This entry represents a zinc finger motif found in nuclear hormone receptors and in erythroid transcription factor GATA-1. Nuclear hormone receptors usually have two copies of this motif, while GATA-1 has one copy. The zinc fingers in nuclear receptors are generally regarded as DNA-binding domains [[cite:PUB00021440]], while those in GATA-1 have been implicated in protein-recognition (of FOG proteins) [[cite:PUB00021697], [cite:PUB00032561]].
","llm":false,"checked":false,"updated":false},{"text":"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 [[cite:PUB00035807], [cite:PUB00035805], [cite:PUB00035806], [cite:PUB00035804], [cite:PUB00014077]]. 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 [[cite:PUB00035812]]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.
","llm":false,"checked":false,"updated":false}],"wikipedia":null,"literature":{"PUB00035807":{"PMID":10529348,"ISBN":null,"volume":"293","issue":"2","year":1999,"title":"Zinc finger peptides for the regulation of gene expression.","URL":null,"raw_pages":"215-8","medline_journal":"J Mol Biol","ISO_journal":"J. Mol. Biol.","authors":["Klug A."],"DOI_URL":"http://dx.doi.org/10.1006/jmbi.1999.3007"},"PUB00035805":{"PMID":15963892,"ISBN":null,"volume":"15","issue":"3","year":2005,"title":"Multiple modes of RNA recognition by zinc finger proteins.","URL":null,"raw_pages":"367-73","medline_journal":"Curr Opin Struct Biol","ISO_journal":"Curr. Opin. Struct. Biol.","authors":["Hall TM."],"DOI_URL":"http://dx.doi.org/10.1016/j.sbi.2005.04.004"},"PUB00035806":{"PMID":15718139,"ISBN":null,"volume":"15","issue":"1","year":2005,"title":"Zinc finger proteins: getting a grip on RNA.","URL":null,"raw_pages":"94-8","medline_journal":"Curr Opin Struct Biol","ISO_journal":"Curr. Opin. Struct. Biol.","authors":["Brown RS."],"DOI_URL":"http://dx.doi.org/10.1016/j.sbi.2005.01.006"},"PUB00035804":{"PMID":17210253,"ISBN":null,"volume":"32","issue":"2","year":2007,"title":"Sticky fingers: zinc-fingers as protein-recognition motifs.","URL":null,"raw_pages":"63-70","medline_journal":"Trends Biochem Sci","ISO_journal":"Trends Biochem. Sci.","authors":["Gamsjaeger R","Liew CK","Loughlin FE","Crossley M","Mackay JP."],"DOI_URL":"http://dx.doi.org/10.1016/j.tibs.2006.12.007"},"PUB00021697":{"PMID":10212985,"ISBN":null,"volume":"13","issue":"3","year":1999,"title":"The solution structure of the N-terminal zinc finger of GATA-1 reveals a specific binding face for the transcriptional co-factor FOG.","URL":null,"raw_pages":"249-62","medline_journal":"J Biomol NMR","ISO_journal":"J. Biomol. NMR","authors":["Kowalski K","Czolij R","King GF","Crossley M","Mackay JP."],"DOI_URL":"http://dx.doi.org/10.1023/A:1008309602929"},"PUB00021440":{"PMID":10698945,"ISBN":null,"volume":"19","issue":"5","year":2000,"title":"Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1.","URL":null,"raw_pages":"1045-54","medline_journal":"EMBO J","ISO_journal":"EMBO J.","authors":["Rastinejad F","Wagner T","Zhao Q","Khorasanizadeh S."],"DOI_URL":"http://dx.doi.org/10.1093/emboj/19.5.1045"},"PUB00035812":{"PMID":11179890,"ISBN":null,"volume":"11","issue":"1","year":2001,"title":"Zinc finger proteins: new insights into structural and functional diversity.","URL":null,"raw_pages":"39-46","medline_journal":"Curr Opin Struct Biol","ISO_journal":"Curr. Opin. Struct. Biol.","authors":["Laity JH","Lee BM","Wright PE."],"DOI_URL":"http://dx.doi.org/10.1016/S0959-440X(00)00167-6"},"PUB00014077":{"PMID":12665246,"ISBN":null,"volume":"54","issue":"6","year":2002,"title":"Zinc fingers--folds for many occasions.","URL":null,"raw_pages":"351-5","medline_journal":"IUBMB Life","ISO_journal":"IUBMB Life","authors":["Matthews JM","Sunde M."],"DOI_URL":"http://dx.doi.org/10.1080/15216540216035"},"PUB00032561":{"PMID":15644435,"ISBN":null,"volume":"102","issue":"3","year":2005,"title":"Zinc fingers as protein recognition motifs: structural basis for the GATA-1/friend of GATA interaction.","URL":null,"raw_pages":"583-8","medline_journal":"Proc Natl Acad Sci U S A","ISO_journal":"Proc. Natl. Acad. Sci. U.S.A.","authors":["Liew CK","Simpson RJ","Kwan AH","Crofts LA","Loughlin FE","Matthews JM","Crossley M","Mackay JP."],"DOI_URL":"http://dx.doi.org/10.1073/pnas.0407511102"}},"set_info":null,"overlaps_with":[{"accession":"IPR005584","name":"DNA gyrase inhibitor YacG","type":"family"},{"accession":"IPR000679","name":"Zinc finger, GATA-type","type":"domain"},{"accession":"IPR001628","name":"Zinc finger, nuclear hormone receptor-type","type":"domain"},{"accession":"IPR001723","name":"Nuclear hormone receptor","type":"family"},{"accession":"IPR003070","name":"Nuclear receptor subfamily 4 group A member 1-3","type":"family"},{"accession":"IPR000003","name":"Retinoid X receptor/HNF4","type":"family"},{"accession":"IPR003077","name":"Peroxisome proliferator-activated receptor gamma","type":"family"},{"accession":"IPR003078","name":"Retinoic acid receptor","type":"family"},{"accession":"IPR000324","name":"Vitamin D receptor","type":"family"},{"accession":"IPR049636","name":"Hepatocyte nuclear factor 4-like, DNA-binding domain","type":"domain"},{"accession":"IPR044101","name":"Retinoid-related orphan receptors, DNA-binding domain","type":"domain"},{"accession":"IPR023257","name":"Liver X receptor","type":"family"},{"accession":"IPR047159","name":"Retinoic acid receptor, DNA-binding domain","type":"domain"},{"accession":"IPR048245","name":"Nuclear receptor subfamily 2 group C member 1/2-like, DNA-binding domain","type":"domain"},{"accession":"IPR042153","name":"VDR, DNA-binding domain","type":"domain"}],"counters":{"subfamilies":0,"domain_architectures":0,"interactions":6,"matches":160601,"pathways":283,"proteins":149069,"proteomes":9063,"sets":0,"structural_models":{"alphafold":132675,"bfvd":2},"structures":146,"taxa":21136},"entry_annotations":{},"cross_references":{},"is_llm":false,"is_reviewed_llm":false,"is_updated_llm":false,"representative_structure":{"accession":"4hc9","name":"DNA binding by GATA transcription factor-complex 3"}}}