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56  structures 1363  species 0  interactions 19707  sequences 310  architectures

Family: GATA (PF00320)

Summary: GATA zinc finger

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 "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). Some members of this class of zinc fingers specifically bind the DNA sequence (A/T)GATA(A/G) in the regulatory regions of genes.,[1] giving rise to the name of the domain. In these domains, a single 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. 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 GATA-family transcription factors. However, there are several proteins that only contains a single copy of the domain. It is also worth noting that many GATA-type Znfs (such as those found in the proteins GATAD2B and MTA1) have not been experimentally demonstrated to be DNA-binding domains. Furthermore, several GATA-type Znfs have been demonstrated to act as protein-recognition domains. For example, the N-terminal Znf of GATA1 binds specifically to a zinc finger from the transcriptional coregulator FOG1 (ZFPM1).[4]

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. 
  4. ^ Liew CK, Simpson RJ, Kwan AH, Crofts LA, Loughlin FE, Matthews JM, Crossley M, Mackay JP (March 2005). "Zinc fingers as protein recognition motifs: structural basis for the GATA-1/friend of GATA interaction". PNAS USA. 102 (3): 583–8. doi:10.1073/pnas.0407511102. PMC 545545Freely accessible. PMID 15644435. 

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

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.

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 contain 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

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 four cysteine residues [ PUBMED:2776214 , PUBMED:8332909 ]. NMR studies have shown the core of the Znf to comprise two 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 two 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.

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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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
(56)
Full
(19707)
Representative proteomes UniProt
(31610)
RP15
(3136)
RP35
(9189)
RP55
(16218)
RP75
(21660)
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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
(56)
Full
(19707)
Representative proteomes UniProt
(31610)
RP15
(3136)
RP35
(9189)
RP55
(16218)
RP75
(21660)
Alignment:
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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
(56)
Full
(19707)
Representative proteomes UniProt
(31610)
RP15
(3136)
RP35
(9189)
RP55
(16218)
RP75
(21660)
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: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 56
Number in full: 19707
Average length of the domain: 35.50 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 8.09 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.8 26.8
Trusted cut-off 26.8 26.8
Noise cut-off 26.7 26.7
Model length: 36
Family (HMM) version: 29
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 GATA domain has been found. There are 56 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
A0A060CYH3 View 3D Structure Click here
A0A060D834 View 3D Structure Click here
A0A0G2JTK6 View 3D Structure Click here
A0A0P0WQZ5 View 3D Structure Click here
A0A0P0XV13 View 3D Structure Click here
A0A0P0XV13 View 3D Structure Click here
A0A0P0XV13 View 3D Structure Click here
A0A0P0XXK4 View 3D Structure Click here
A0A0P0Y3U1 View 3D Structure Click here
A0A0R0H114 View 3D Structure Click here
A0A0R0I1E4 View 3D Structure Click here
A0A0R0IF15 View 3D Structure Click here
A0A0R0IV54 View 3D Structure Click here
A0A0R0IW01 View 3D Structure Click here
A0A0R0J5P6 View 3D Structure Click here
A0A0R0K1U4 View 3D Structure Click here
A0A0R0KTZ8 View 3D Structure Click here
A0A0R0L3S5 View 3D Structure Click here
A0A0R0L803 View 3D Structure Click here
A0A0R4ILP3 View 3D Structure Click here
A0A0R4ILP3 View 3D Structure Click here
A0A0R4IN87 View 3D Structure Click here
A0A1D6E4G0 View 3D Structure Click here
A0A1D6EIM0 View 3D Structure Click here
A0A1D6FKM8 View 3D Structure Click here
A0A1D6FL14 View 3D Structure Click here
A0A1D6GI61 View 3D Structure Click here
A0A1D6GUV7 View 3D Structure Click here
A0A1D6HEP8 View 3D Structure Click here
A0A1D6HNS2 View 3D Structure Click here
A0A1D6IJK6 View 3D Structure Click here
A0A1D6IU09 View 3D Structure Click here
A0A1D6JB89 View 3D Structure Click here
A0A1D6JBJ0 View 3D Structure Click here
A0A1D6K8G2 View 3D Structure Click here
A0A1D6KGN8 View 3D Structure Click here
A0A1D6KGN8 View 3D Structure Click here
A0A1D6KZF6 View 3D Structure Click here
A0A1D6L3K1 View 3D Structure Click here
A0A1D6LNQ5 View 3D Structure Click here
A0A1D6MDM9 View 3D Structure Click here
A0A1D6NGI0 View 3D Structure Click here
A0A1D6PJR4 View 3D Structure Click here
A0A1D6QH03 View 3D Structure Click here
A0A1D6QH04 View 3D Structure Click here
A0A1D6QH40 View 3D Structure Click here
A0A1D8PNX9 View 3D Structure Click here
A0A1R3MKD7 View 3D Structure Click here
A0A2R8RTX5 View 3D Structure Click here
A0A2R9YJP8 View 3D Structure Click here
A0A2R9YJP8 View 3D Structure Click here
B0G188 View 3D Structure Click here
B2GV01 View 3D Structure Click here
B4F991 View 3D Structure Click here
B4F9D9 View 3D Structure Click here
B4F9D9 View 3D Structure Click here
B4FVT9 View 3D Structure Click here
B6STZ1 View 3D Structure Click here
B6TR29 View 3D Structure Click here
B7EMP8 View 3D Structure Click here
B7WN96 View 3D Structure Click here
B7ZZ65 View 3D Structure Click here
B9FGD6 View 3D Structure Click here
C0HE33 View 3D Structure Click here
C0HE33 View 3D Structure Click here
C0PFG1 View 3D Structure Click here
C0PFJ8 View 3D Structure Click here
D3ZEB4 View 3D Structure Click here
D3ZEM6 View 3D Structure Click here
E7EY65 View 3D Structure Click here
E7F226 View 3D Structure Click here
E7FCG5 View 3D Structure Click here
F1QD30 View 3D Structure Click here
F1QD30 View 3D Structure Click here
F1QEY1 View 3D Structure Click here
F1QLG2 View 3D Structure Click here
F1QQG0 View 3D Structure Click here
F1QQG0 View 3D Structure Click here
F1QVT3 View 3D Structure Click here
G5EDN4 View 3D Structure Click here
G5EF25 View 3D Structure Click here
G5EF71 View 3D Structure Click here
G5EGN3 View 3D Structure Click here
I1J8P1 View 3D Structure Click here
I1J9R1 View 3D Structure Click here
I1JCP8 View 3D Structure Click here
I1JMW7 View 3D Structure Click here
I1JR72 View 3D Structure Click here
I1JSK1 View 3D Structure Click here
I1JUW3 View 3D Structure Click here
I1JV86 View 3D Structure Click here
I1JV87 View 3D Structure Click here
I1K0V3 View 3D Structure Click here
I1K730 View 3D Structure Click here
I1K9E7 View 3D Structure Click here
I1K9S5 View 3D Structure Click here
I1K9S6 View 3D Structure Click here
I1KJP6 View 3D Structure Click here
I1KL59 View 3D Structure Click here
I1KMU4 View 3D Structure Click here
I1KQX6 View 3D Structure Click here
I1L1G9 View 3D Structure Click here
I1LGU6 View 3D Structure Click here
I1LL49 View 3D Structure Click here
I1LTK1 View 3D Structure Click here
I1LVJ1 View 3D Structure Click here
I1M4J7 View 3D Structure Click here
I1MB13 View 3D Structure Click here
I1MH70 View 3D Structure Click here
I1MNF7 View 3D Structure Click here
I1MNT7 View 3D Structure Click here
I1MRN5 View 3D Structure Click here
I1MSH4 View 3D Structure Click here
I1MV65 View 3D Structure Click here
I1MWA9 View 3D Structure Click here
I1MXA9 View 3D Structure Click here
I1N869 View 3D Structure Click here
I1NHG2 View 3D Structure Click here
K7K6I9 View 3D Structure Click here
K7K9Y2 View 3D Structure Click here
K7KI74 View 3D Structure Click here
K7KQQ3 View 3D Structure Click here
K7L7H0 View 3D Structure Click here
K7LAL8 View 3D Structure Click here
K7LKL8 View 3D Structure Click here
K7LNF5 View 3D Structure Click here
K7LP59 View 3D Structure Click here
K7LQQ6 View 3D Structure Click here
K7LTK4 View 3D Structure Click here
K7M5W0 View 3D Structure Click here
K7M6T4 View 3D Structure Click here
K7MF59 View 3D Structure Click here
K7MHJ9 View 3D Structure Click here
K7MZU9 View 3D Structure Click here
K7TXE3 View 3D Structure Click here
K7TXE3 View 3D Structure Click here
K7UI23 View 3D Structure Click here
K7V265 View 3D Structure Click here
K7V265 View 3D Structure Click here
K7V551 View 3D Structure Click here
K7VQ40 View 3D Structure Click here
O09100 View 3D Structure Click here
O09100 View 3D Structure Click here
O49741 View 3D Structure Click here
O49743 View 3D Structure Click here
O61924 View 3D Structure Click here
O65515 View 3D Structure Click here
O82632 View 3D Structure Click here
O94720 View 3D Structure Click here
O94720 View 3D Structure Click here
O94776 View 3D Structure Click here
P09007 View 3D Structure Click here
P0C6A0 View 3D Structure Click here
P15976 View 3D Structure Click here
P15976 View 3D Structure Click here
P17679 View 3D Structure Click here
P17679 View 3D Structure Click here
P18494 View 3D Structure Click here
P23769 View 3D Structure Click here
P23769 View 3D Structure Click here
P23771 View 3D Structure Click here
P23771 View 3D Structure Click here
P23772 View 3D Structure Click here
P23772 View 3D Structure Click here
P26343 View 3D Structure Click here
P28515 View 3D Structure Click here
P28515 View 3D Structure Click here
P34233 View 3D Structure Click here
P40209 View 3D Structure Click here
P40569 View 3D Structure Click here
P42944 View 3D Structure Click here
P43429 View 3D Structure Click here
P43429 View 3D Structure Click here
P43574 View 3D Structure Click here
P43694 View 3D Structure Click here
P43694 View 3D Structure Click here
P46152 View 3D Structure Click here
P46152 View 3D Structure Click here
P46153 View 3D Structure Click here
P46153 View 3D Structure Click here
P52168 View 3D Structure Click here
P52168 View 3D Structure Click here
P52172 View 3D Structure Click here
P69781 View 3D Structure Click here
P91623 View 3D Structure Click here
P91623 View 3D Structure Click here
P97489 View 3D Structure Click here
P97489 View 3D Structure Click here
Q02710 View 3D Structure Click here
Q05AJ3 View 3D Structure Click here
Q05AJ3 View 3D Structure Click here
Q07928 View 3D Structure Click here
Q08369 View 3D Structure Click here
Q08369 View 3D Structure Click here
Q09228 View 3D Structure Click here
Q0DKL8 View 3D Structure Click here
Q0DNU1 View 3D Structure Click here
Q0IPT9 View 3D Structure Click here
Q0IPT9 View 3D Structure Click here
Q10134 View 3D Structure Click here
Q10134 View 3D Structure Click here
Q10280 View 3D Structure Click here
Q10655 View 3D Structure Click here
Q10F25 View 3D Structure Click here
Q10QV7 View 3D Structure Click here
Q13330 View 3D Structure Click here
Q1WG82 View 3D Structure Click here
Q2QLX6 View 3D Structure Click here
Q4V8E1 View 3D Structure Click here
Q53P56 View 3D Structure Click here
Q54FV1 View 3D Structure Click here
Q54HA4 View 3D Structure Click here
Q54KX0 View 3D Structure Click here
Q54L80 View 3D Structure Click here
Q54L82 View 3D Structure Click here
Q54NM5 View 3D Structure Click here
Q54TE3 View 3D Structure Click here
Q54TM6 View 3D Structure Click here
Q54V32 View 3D Structure Click here
Q54V37 View 3D Structure Click here
Q54WY0 View 3D Structure Click here
Q550D5 View 3D Structure Click here
Q55C49 View 3D Structure Click here
Q55EQ0 View 3D Structure Click here
Q55GK0 View 3D Structure Click here
Q59LY1 View 3D Structure Click here
Q59TU4 View 3D Structure Click here
Q5A201 View 3D Structure Click here
Q5A432 View 3D Structure Click here
Q5A5Q6 View 3D Structure Click here
Q5ALK1 View 3D Structure Click here
Q5AP95 View 3D Structure Click here
Q5AP95 View 3D Structure Click here
Q5HZ36 View 3D Structure Click here
Q5JNB8 View 3D Structure Click here
Q5KSV0 View 3D Structure Click here
Q5PP38 View 3D Structure Click here
Q5U2V0 View 3D Structure Click here
Q5U2V0 View 3D Structure Click here
Q5Z4U5 View 3D Structure Click here
Q5Z624 View 3D Structure Click here
Q61169 View 3D Structure Click here
Q61169 View 3D Structure Click here
Q62599 View 3D Structure Click here
Q62901 View 3D Structure Click here
Q6DBP8 View 3D Structure Click here
Q6F2Z7 View 3D Structure Click here
Q6H635 View 3D Structure Click here
Q6L5E5 View 3D Structure Click here
Q6NW63 View 3D Structure Click here
Q6NW63 View 3D Structure Click here
Q6QPM2 View 3D Structure Click here
Q6YSY7 View 3D Structure Click here
Q6YW48 View 3D Structure Click here
Q6Z433 View 3D Structure Click here
Q75JZ0 View 3D Structure Click here
Q75JZ1 View 3D Structure Click here
Q7XN01 View 3D Structure Click here
Q80TZ9 View 3D Structure Click here
Q850Z5 View 3D Structure Click here
Q86YP4 View 3D Structure Click here
Q8GW81 View 3D Structure Click here
Q8GXL7 View 3D Structure Click here
Q8H036 View 3D Structure Click here
Q8H1G0 View 3D Structure Click here
Q8K4B0 View 3D Structure Click here
Q8L4M6 View 3D Structure Click here
Q8LAU9 View 3D Structure Click here
Q8LC59 View 3D Structure Click here
Q8LC79 View 3D Structure Click here
Q8LG10 View 3D Structure Click here
Q8LIZ3 View 3D Structure Click here
Q8LQW5 View 3D Structure Click here
Q8LR32 View 3D Structure Click here
Q8MQA7 View 3D Structure Click here
Q8VHR5 View 3D Structure Click here
Q8VZP4 View 3D Structure Click here
Q8W4H1 View 3D Structure Click here
Q8WXI9 View 3D Structure Click here
Q91428 View 3D Structure Click here
Q91428 View 3D Structure Click here
Q924K8 View 3D Structure Click here
Q924Y4 View 3D Structure Click here
Q924Y4 View 3D Structure Click here
Q925H1 View 3D Structure Click here
Q92908 View 3D Structure Click here
Q92908 View 3D Structure Click here
Q99NH5 View 3D Structure Click here
Q99NH5 View 3D Structure Click here
Q9BTC8 View 3D Structure Click here
Q9BWX5 View 3D Structure Click here
Q9BWX5 View 3D Structure Click here
Q9FH57 View 3D Structure Click here
Q9FJ10 View 3D Structure Click here
Q9LIB5 View 3D Structure Click here
Q9LRH6 View 3D Structure Click here
Q9LT45 View 3D Structure Click here
Q9M1U2 View 3D Structure Click here
Q9P2R6 View 3D Structure Click here
Q9R190 View 3D Structure Click here
Q9SD38 View 3D Structure Click here
Q9SKN6 View 3D Structure Click here
Q9SV30 View 3D Structure Click here
Q9SZI6 View 3D Structure Click here
Q9UHF7 View 3D Structure Click here
Q9URT4 View 3D Structure Click here
Q9USM3 View 3D Structure Click here
Q9VF00 View 3D Structure Click here
Q9VKZ0 View 3D Structure Click here
Q9W6U0 View 3D Structure Click here
Q9W6U0 View 3D Structure Click here
Q9XUW7 View 3D Structure Click here
Q9ZPX0 View 3D Structure Click here
U4PMB4 View 3D Structure Click here