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5  structures 183  species 1  interaction 10834  sequences 96  architectures

Family: AP2 (PF00847)

Summary: AP2 domain

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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]
Symbol AP2
Pfam PF00847
Pfam clan CL0081
InterPro IPR001471
SCOP 3gcc
Apetala 2
Symbol AP2
Entrez 829845
UniProt P47927
Not to be confused with AP2 adaptors.

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]


  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 1170874free to read. 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 1178005free to read. 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 148202free to read. PMID 9862967. 

External links

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 has the following description:

This clan contains proteins with a distinctive three stranded DNA-binding domain [1].

The clan contains the following 7 members:

AP2 DUF3596 Integrase_AP2 Integrase_DNA MBD MBDa Phage_integ_N


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Curation and family details

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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: 76
Number in full: 10834
Average length of the domain: 52.50 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 16.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 54
Family (HMM) version: 18
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Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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There is 1 interaction for this family. More...



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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