The AT-rich interaction domain (ARID) is an ~100-amino acid DNA-binding module found in a large number of eukaryotic transcription factors that regulate cellproliferation, differentiation and development [, ]. The ARID domain appearsas a single-copy motif and can be found in association with other domains,such as JmjC, JmjN, Tudor and PHD-type zinc finger [].The basic structure of the ARID domain domain appears to be a series of sixα-helices separated by β-strands, loops, or turns, but the structuredregion may extend to an additional helix at either or both ends of the basicsix. Based on primary sequence homology, they can be partitioned into threestructural classes:Minimal ARID proteins that consist of a core domain formed by six alpha-helices;ARID proteins that supplement the core domain with an N-terminal alpha-helix;Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.Minimal ARIDs are distributed in all eukaryotes, while extended ARIDs arerestricted to metazoans. The ARID domain binds DNA as a monomer, recognizingthe duplex through insertion of a loop and an α-helix into the majorgroove, and by extensive non-specific anchoring contacts to the adjacentsugar-phosphate backbone [, , ].Some proteins known to contain a ARID domain are listed below:Eukaryotic transcription factors of the jumonji family.Mammalian Bright, a B-cell-specific trans-activator of IgH transcription.Mammalian PLU-1, a protein that is upregulated in breast cancer cells.Mammalian RBP1 and RBP2, retinoblastoma binding factors.Mammalian Mrf-1 and Mrf-2, transcriptional modulators of thecytomegalovirus major intermediate-early promoter.Drosophila melanogaster Dead ringer protein, a transcriptional regulatoryprotein required for early embryonic development.Yeast SWI1 protein, from the SWI/SNF complex involved in chromatinremodeling and broad aspects of transcription regulation.Drosophila melanogaster Osa. It is structurally related to SWI1 andassociates with the brahma complex, which is the Drosophila equivalent ofthe SWI/SNF complex.
The AT-rich interaction domain (ARID) is an ~100-amino acid DNA-binding module found in a large number of eukaryotic transcription factors that regulate cellproliferation, differentiation and development [, ]. The ARID domain appearsas a single-copy motif and can be found in association with other domains,such as JmjC, JmjN, Tudor and PHD-type zinc finger [].The basic structure of the ARID domain domain appears to be a series of sixα-helices separated by β-strands, loops, or turns, but the structuredregion may extend to an additional helix at either or both ends of the basicsix. Based on primary sequence homology, they can be partitioned into threestructural classes:Minimal ARID proteins that consist of a core domain formed by six alpha-helices;ARID proteins that supplement the core domain with an N-terminal alpha-helix;Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.Minimal ARIDs are distributed in all eukaryotes, while extended ARIDs arerestricted to metazoans. The ARID domain binds DNA as a monomer, recognizingthe duplex through insertion of a loop and an α-helix into the majorgroove, and by extensive non-specific anchoring contacts to the adjacentsugar-phosphate backbone [, , ].Some proteins known to contain a ARID domain are listed below:Eukaryotic transcription factors of the jumonji family.Mammalian Bright, a B-cell-specific trans-activator of IgH transcription.Mammalian PLU-1, a protein that is upregulated in breast cancer cells.Mammalian RBP1 and RBP2, retinoblastoma binding factors.Mammalian Mrf-1 and Mrf-2, transcriptional modulators of thecytomegalovirus major intermediate-early promoter.Drosophila melanogaster Dead ringer protein, a transcriptional regulatoryprotein required for early embryonic development.Yeast SWI1 protein, from the SWI/SNF complex involved in chromatinremodeling and broad aspects of transcription regulation.Drosophila melanogaster Osa. It is structurally related to SWI1 andassociates with the brahma complex, which is the Drosophila equivalent ofthe SWI/SNF complex.
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 [, , , , ]. 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 []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH [].TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ].The TFIIB zinc finger adopts a zinc ribbon fold characterised by two β-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I [].
