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73  structures 1491  species 0  interactions 32564  sequences 313  architectures

Family: bZIP_1 (PF00170)

Summary: bZIP transcription factor

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This is the Wikipedia entry entitled "BZIP domain". More...

BZIP domain Edit Wikipedia article

bZIP transcription factor
CREB.png
CREB (top) is a transcription factor capable of binding DNA via the bZIP domain (bottom) and regulating gene expression.
Identifiers
SymbolbZIP_1
PfamPF00170
InterProIPR011616
PROSITEPDOC00036
SCOPe1ysa / SUPFAM
CDDcd14686
Membranome235

The Basic Leucine Zipper Domain (bZIP domain) is found in many DNA binding eukaryotic proteins. One part of the domain contains a region that mediates sequence specific DNA binding properties and the leucine zipper that is required to hold together (dimerize) two DNA binding regions. The DNA binding region comprises a number of basic amino acids such as arginine and lysine. Proteins containing this domain are transcription factors.[1][2]

bZIP transcription factors

bZIP transcription factors are found in all eukaryotes and form one of the largest families of dimerizing TFs.[3][4] An evolutionary study from 2008 revealed that 4 bZIP genes were encoded by the genome of the most recent common ancestor of all plants.[5] Interactions between bZIP transcription factors are numerous and complex [6][7][3] and play important roles in cancer development[8] in epithelial tissues, steroid hormone synthesis by cells of endocrine tissues,[9] factors affecting reproductive functions,[10] and several other phenomena that affect human health.

bZIP domain containing proteins

  • AP-1 fos/jun heterodimer that forms a transcription factor
  • Jun-B transcription factor
  • CREB cAMP response element transcription factor
  • OPAQUE2 (O2) transcription factor of the 22-kD zein gene that encodes a class of storage proteins in the endosperm of maize (Zea Mays) kernels
  • NFE2L2 or Nrf2
  • Bzip Maf transcription factors

Human proteins containing this domain

ATF1; ATF2; ATF4; ATF5; ATF6; ATF7; BACH1; BACH2; BATF; BATF2; CEBPA; CEBPB; CEBPD; CEBPE; CEBPG; CEBPZ; CREB1; CREB3; CREB3L1; CREB3L2; CREB3L3; CREB3L4; CREB5; CREBL1; CREM; E4BP4; FOSL1; FOSL2; JUN; JUNB; JUND; MAFA; MAFB; NFE2; NFE2L2; NFE2L3; SNFT; XBP1

References

  1. ^ Ellenberger T (1994). "Getting a grip in DNA recognition: structures of the basic region leucine zipper, and the basic region helix-loop-helix DNA-binding domains". Curr. Opin. Struct. Biol. 4 (1): 12–21. doi:10.1016/S0959-440X(94)90054-X.
  2. ^ Hurst HC (1995). "Transcription factors 1: bZIP proteins". Protein Profile. 2 (2): 101–68. PMID 7780801.
  3. ^ a b Amoutzias, G. D.; Veron, A. S.; Weiner, J.; Robinson-Rechavi, M.; Bornberg-Bauer, E.; Oliver, S. G.; Robertson, D. L. (2007-03-01). "One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity". Molecular Biology and Evolution. 24 (3): 827–835. doi:10.1093/molbev/msl211. ISSN 0737-4038. PMID 17194801.
  4. ^ Amoutzias, Grigoris D.; Robertson, David L.; Van de Peer, Yves; Oliver, Stephen G. (2008-05-01). "Choose your partners: dimerization in eukaryotic transcription factors". Trends in Biochemical Sciences. 33 (5): 220–229. doi:10.1016/j.tibs.2008.02.002. ISSN 0968-0004. PMID 18406148.
  5. ^ Corrêa LG, Riaño-Pachón DM, Schrago CG, dos Santos RV, Mueller-Roeber B, Vincentz M (2008). Shiu S (ed.). "The Role of bZIP Transcription Factors in Green Plant Evolution: Adaptive Features Emerging from Four Founder Genes". PLoS ONE. 3 (8): e2944. doi:10.1371/journal.pone.0002944. PMC 2492810. PMID 18698409.
  6. ^ Vinson, Charles; Acharya, Asha; Taparowsky, Elizabeth J. (2006-01-01). "Deciphering B-ZIP transcription factor interactions in vitro and in vivo" (PDF). Biochimica et Biophysica Acta. 1759 (1–2): 4–12. doi:10.1016/j.bbaexp.2005.12.005. ISSN 0006-3002. PMID 16580748.
  7. ^ Newman, John R. S.; Keating, Amy E. (2003-06-27). "Comprehensive identification of human bZIP interactions with coiled-coil arrays". Science. 300 (5628): 2097–2101. doi:10.1126/science.1084648. ISSN 1095-9203. PMID 12805554.
  8. ^ Vlahopoulos SA, Logotheti S, Mikas D, Giarika A, Gorgoulis V, Zoumpourlis V (April 2008). "The role of ATF-2 in oncogenesis". BioEssays. 30 (4): 314–27. doi:10.1002/bies.20734. PMID 18348191.
  9. ^ Manna PR, Dyson MT, Eubank DW, Clark BJ, Lalli E, Sassone-Corsi P, Zeleznik AJ, Stocco DM (January 2002). "Regulation of steroidogenesis and the steroidogenic acute regulatory protein by a member of the cAMP response-element binding protein family". Mol. Endocrinol. 16 (1): 184–99. doi:10.1210/me.16.1.184. PMID 11773448.
  10. ^ Hoare S, Copland JA, Wood TG, Jeng YJ, Izban MG, Soloff MS (May 1999). "Identification of a GABP alpha/beta binding site involved in the induction of oxytocin receptor gene expression in human breast cells, potentiation by c-Fos/c-Jun". Endocrinology. 140 (5): 2268–79. doi:10.1210/en.140.5.2268. PMID 10218980.

External links

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The Pfam entry includes the basic region and the leucine zipper region.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004827

The basic-leucine zipper (bZIP) domain transcription factors [ PUBMED:7780801 ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region required for dimerisation.

Several structure of bZIP have been solved. The basic region and the leucine zipper form a contiguous alpha helice where the four hydrophobic residues of the leucine zipper are oriented on one side. This conformation allows dimerization in parallel and it bends the helices so that the newly functional dimer forms a flexible fork where the basic domains, at the N-terminal open end, can then interact with DNA. The two leucine zipper are therefore oriented perpendicular to the DNA [ PUBMED:1473154 ].

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 bZIP (CL0018), which has the following description:

This family of eukaryotic transcription factors contain a basic region adjacent to a leucine zipper.

The clan contains the following 3 members:

bZIP_1 bZIP_2 bZIP_Maf

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 and the UniProtKB 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
(15)
Full
(32564)
Representative proteomes UniProt
(52271)
RP15
(4351)
RP35
(13296)
RP55
(24973)
RP75
(34171)
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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
(15)
Full
(32564)
Representative proteomes UniProt
(52271)
RP15
(4351)
RP35
(13296)
RP55
(24973)
RP75
(34171)
Alignment:
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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
(15)
Full
(32564)
Representative proteomes UniProt
(52271)
RP15
(4351)
RP35
(13296)
RP55
(24973)
RP75
(34171)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Prosite
Previous IDs: bZIP;
Type: Coiled-coil
Sequence Ontology: SO:0001080
Author: Sonnhammer ELL
Number in seed: 15
Number in full: 32564
Average length of the domain: 61.00 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 16.59 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.6 27.6
Trusted cut-off 27.6 27.6
Noise cut-off 27.5 27.5
Model length: 64
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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

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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 bZIP_1 domain has been found. There are 73 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A060D1N2 View 3D Structure Click here
A0A060D700 View 3D Structure Click here
A0A060D918 View 3D Structure Click here
A0A0G2K331 View 3D Structure Click here
A0A0N7KI44 View 3D Structure Click here
A0A0N7KMD3 View 3D Structure Click here
A0A0N7KSG4 View 3D Structure Click here
A0A0N7KUB6 View 3D Structure Click here
A0A0P0UYZ1 View 3D Structure Click here
A0A0P0V9J7 View 3D Structure Click here
A0A0P0VFR9 View 3D Structure Click here
A0A0P0VG62 View 3D Structure Click here
A0A0P0VWV8 View 3D Structure Click here
A0A0P0WFC8 View 3D Structure Click here
A0A0P0WNV7 View 3D Structure Click here
A0A0P0X1A0 View 3D Structure Click here
A0A0P0X3I8 View 3D Structure Click here
A0A0P0XR34 View 3D Structure Click here
A0A0R0EGQ1 View 3D Structure Click here
A0A0R0EMF9 View 3D Structure Click here
A0A0R0FII4 View 3D Structure Click here
A0A0R0G544 View 3D Structure Click here
A0A0R0GJQ0 View 3D Structure Click here
A0A0R0GWQ9 View 3D Structure Click here
A0A0R0HDY8 View 3D Structure Click here
A0A0R0HI77 View 3D Structure Click here
A0A0R0HQF0 View 3D Structure Click here
A0A0R0IG25 View 3D Structure Click here
A0A0R0IKI9 View 3D Structure Click here
A0A0R0IQB8 View 3D Structure Click here
A0A0R0IVB6 View 3D Structure Click here
A0A0R0KB07 View 3D Structure Click here
A0A0R0KCM8 View 3D Structure Click here
A0A0R0KHW1 View 3D Structure Click here
A0A0R0LBJ6 View 3D Structure Click here
A0A0R0LBM0 View 3D Structure Click here
A0A0R0LE00 View 3D Structure Click here
A0A0R4IAV4 View 3D Structure Click here
A0A0R4IB23 View 3D Structure Click here
A0A0R4IFU8 View 3D Structure Click here