The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors 1 1Edited by P. E. Wright

Starich, Mary R.; Wikström, Mats; Arst, Herbert N.; Clore, G. Marius; Gronenborn, Angela M.

doi:10.1006/jmbi.1998.1625

Cited by 61 publications

(92 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Shown are electrophoretic mobility shift assays comparing the binding specificities of peptides CC14 (D) and CC13 (E) for various dsDNA oligomers, corresponding to data presented in A and C, respectively. the recognition of the GAT motif, in a manner similar to the corresponding PL-RR residues of the AREA zinc finger (12).…”

Section: Discussionmentioning

confidence: 99%

“…Shown are sequences of the N-terminal and C-terminal zinc finger peptides described in this study with modified or additional residues highlighted in bold black characters. Residues indicated in red represent the zinc chelating CXXC, whereas residues highlighted in bold blue characters represent the core zinc finger residues responsible for the recognition of the GAT DNA motif (11,12). The region encompassing the single ␣-helix of the core finger is underlined.…”

Section: Binding Site Selections Experimentsmentioning

confidence: 99%

“…The residues involved in these interactions all belong to the basic QTRNRK motif (residues Gln-209 to Lys-214 of cGATA-1). 1 The importance of these basic linker residues for the high affinity interactions of the C-terminal finger of GATA-1 with DNA has been further emphasized in a recent solution structure of the fungal AREA-DNA complex (12). The basic C-terminal arm of AREA, which lacks the QTRNRK motif, wraps around the DNA.…”

mentioning

confidence: 99%

“…However, rather than lying in the minor groove, the arm runs parallel to the sugar phosphate backbone along the edge of the minor groove. It has been proposed that this accounts for the ϳ1000-fold difference in affinity noted for the C-terminal finger of GATA-1 and the AREA single finger (12). Do these different modes of C-terminal arm binding influence the DNA binding specificity of the GATA zinc fingers?…”

mentioning

confidence: 99%

See 3 more Smart Citations

Determinants of GATA-1 Binding to DNA

Ghirlando

Trainor

2003

Journal of Biological Chemistry

View full text Add to dashboard Cite

Mammalian GATA transcription factors are expressed in various tissues in a temporally regulated manner. The prototypic member, GATA-1, is required for normal erythroid, megakaryocytic, and mast cell development. This family of DNA-binding proteins recognizes a consensus (A/T)GATA(A/G) motif and possesses homologous DNA binding domains consisting of two zinc fingers. The C-terminal finger of GATA-1 recognizes the consensus motif with nanomolar affinities, whereas the N-terminal finger shows a binding preference for a GATC motif, albeit with much reduced affinity (K d Ϸ M). The Nterminal finger of GATA-2 also shows a preference for an AGATCT binding site, with an increased affinity attributed to N-and C-terminal flanking basic residues (K d Ϸ nM). To understand the differences in the binding specificities of the N-and C-terminal zinc fingers of GATA-1, we have constructed a series of swapped domain peptides. We show that the specificity for AGATAA over AGATCT arises from the C-terminal non-finger basic domain. Thus, the N-terminal finger binds preferentially to AGATAA once appended to the C-terminal arm of the C-terminal finger. We further show that this specificity arises from the highly conserved QTRNRK residues. The converse is, however, untrue in the case of the C-terminal finger; swapping of QTRNRK with the corresponding LVSKRA does not switch the DNA binding specificity from AGATAA to AGATCT. These results highlight the important role of residues adjacent to the CXXCX 17 CNAC zinc finger motif (i.e. non-finger residues) in the specific recognition of DNA residues.DNA binding zinc fingers of the form CXXCX 17 CNAC characterize the GATA family of transcription factors. GATA-1, the original member of the family possesses two such zinc fingers (1, 2). The C-terminal finger and flanking basic arm are both necessary and sufficient for binding to the GATA recognition sequence, (A/T)GATA(A/G) (3, 4). Even though the single Nterminal finger does not bind DNA independently with high affinity, it does stabilize GATA-1 interactions with some sites crucial for gene expression (3,(5)(6)(7)(8). Recent reports, however, indicate that the N-terminal finger binds DNA with an affinity much lower than that observed for the C-terminal finger with binding occurring preferentially to GATC motifs (9). Despite the similarities between the C-and N-terminal fingers (Fig. 1, peptides CC11 and NN4, respectively), the N-terminal finger does not recognize the AGATAA consensus motif, indicating that the flanking or poorly conserved linker residues may play a key role in DNA recognition. A role for the flanking residues has been pointed out in the case of the N-terminal finger of GATA-2 (10). Like the N-terminal finger of GATA-1, this homologous finger shows a binding preference for GATC motifs. However, because of the additional basic region at the N terminus a higher binding affinity has been reported for this finger.Solution NMR studies of the complex formed between the C-terminal finger of cGATA-1 and the AGATAA DNA sequence highlight t...

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Binding Site Selections Experimentsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Determinants of GATA-1 Binding to DNA

Ghirlando

Trainor

2003

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…17,18 Structural studies have shown that NmrA binds directly to the zinc finger of AreA mainly through interactions with alpha helices 1, 6, and 11, and amino acid substitutions in alpha helix 6 (E193Q/D195N or Q202E/ F204Y) reduce the affinity of this interaction. 9,11 Comparison with a nuclear magnetic resonance solution structure of the AreA Zf in a complex with a GATAcontaining double stranded oligonucleotide 19,20 shows parts of helices a-6 and a-11 of NmrA are positioned close to the GATA motif in the DNA, mimicking the major groove of the DNA. 9 We show here for the first time that A. nidulans has three protease activities that digest NmrA(Mr 38.8 kDa) in an ordered manner to generate an N-terminal protease resistant 32 kDa fragment and that in vitro the presence of oxidized dinucleotides substantially enhances the resistance of this N-terminal fragment to further digestion by these proteases.…”

Section: Introductionmentioning

confidence: 99%

The transcription repressor NmrA is subject to proteolysis by three Aspergillus nidulans proteases

et al. 2010

View full text Add to dashboard Cite

The role of specific cleavage of transcription repressor proteins by proteases and how this may be related to the emerging theme of dinucleotides as cellular signaling molecules is poorly characterized. The transcription repressor NmrA of Aspergillus nidulans discriminates between oxidized and reduced dinucleotides, however, dinucleotide binding has no effect on its interaction with the zinc finger in the transcription activator AreA. Protease activity in A. nidulans was assayed using NmrA as the substrate, and was absent in mycelium grown under nitrogen sufficient conditions but abundant in mycelium starved of nitrogen. One of the proteases was purified and identified as the protein Q5BAR4 encoded by the gene AN2366.2. Fluorescence confocal microscopy showed that the nuclear levels of NmrA were reduced approximately 38% when mycelium was grown on nitrate compared to ammonium and absent when starved of nitrogen. Proteolysis of NmrA occurred in an ordered manner by preferential digestion within a C-terminal surface exposed loop and subsequent digestion at other sites. NmrA digested at the C-terminal site was unable to bind to the AreA zinc finger. These data reveal a potential new layer of control of nitrogen metabolite repression by the ordered proteolytic cleavage of NmrA. NmrA digested at the C-terminal site retained the ability to bind NAD 1 and showed a resistance to further digestion that was enhanced by the presence of NAD 1 . This is the first time that an effect of dinucleotide binding to NmrA has been demonstrated.

show abstract

Gronenborn, A. M.: NMR - Nothing More Rewarding

Gronenborn

2011

Encyclopedia of Magnetic Resonance

View full text Add to dashboard Cite

The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors 1 1Edited by P. E. Wright

Cited by 61 publications

References 49 publications

Determinants of GATA-1 Binding to DNA

Determinants of GATA-1 Binding to DNA

The transcription repressor NmrA is subject to proteolysis by three Aspergillus nidulans proteases

Gronenborn, A. M.: NMR - Nothing More Rewarding

Contact Info

Product

Resources

About