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288  structures 523  species 0  interactions 5966  sequences 81  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
Symbol bZIP_1
Pfam PF00170
InterPro IPR011616
PROSITE PDOC00036
SCOP 1ysa
SUPERFAMILY 1ysa

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[edit]

bZIP transcription factors are found in all organisms. A recent evolutionary study revealed that 4 bZIP genes were encoded by the genome of the most recent common ancestor of all plants.[3] Interactions between bZIP transcription factors play important roles in cancer development[4] in epithelial tissues, steroid hormone synthesis by cells of endocrine tissues,[5] factors affecting reproductive functions,[6] and several other phenomena that affect human health.

bZIP domain containing proteins[edit]

  • 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[edit]

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

External links[edit]

References[edit]

  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. ^ Corrêa LGG, Riaño-Pachón DM, Schrago CG, dos Santos RV, Mueller-Roeber B, Vincentz M. (2008). "The Role of bZIP Transcription Factors in Green Plant Evolution: Adaptive Features Emerging from Four Founder Genes". In Shiu, Shin-Han. PLoS ONE 3 (8): e2944. doi:10.1371/journal.pone.0002944. PMC 2492810. PMID 18698409. 
  4. ^ 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. 
  5. ^ 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. 
  6. ^ 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. 

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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 IPR011616

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

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 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
(22)
Full
(5966)
Representative proteomes NCBI
(7374)
Meta
(40)
RP15
(830)
RP35
(1626)
RP55
(2510)
RP75
(3305)
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Format an alignment

  Seed
(22)
Full
(5966)
Representative proteomes NCBI
(7374)
Meta
(40)
RP15
(830)
RP35
(1626)
RP55
(2510)
RP75
(3305)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(22)
Full
(5966)
Representative proteomes NCBI
(7374)
Meta
(40)
RP15
(830)
RP35
(1626)
RP55
(2510)
RP75
(3305)
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: Prosite
Previous IDs: bZIP;
Type: Family
Author: Sonnhammer ELL
Number in seed: 22
Number in full: 5966
Average length of the domain: 61.00 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 17.17 %

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 22.3 22.3
Trusted cut-off 22.3 22.3
Noise cut-off 22.2 22.2
Model length: 64
Family (HMM) version: 16
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 bZIP_1 domain has been found. There are 288 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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