsis thaliana ERF1 to 6.
  • Tobacco ethylene-responsive element-binding proteins (EREBPs), homologues of ERF proteins.
  • Arabidopsis thaliana AP2 protein. It regulates meristeme identity, floral organ specification and seed coat development.
  • Arabidopsis thaliana C-repeat/dehydration-responsive element (DRE) binding factor 1 (CBF1 or DREB1) and DREB2. They bind a GCC-box-like element found in dehydratation responsive element. Binding to this element mediates cold-inducible transcription.
  • Arabidopsis thaliana and maize abscisic acid (ABA)-insensitive 4 (ABI4) proteins. They bind to a GCC-box-like element found in ABA-responsive genes.
  • Octadecanoid-derivative responsive catharenthus AP2-domain (ORCA2) protein. It binds a GCC-box-like element in the jasmonate responsive element of Str promoter.
  • Tomato Pto-interacting proteins 4 to 6 (Pti4 to Pti6). Pti5 and 6 bind a GCC-box-like element in regulatory regions of various pathogenesis-related (PR) genes.
  • Trichodesmium erythraeum, Tetrahymena thermophila, Enterobacteria phage RB49 and bacteriophage Felix 01 HNH endonucleases. HNH endonucleases are homing endonucleases that move extensively via lateral gene transfer [PUBMED:15319480].

This entry represents the AP2/ERF domain.

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 MBD-like (CL0081), which contains the following 6 members:

AP2 DUF3596 Integrase_AP2 Integrase_DNA MBD Phage_integ_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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(206)
Full
(5868)
Representative proteomes NCBI
(5799)
Meta
(189)
RP15
(596)
RP35
(1740)
RP55
(2384)
RP75
(2816)
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Format an alignment

  Seed
(206)
Full
(5868)
Representative proteomes NCBI
(5799)
Meta
(189)
RP15
(596)
RP35
(1740)
RP55
(2384)
RP75
(2816)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(206)
Full
(5868)
Representative proteomes NCBI
(5799)
Meta
(189)
RP15
(596)
RP35
(1740)
RP55
(2384)
RP75
(2816)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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:

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: Pfam-B_409 (release 3.0)
Previous IDs: AP2-domain;
Type: Domain
Author: Bateman A
Number in seed: 206
Number in full: 5868
Average length of the domain: 52.10 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 17.05 %

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 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 56
Family (HMM) version: 15
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 AP2 domain has been found. There are 5 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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