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5  structures 183  species 1  interaction 10834  sequences 96  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

Not to be confused with AP2 adaptors.
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]

Structure and Biological Content of AP2

Through recent studies, Apetala 2 is found to have a major role in hormone regulation,specific in flowers and plants, such as the AGAMOUS.[5] The study that determined this, done by Ogawa, was created to clarify the relationship between Apetala 2 and AtEBP in gene expression. The results showed that over-expression of AtEBP caused upregulation of AP2 expression in leaves which suggested that the N-terminal region is not required to produce AP2-like phenotypes.[6] AP2 also makes up another compound called ANT, which is composed of two AP2 domains homologous with the DNA binding domain of ethylene response element binding proteins.[7] Another study by Maes, T. titled Petunia Ap2-like genes and their role in flower and seed development, discovered three AP2-like proteins from petunia and by studying their expression patterns in situ hybridization: PhAP2A, PhAP2B, and PhAP2C. PhAP2A was found to have extremely similar functions of AP2 in A. thaliana and has an almost exact gene sequence. PhAP2B and PhAP2C encode for AP2-like proteins that belong to a different subgroup of the AP2 family of transcription factors and exhibit very different expression patterns during flower development compared to PhAP2A.[8]

Associations of AP2 with Chemical Compounds

Apetala 2 mutations cause changes in the ratio of hexose to sucrose during seed development, opening the possibility that AP2 may control seed mass through its effects on sugar metabolism.[9] As a protein, it regulates the amount of sugars in the system and is involved in transportation, shaping, and signaling. Another study showed that analyzed the functionality of DBF1 in abiotic stress responses and found that Arabidopsis plants over-expressing DBF1 were more tolerant to osmotic stress than control plants.[10] DBF1 is the binding factor that is found in the helping Apetala 2 carry out transcription factors.

Diseases

DNA is constantly subject to mutations, which can cause a complete shift in function of the protein due to the malformed protein, causing diseases in some cases. In an AP2 study for instance, an ERF/AP2-type transcription factor was isolated by differential-display reverse transcription-PCR, which induced a hypersensitive response in the leaves.[11] The Arabidopsis CBF gene family is composed of three genes encoding AP2domain-containing proteins, which are all regulated by low temperature to be able to carry out gene expression, but not by abscisic acid or dehydration.[12]

References

  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 1170874Freely accessible. 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 1178005Freely accessible. 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 148202Freely accessible. PMID 9862967. 
  5. ^ Mutual Regulation of Arabidopsis thaliana Ethylene-responsive Element Binding Protein and a Plant Floral Homeotic Gene, APETALA2. Ogawa, T., Uchimiya, H., Kawai-Yamada, M. Ann. Bot. (2007)
  6. ^ Functional domains of the floral regulator AGAMOUS: characterization of the DNA binding domain and analysis of dominant negative mutations. Mizukami, Y., Huang, H., Tudor, M., Hu, Y., Ma, H. Plant Cell (1996)
  7. ^ The AINTEGUMENTA gene of Arabidopsis required for ovule and female gametophyte development is related to the floral homeotic gene APETALA2. Klucher, K.M., Chow, H., Reiser, L., Fischer, R.L. Plant Cell (1996)
  8. ^ Petunia Ap2-like genes and their role in flower and seed development. Maes, T., Van de Steene, N., Zethof, J., Karimi, M., D'Hauw, M., Mares, G., Van Montagu, M., Gerats, T. Plant Cell (2001)
  9. ^ Control of seed mass by APETALA2. Ohto, M.A., Fischer, R.L., Goldberg, R.B., Nakamura, K., Harada, J.J. Proc. Natl. Acad. Sci. U.S.A. (2005)
  10. ^ Maize DBF1-interactor protein 1 containing an R3H domain is a potential regulator of DBF1 activity in stress responses. Saleh, A., Lumbreras, V., Lopez, C., Kizis, E.D., Pagès, M. Plant J. (2006)
  11. ^ The pepper transcription factor CaPF1 confers pathogen and freezing tolerance in Arabidopsis. Yi, S.Y., Kim, J.H., Joung, Y.H., Lee, S., Kim, W.T., Yu, S.H., Choi, D. Plant Physiol. (2004)
  12. ^ The Arabidopsis CBF gene family is composed of three genes encoding AP2 domain-containing proteins whose expression Is regulated by low temperature but not by abscisic acid or dehydration. Medina, J., Bargues, M., Terol, J., Pérez-Alonso, M., Salinas, J. Plant Physiol. (1999)

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 "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

  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 1170874Freely accessible. 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 160773Freely accessible. 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 20889Freely accessible. PMID 9159183. 

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

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
(76)
Full
(10834)
Representative proteomes UniProt
(18041)
NCBI
(21239)
Meta
(107)
RP15
(1353)
RP35
(5186)
RP55
(9410)
RP75
(11158)
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PP/heatmap 1                

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

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  Seed
(76)
Full
(10834)
Representative proteomes UniProt
(18041)
NCBI
(21239)
Meta
(107)
RP15
(1353)
RP35
(5186)
RP55
(9410)
RP75
(11158)
Alignment:
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  Seed
(76)
Full
(10834)
Representative proteomes UniProt
(18041)
NCBI
(21239)
Meta
(107)
RP15
(1353)
RP35
(5186)
RP55
(9410)
RP75
(11158)
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

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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

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: 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
Download: download the raw HMM for this family

Species distribution

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Interactions

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

AP2

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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