BRLZ

basic region leucin zipper

• SMART accession number: SM00338
• Interpro abstract (IPR004827): The basic-leucine zipper (bZIP) transcription factors (PUBMED:7780801), of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158) required for dimerization.
• GO process: regulation of transcription, DNA-dependent (GO:0006355)
• GO component: nucleus (GO:0005634)
• GO function: transcription factor activity (GO:0003700), protein dimerization activity (GO:0046983), sequence-specific DNA binding (GO:0043565)

There are 3143 BRLZ domains in 3139 proteins in SMART's nrdb database.

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Muller CW, Herrmann BG
• Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor.
• Nature. 1997; 389: 884-8

The mouse Brachyury (T) gene is the prototype of a growing family of so-called T-box genes which encode transcriptional regulators and have been identified in a variety of invertebrates and vertebrates, including humans. Mutations in Brachyury and other T-box genes result in drastic embryonic phenotypes, indicating that T-box gene products are essential in tissue specification, morphogenesis and organogenesis. The T-box encodes a DNA-binding domain of about 180 amino-acid residues, the T domain. Here we report the X-ray structure of the T domain from Xenopus laevis in complex with a 24-nucleotide palindromic DNA duplex. We show that the protein is bound as a dimer, interacting with the major and the minor grooves of the DNA. A new type of specific DNA contact is seen, in which a carboxy-terminal helix is deeply embedded into an enlarged minor groove without bending the DNA. Hydrophobic interactions and an unusual main-chain carbonyl contact to a guanine account for sequence-specific recognition in the minor groove by this helix. Thus the structure of this T domain complex with DNA reveals a new way in which a protein can recognize DNA.

• Hurst HC
• Transcription factors 1: bZIP proteins.
• Protein Profile. 1995; 2: 101-68

• Ellenberger T, Fass D, Arnaud M, Harrison SC
• Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer.
• Genes Dev. 1994; 8: 970-80

A large group of transcription factors regulating cell growth and differentiation share a dimeric alpha-helical DNA-binding domain termed the basic region helix-loop-helix (bHLH). bHLH proteins associate as homodimers and heterodimers having distinctive DNA-binding activities and transcriptional activities that are central to the regulated differentiation of a number of tissues. Some of the bHLH residues specifying these activities have been identified, but a full understanding of their function has awaited further structural information. We report here the crystal structure of the transcription factor E47 bHLH domain bound to DNA. The bHLH of E47 is a parallel, four-helix bundle with structural features that distinguish it from the bHLH-zipper protein Max. The E47 dimer makes nonequivalent contacts to each half of the -CACCTG- binding site. Sequence discrimination at the center of the E box may result from interaction with both the DNA bases and the phosphodiester backbone.

• Anthony-Cahill SJ et al.
• Molecular characterization of helix-loop-helix peptides.
• Science. 1992; 255: 979-83

A class of regulators of eukaryotic gene expression contains a conserved amino acid sequence responsible for protein oligomerization and binding to DNA. This structure consists of an arginine- and lysine-rich basic region followed by a helix-loop-helix motif, which together mediate specific binding to DNA. Peptides were prepared that span this motif in the MyoD protein; in solution, they formed alpha-helical dimers and tetramers. They bound to DNA as dimers and their alpha-helical content increased on binding. Parallel and antiparallel four-helix models of the DNA-bound dimer were constructed. Peptides containing disulfide bonds were engineered to test the correctness of the two models. A disulfide that is compatible with the parallel model promotes specific interaction with DNA, whereas a disulfide compatible with the antiparallel model abolishes specific binding. Electron paramagnetic resonance (EPR) measurements of nitroxide-labeled peptides provided intersubunit distance measurements that also supported the parallel model.

• Landschulz WH, Johnson PF, McKnight SL
• The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins.
• Science. 1988; 240: 1759-64

A 30-amino-acid segment of C/EBP, a newly discovered enhancer binding protein, shares notable sequence similarity with a segment of the cellular Myc transforming protein. Display of these respective amino acid sequences on an idealized alpha helix revealed a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns. The periodic array of at least four leucines was also noted in the sequences of the Fos and Jun transforming proteins, as well as that of the yeast gene regulatory protein, GCN4. The polypeptide segments containing these periodic arrays of leucine residues are proposed to exist in an alpha-helical conformation, and the leucine side chains extending from one alpha helix interdigitate with those displayed from a similar alpha helix of a second polypeptide, facilitating dimerization. This hypothetical structure is referred to as the "leucine zipper," and it may represent a characteristic property of a new category of DNA binding proteins.

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
18.00	map05215	Prostate cancer
13.33	map04916	Melanogenesis
13.00	map04010	MAPK signaling pathway
5.67	map05210	Colorectal cancer
5.67	map04620	Toll-like receptor signaling pathway
5.67	map04662	B cell receptor signaling pathway
5.67	map04660	T cell receptor signaling pathway
5.00	map04912	GnRH signaling pathway
5.00	map04310	Wnt signaling pathway
3.00	map05060	Prion disease
2.67	map05120	Epithelial cell signaling in Helicobacter pylori infection
2.67	map04510	Focal adhesion
2.67	map04012	ErbB signaling pathway
2.67	map05211	Renal cell carcinoma
2.33	map04612	Antigen processing and presentation
2.33	map04720	Long-term potentiation
1.67	map05221	Acute myeloid leukemia
1.33	map04950	Maturity onset diabetes of the young
1.33	map04930	Type II diabetes mellitus
0.33	map04080	Neuroactive ligand-receptor interaction

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with BRLZ domain which could be assigned to a KEGG orthologous group, and not all proteins containing BRLZ domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

Structure (3D structures containing this domain)

3D Structures of BRLZ domains in PDB

PDB code	Title
1a02	Structure of the dna binding domains of nfat, fos and jun bound to dna
1ci6	Transcription factor atf4-c/ebp beta bzip heterodimer
1dgc	The x-ray structure of the gcn4-bzip bound to atf/creb site dna shows the complex depends on dna flexibility
1dh3	Crystal structure of a creb bzip-cre complex reveals the basis for creb faimly selective dimerization and dna binding
1fos	Two human c-fos:c-jun:dna complexes
1gd2	Crystal structure of bzip transcription factor pap1 bound to dna
1gtw	Crystal structure of c/ebpbeta bzip homodimer bound to a dna fragment from the tom-1a promoter
1gu4	Crystal structure of c/ebpbeta bzip homodimer bound to a high affinity dna fragment
1gu5	Crystal structure of c/ebpbeta bzip homodimer bound to a dna fragment from the mim-1 promoter
1h88	Crystal structure of ternary protein-dna complex1
1h89	Crystal structure of ternary protein-dna complex2
1h8a	Crystal structure of ternary protein-dna complex3
1hjb	Crystal structure of runx-1/aml1/cbfalpha runt domain and c/ebpbeta bzip homodimer bound to a dna fragment from the csf-1r promoter
1io4	Crystal structure of runx-1/aml1/cbfalpha runt domain- cbfbeta core domain heterodimer and c/ebpbeta bzip homodimer bound to a dna fragment from the csf-1r promoter
1jnm	Crystal structure of the jun/cre complex
1ld4	Placement of the structural proteins in sindbis virus
1nwq	Crystal structure of c/ebpalpha-dna complex
1s9k	Crystal structure of human nfat1 and fos-jun on the il-2 arre1 site
1t2k	Structure of the dna binding domains of irf3, atf-2 and jun bound to dna
1ysa	The gcn4 basic region leucine zipper binds dna as a dimer of uninterrupted alpha helices: crystal structure of the protein-dna complex
2dgc	Gcn4 basic domain, leucine zipper complexed with atf/creb site dna
2e42	Crystal structure of c/ebpbeta bzip homodimer v285a mutant bound to a high affinity dna fragment
2e43	Crystal structure of c/ebpbeta bzip homodimer k269a mutant bound to a high affinity dna fragment
2h7h	Crystal structure of the jun bzip homodimer complexed with ap-1 dna
3a5t

Links (links to other resources describing this domain)

• PFAM: bZIP
• INTERPRO: IPR004827
• PROSITE: BZIP_BASIC