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40  structures 384  species 1  interaction 3798  sequences 92  architectures

Family: GATA (PF00320)

Summary: GATA zinc finger

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This is the Wikipedia entry entitled "GATA zinc finger". More...

GATA zinc finger Edit Wikipedia article

GATA zinc finger
PDB 1y0j EBI.jpg
zinc fingers as protein recognition motifs: structural basis for the gata-1/friend of gata interaction
Identifiers
Symbol GATA
Pfam PF00320
Pfam clan CL0167
InterPro IPR000679
PROSITE PDOC00300
SCOP 1gat
SUPERFAMILY 1gat
CDD cd00202

In molecular biology, GATA zinc fingers are zinc-containing domains found in a number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins). They specifically bind the DNA sequence (A/T)GATA(A/G) in the regulatory regions of genes.[1] They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved zinc finger (Znf) domains in which the zinc ion is coordinated by 4 cysteine residues.[2][3] NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed.[3] Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain.

References

  1. ^ Yamamoto M, Ko LJ, Leonard MW, Beug H, Orkin SH, Engel JD (October 1990). "Activity and tissue-specific expression of the transcription factor NF-E1 multigene family". Genes Dev. 4 (10): 1650–62. doi:10.1101/gad.4.10.1650. PMID 2249770. 
  2. ^ Evans T, Felsenfeld G (September 1989). "The erythroid-specific transcription factor Eryf1: a new finger protein". Cell 58 (5): 877–85. doi:10.1016/0092-8674(89)90940-9. PMID 2776214. 
  3. ^ a b Omichinski JG, Clore GM, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl SJ, Gronenborn AM (July 1993). "NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1". Science 261 (5120): 438–46. doi:10.1126/science.8332909. PMID 8332909. 

This article incorporates text from the public domain Pfam and InterPro IPR000679

External links

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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.

GATA zinc finger Provide feedback

This domain uses four cysteine residues to coordinate a zinc ion. This domain binds to DNA. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain.

Literature references

  1. Omichinski JG, Clore GM, Schaad O, Felsenfeld G, Trainor C, Appella E, Stahl SJ, Gronenborn AM; , Science 1993;261:438-446.: NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. PUBMED:8332909 EPMC:8332909


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000679

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [PUBMED:10529348, PUBMED:15963892, PUBMED:15718139, PUBMED:17210253, PUBMED:12665246]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [PUBMED:11179890]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [PUBMED:2249770] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [PUBMED:2776214, PUBMED:8332909]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed [PUBMED:8332909]. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain.

More information about these proteins can be found at Protein of the Month: Zinc Fingers [PUBMED:].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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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
(69)
Full
(3798)
Representative proteomes NCBI
(3654)
Meta
(15)
RP15
(638)
RP35
(1149)
RP55
(1789)
RP75
(2299)
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  Seed
(69)
Full
(3798)
Representative proteomes NCBI
(3654)
Meta
(15)
RP15
(638)
RP35
(1149)
RP55
(1789)
RP75
(2299)
Alignment:
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Sequence:
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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
(69)
Full
(3798)
Representative proteomes NCBI
(3654)
Meta
(15)
RP15
(638)
RP35
(1149)
RP55
(1789)
RP75
(2299)
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.

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.

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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: Prosite
Previous IDs: none
Type: Domain
Author: Finn RD
Number in seed: 69
Number in full: 3798
Average length of the domain: 35.30 aa
Average identity of full alignment: 45 %
Average coverage of the sequence by the domain: 8.26 %

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 20.7 20.7
Trusted cut-off 20.7 20.7
Noise cut-off 20.6 20.6
Model length: 36
Family (HMM) version: 22
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Species distribution

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Interactions

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

zf-C2H2

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 GATA domain has been found. There are 40 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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