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Steitz TA. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q Rev Biophys 1990; 23:205-80. [PMID: 2204954 DOI: 10.1017/s0033583500005552] [Citation(s) in RCA: 460] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Structural studies of DNA-binding proteins and their complexes with DNA have proceeded at an accelerating pace in recent years due to important technical advances in molecular genetics, DNA synthesis, protein crystallography and nuclear magnetic resonance. The last major review on this subject by Pabo & Sauer (1984) summarized the structural and functional studies of the three sequence-specific DNA-binding proteins whose crystal structures were then known, theE. colicatabolite gene activator protein (CAP) (McKay & Steitz, 1981; McKayet al.1982; Weber & Steitz, 1987), acrorepressor from phage λ (Andersonet al.1981), and the DNA-binding proteolytic fragment ofλcIrepressor protein (Pabo & Lewis, 1982) Although crystallographic studies of theE. coli lacrepressor protein were initiated as early as 1971 when it was the only regulatory protein available in sufficient quantities for structural studies (Steitzet al.1974), little was established about the structural aspects of DNA-binding proteins until the structure of CAP was determined in 1980 followed shortly thereafter by the structure ofλcrorepressor and subsequently that of the λ repressor fragment. There are now determined at high resolution the crystal structures of seven prokaryotic gene regulatory proteins or fragments [CAP,λcro,λcIrepressor fragment, 434 repressor fragment (Andersonet al.1987), 434crorepressor (Wolbergeret al.1988),E. coli trprepressor (Schevitzet al.1985),E. coli metrepressor (Raffertyet al.1989)],EcoRI restriction endonuclease (McClarinet al.1986), DNAse I (Suck & Ofner, 1986), the catalytic domain of γδ resolvase (Hatfullet al.1989) and two sequence-independent double-stranded DNA-binding proteins [the Klenow fragment ofE. coliDNA polymerase I (Olliset al.1985) and theE. coliHu protein (Tanakaet al., 1984)].
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Affiliation(s)
- T A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University
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203
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Härd T, Kellenbach E, Boelens R, Maler BA, Dahlman K, Freedman LP, Carlstedt-Duke J, Yamamoto KR, Gustafsson JA, Kaptein R. Solution structure of the glucocorticoid receptor DNA-binding domain. Science 1990; 249:157-60. [PMID: 2115209 DOI: 10.1126/science.2115209] [Citation(s) in RCA: 487] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The three-dimensional structure of the DNA-binding domain (DBD) of the glucocorticoid receptor has been determined by nuclear magnetic resonance spectroscopy and distance geometry. The structure of a 71-residue protein fragment containing two "zinc finger" domains is based on a large set of proton-proton distances derived from nuclear Overhauser enhancement spectra, hydrogen bonds in previously identified secondary structure elements, and coordination of two zinc atoms by conserved cysteine residues. The DBD is found to consist of a globular body from which the finger regions extend. A model of the dimeric complex between the DBD and the glucocorticoid response element is proposed. The model is consistent with previous results indicating that specific amino acid residues of the DBD are involved in protein-DNA and protein-protein interactions.
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Affiliation(s)
- T Härd
- Department of Chemistry, University of Utrecht, The Netherlands
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204
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Churchill ME, Tullius TD, Klug A. Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus. Proc Natl Acad Sci U S A 1990; 87:5528-32. [PMID: 2164687 PMCID: PMC54358 DOI: 10.1073/pnas.87.14.5528] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The zinc finger protein TFIIIA, a positive transcription factor of the 5S RNA gene, binds to an internal control region of 50 nucleotides. Two modes of binding have been considered for the TFIIIA-DNA complex, one of which has been proposed on the basis of nuclease and chemical protection experiments and the other on model building. Since then, evidence has accumulated on the structures of individual components of the complex--for example, zinc finger polypeptides studied by NMR and a segment of the binding site analyzed by x-ray crystallography, but no high-resolution structural data on the TFIIIA-DNA complex itself are available. Probes used previously to study the TFIIIA-DNA complex do not react with every nucleotide of DNA, unlike hydroxyl radical, which cleaves DNA at every backbone position. We describe here the quantitative analysis of high-resolution hydroxyl radical footprints and suggest how the array of zinc fingers might interact with the double helix.
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Affiliation(s)
- M E Churchill
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England
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205
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206
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South TL, Kim B, Hare DR, Summers MF. Zinc fingers and molecular recognition. Structure and nucleic acid binding studies of an HIV zinc finger-like domain. Biochem Pharmacol 1990; 40:123-9. [PMID: 2115335 DOI: 10.1016/0006-2952(90)90187-p] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- T L South
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore 21228
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207
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Weiss MA, Mason KA, Dahl CE, Keutmann HT. Alternating zinc-finger motifs in the human male-associated protein ZFY. Biochemistry 1990; 29:5660-4. [PMID: 2116899 DOI: 10.1021/bi00476a002] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
ZFY, a putative transcription factor encoded by the human Y chromosome, contains a distinctive two-finger repeat: odd-numbered and even-numbered CC/HH metal-binding motifs exhibit systematic alternation in sequence pattern. Such alternation, which is not generally observed in zinc-finger proteins, has also been described in an extensive family of Kruppel-like genes in Xenopus laevis and in the AIDS-associated human DNA-binding protein HIV-EP1. The strict conservation of a two-finger repeat among ZFY-, Kruppel- and HIV-related zinc-finger proteins suggests distinct mechanisms of protein-nucleic acid recognition. To test whether this sequence pattern reflects an underlying alternation in domain structure, we have synthesized and characterized single-finger peptides from the human ZFY gene. Remarkably, systematic differences in metal-dependent folding are observed in the circular dichroism spectra of even- and odd-numbered domains. Our results suggest the existence of distinct CC/HH finger submotifs, which may play different roles in nucleic acid recognition.
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Affiliation(s)
- M A Weiss
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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208
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Taylor WE, Young ET. cAMP-dependent phosphorylation and inactivation of yeast transcription factor ADR1 does not affect DNA binding. Proc Natl Acad Sci U S A 1990; 87:4098-102. [PMID: 2161531 PMCID: PMC54054 DOI: 10.1073/pnas.87.11.4098] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Transcription factor ADR1 increases the level of ADH2 gene expression 200-fold by binding to a palindromic upstream activation sequence (UAS1) in the glucose-repressible ADH2 promoter in Saccharomyces cerevisiae. cAMP-dependent protein kinase (cAPK) phosphorylates ADR1 in vitro and a yeast strain with elevated cAPK activity inhibits the ability of ADR1 to activate ADH2 transcription in vivo [Cherry, J. R., Johnson, T. R., Dollard, C., Schuster, J. R. & Denis, C. L. (1988) Cell 56, 409-419]. Intact ADR1 protein was detected at comparable levels in extracts made from repressed or derepressed yeast cells, indicating that glucose repression is not due to absence of ADR1. ADR1 in extracts made from glucose-repressed and -derepressed cells bound UAS1 DNA with similar affinities despite having greatly different abilities to activate ADH2 gene expression in vivo. A mutant form of ADR1 encoded by ADR1-5c, which has an altered consensus sequence for phosphorylation by cAPK conferred constitutive expression on ADH2 but bound DNA to the same extent as wild-type ADR1 protein. Similarly, normal DNA binding was seen for ADR1 produced in mutants with altered levels of cAPK activity. Because inactivation of ADR1 by phosphorylation has no detectable effect on either DNA binding or ADR1 levels, ADR1 probably binds to UAS1 constitutively and phosphorylation prevents it from promoting transcription.
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Affiliation(s)
- W E Taylor
- Department of Biochemistry, University of Washington, Seattle 98195
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209
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The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)38926-4] [Citation(s) in RCA: 481] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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210
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Lee TC, Christie GE. Purification and properties of the bacteriophage P2 ogr gene product. A prokaryotic zinc-binding transcriptional activator. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39137-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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211
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Berg JM. Zinc fingers and other metal-binding domains. Elements for interactions between macromolecules. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39172-0] [Citation(s) in RCA: 227] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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212
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Neuhaus D, Nakaseko Y, Nagai K, Klug A. Sequence-specific [1H]NMR resonance assignments and secondary structure identification for 1- and 2-zinc finger constructs from SW15. A hydrophobic core involving four invariant residues. FEBS Lett 1990; 262:179-84. [PMID: 2110530 DOI: 10.1016/0014-5793(90)80184-k] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Complete [1H]NMR resonance assignments are presented for the second of the three zinc fingers from SW15 as it appears in both 1- and 2-finger constructs. Signals from finger 2 are unaffected by the presence or absence of finger 1, showing that the protein has a modular construction. The structure of finger 2 comprises a helix running from N56 to Q67, and a region approximating to an anti-parallel beta-sheet running from Y42 to F53. These features combine to produce a hydrophobic core in the structure involving the invariant residues Y42, F53, L59 and H62.
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Affiliation(s)
- D Neuhaus
- MRC Laboratory for Molecular Biology, Cambridge, England
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213
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Identification, nuclear localization, and DNA-binding activity of the zinc finger protein encoded by the Evi-1 myeloid transforming gene. Mol Cell Biol 1990. [PMID: 2106070 DOI: 10.1128/mcb.10.3.1259] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Activation of the Evi-1 zinc finger gene is a common event associated with transformation of murine myeloid leukemias. To characterize the gene product, we developed antisera against various protein domains. These antisera primarily detected a 145-kilodalton nuclear protein that bound double-stranded DNA. Binding was inhibited by chelating agents and partially restored by zinc ions.
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214
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Carr MD, Pastore A, Gausepohl H, Frank R, Roesch P. NMR and molecular dynamics studies of the mKr2 'zinc finger'. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 188:455-61. [PMID: 2108027 DOI: 10.1111/j.1432-1033.1990.tb15423.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We determined the structure of a 30-amino-acid 'zinc finger' motif from the mouse Kruppel-like gene mKr2 in solution in the absence of metal ions by two-dimensional NMR, distance geometry and restrained molecular dynamics methods. The most prominent secondary structural feature of the peptide is a helix extending from Ser14 to Ile20. The zinc-containing structure of the peptide was simulated by molecular dynamics calculations with restraints derived from the known geometry of the zinc ion and the ligating amino acid residues Cys6, Cys9, His22, His26. The latter structure does not deviate markedly from the set of structures determined for the zinc-free peptide, i.e. this peptide can accommodate a Zn2+ ion without major structural rearrangements. Thus, we propose that the metal ion stabilizes the existing three-dimensional peptide structural motif rather than introducing novel structural features.
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Affiliation(s)
- M D Carr
- Max-Planck-Institut für Medizinische Forschung, Abteilung Biophysik, Heidelberg, Federal Republic of Germany
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215
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Matsugi T, Morishita K, Ihle JN. Identification, nuclear localization, and DNA-binding activity of the zinc finger protein encoded by the Evi-1 myeloid transforming gene. Mol Cell Biol 1990; 10:1259-64. [PMID: 2106070 PMCID: PMC361017 DOI: 10.1128/mcb.10.3.1259-1264.1990] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Activation of the Evi-1 zinc finger gene is a common event associated with transformation of murine myeloid leukemias. To characterize the gene product, we developed antisera against various protein domains. These antisera primarily detected a 145-kilodalton nuclear protein that bound double-stranded DNA. Binding was inhibited by chelating agents and partially restored by zinc ions.
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Affiliation(s)
- T Matsugi
- Department of Biochemistry, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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216
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Lania L, Donti E, Pannuti A, Pascucci A, Pengue G, Feliciello I, La Mantia G, Lanfrancone L, Pelicci PG. cDNA isolation, expression analysis, and chromosomal localization of two human zinc finger genes. Genomics 1990; 6:333-40. [PMID: 2106481 DOI: 10.1016/0888-7543(90)90574-e] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
On the basis of sequence similarity in the repeated zinc finger domain, we have identified and characterized two human cDNA clones (ZNF7 and ZNF8), both encoding proteins containing potential finger-like nucleic acid binding motifs. Northern blot analysis indicates that both genes are expressed as multiple transcripts and they are ubiquitously present in many human cell lines of different embryological derivation. Moreover, their expression is modulated during in vitro induced terminal differentiation of human myeloid cell line HL-60. By in situ hybridization experiments, we have localized the ZNF7 gene to chromosome 8 (region q24) and the ZNF8 gene to the terminal band of the long arm of chromosome 20 (20q13).
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Affiliation(s)
- L Lania
- Department of Genetics, University of Naples, Italy
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217
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Abstract
The "zinc finger" is a 30-residue repeating motif that has been identified in a variety of eukaryotic transcription factors. Each domain is capable of binding a Zn2+ ion through invariant Cys and His residues. We have determined the three-dimensional structure of a synthetic peptide that corresponds to one of the two zinc finger domains in the yeast transcription factor ADR1, using two-dimensional nuclear magnetic resonance spectroscopy. The Zn2(+)-bound structure of the peptide consists of a loop containing the two Cys residues, a "fingertip," a 12- to 13-residue alpha-helix containing the two His residues, and a C-terminal tail. A majority of the interresidue contacts observed involve the seven conserved residues of the prototypic zinc finger (i.e., the four zinc ligands and the three hydrophobic residues), indicating that these residues are largely responsible for the three-dimensional structure of the domain and that all the zinc finger domains of the TFIIIA class will have similar structures. Potential DNA-binding residues are found throughout the structure, with the highest concentration of such residues on the external face of the alpha-helix.
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Affiliation(s)
- R E Klevit
- Department of Biochemistry, University of Washington, Seattle 98195
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218
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Párraga G, Horvath S, Hood L, Young ET, Klevit RE. Spectroscopic studies of wild-type and mutant "zinc finger" peptides: determinants of domain folding and structure. Proc Natl Acad Sci U S A 1990; 87:137-41. [PMID: 2104978 PMCID: PMC53215 DOI: 10.1073/pnas.87.1.137] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The "zinc finger" model [Miller, J., McLachlan, A. D. & Klug, A. (1985) EMBO J. 4, 1609-1614; Brown, R. S., Sander, C. & Argos, P. (1985) FEBS Lett. 186, 271-274] makes both specific structural and specific functional predictions about zinc finger consensus sequences that can be tested with a combination of genetic, molecular biological, and biophysical techniques. The yeast transcription factor ADR1 contains two adjacent zinc finger domains; genetic and deletion analyses showed that amino acid substitutions and deletions in the zinc finger domains resulted in the loss of protein activity. To test the structural and folding predictions of the zinc finger model, peptides encompassing each of the ADR1 fingers were synthesized (ADR1a and ADR1b) as well as a mutant finger peptide (del138) deleted for a single amino acid residue. The folding and metal-binding characteristics of these were assessed by 1H nuclear magnetic resonance (NMR) and visible spectroscopy. While a single unique conformational species was detected for the two wild-type peptides upon tetrahedral binding of zinc, the deletion peptide did not bind zinc with tetrahedral geometry, nor did it fold into a zinc finger domain. The metal-binding and folding results found with the mutant peptide were similar to those obtained when thiol alkylation or imidazole protonation of the wild-type peptides was performed. These data indicate that ligand spacing and both thiol and imidazole participation in zinc binding are specific and necessary requirements for zinc finger folding, which provides direct support for the initial predictions of the model.
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Affiliation(s)
- G Párraga
- Department of Biochemistry, University of Washington, Seattle 98195
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219
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Iapalucci S, López N, Rey O, Zakin MM, Cohen GN, Franze-Fernández MT. The 5' region of Tacaribe virus L RNA encodes a protein with a potential metal binding domain. Virology 1989; 173:357-61. [PMID: 2510403 DOI: 10.1016/0042-6822(89)90257-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We have just completed the Tacaribe arenavirus (TV) genome structure by sequencing the 5' region of the L RNA. Analysis of the sequence has indicated the existence of an open reading frame (ORF) in the viral sense RNA encoding a 95 amino acid polypeptide. The first in phase AUG codon is in positions 70-72 from the 5' end of the viral RNA surrounded by a sequence favorable for the initiation of protein synthesis. The ORF ends at positions 355-357. The predicted polypeptide (P11) contains a cysteine-rich sequence bearing a remarkable similarity to the "zinc finger" sequences found in a number of proteins. We have recently reported that the 3' region of the TV L RNA encodes a polypeptide comprising 2210 amino acids in the viral-complementary sequence. This latter gene, i.e., the L gene, terminates at positions 442-440 from the 5' end of the viral RNA. The two genes encoded by the L RNA (L and P11) are in opposite strands of the RNA in sequences that do not overlap, but are separated by a noncoding intergenic region of 82 nucleotides. The nucleotide sequence of the intergenic region leads to the prediction of a strong secondary structure.
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Affiliation(s)
- S Iapalucci
- Centro de Virología Animal, Buenos Aires, Argentina
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220
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Abstract
The first step in the transcription of most protein-encoding genes in eukaryotes is the binding of a transcription factor to the TATA-box promoter element. This TATA-box transcription factor was purified from extracts of the yeast Saccharomyces cerevisiae by using reconstitution of in vitro transcription reactions as an assay. The activity copurified with a protein whose sodium dodecyl sulfate/polyacrylamide gel mobility is 25 kDa. The sequence of the amino-terminal 21 residues of this protein was determined by sequential Edman degradation. A yeast genomic library was screened with mixed oligonucleotides encoding six residues of the protein sequence. The yeast TATA-box factor gene was cloned, and DNA sequencing revealed a 720-base-pair open reading frame encoding a 27,016-Da protein. The identity of the clone was confirmed by expressing the gene in Escherichia coli and detecting TATA-box factor DNA binding and transcriptional activities in extracts of the recombinant E. coli. The TATA-box factor gene was mapped to chromosome five of S. cerevisiae. RNA blot hybridization and nuclease S1 analysis indicated that the major TATA-box factor mRNA is 1.3 kilobases, including an unusually long 5' untranslated region of 188 +/- 5 nucleotides. Homology searches showed a region of distant similarity to the calcium-binding structures of calpains, a structure that has a conformation similar to the helix-turn-helix motif of DNA binding proteins.
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Affiliation(s)
- M C Schmidt
- Molecular Biology Institute, University of California, Los Angeles CA 90024-1570
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221
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Parraga G, Young L, Klevit RE. Zinc-finger motifs and DNA binding. Trends Biochem Sci 1989; 14:398. [PMID: 2510374 DOI: 10.1016/0968-0004(89)90283-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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222
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Localization of a minimal binding domain and activation regions in yeast regulatory protein ADR1. Mol Cell Biol 1989. [PMID: 2503705 DOI: 10.1128/mcb.9.6.2360] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ADR1 is a transcription factor required for activation of the glucose-repressible alcohol dehydrogenase 2 (ADH2) gene in Saccharomyces cerevisiae. ADR1 has two zinc finger domains between amino acids 102 and 159, and it binds to an upstream activation sequence (UAS1) in the ADH2 promoter. A functional dissection of ADR1 was performed by using a series of amino- and carboxy-terminal deletion mutants of ADR1, most of which were fused to the Escherichia coli beta-galactosidase. These deletion mutants were assayed for binding to UAS1 in vitro, for the ability to activate ADH2 transcription in vivo, and for level of expression. Deletion of ADR1 amino acids 150 to 172 and 76 to 98 eliminated DNA binding in vitro, which accounted for the loss of transcriptional activation in vivo. Results with the former deletion mutant indicated that both of the ADR1 zinc fingers are necessary for sequence-specific DNA binding. Results with the latter deletion mutant suggested that at least part of the sequence between amino acids 76 to 98, in addition to the two finger domains, is required for high-affinity DNA binding. The smallest fusion protein able to activate ADH2 transcription, containing ADR1 amino acids 76 to 172, was much less active in vivo than was the longest fusion protein containing amino acids 1 to 642 of ADR1. In addition, multiple regions of the ADR1 polypeptide (including amino acids 40 to 76, 260 to 302, and 302 to 505), which are required for full activation of ADH2, were identified. An ADR1-beta-galactosidase fusion protein containing only the amino-terminal 16 amino acids of ADR1 was present at a much higher level than were larger fusion proteins, which suggested that the sequences within ADR1 influence the expression of the gene fusion.
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223
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Abstract
The erythroid-specific transcription factor Eryf1 binds to DNA sites within regulatory regions of every member of both the alpha- and beta-globin families in chicken. The distribution of these sites suggests that Eryf1 may serve as a general "switch" factor for erythroid development. We have cloned the cDNA for Eryf1 and show that the corresponding mRNA is present in all erythroid lineages, but is absent from non-erythroid cells. We demonstrate that the cDNA encodes the specific Eryf1 binding activity found in erythrocytes. Eryf1 is a basic 38 kd protein containing a pair of highly similar "fingers" with the motif Cys-x-x-Cys-x17-Cys-x-x-Cys. The amino acid sequences of these regions bear no resemblance to those found in other regulatory proteins with a similar arrangement of cysteine residues. Our evidence suggests, furthermore, that transition metal ions are unusually tightly bound, or may not be necessary for the sequence-specific DNA binding of Eryf1.
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Affiliation(s)
- T Evans
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892
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224
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Lee MS, Cavanagh J, Wright PE. Complete assignment of the 1H NMR spectrum of a synthetic zinc finger from Xfin. Sequential resonance assignments and secondary structure. FEBS Lett 1989; 254:159-64. [PMID: 2506074 DOI: 10.1016/0014-5793(89)81030-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A 25-residue synthetic peptide corresponding to zinc finger 31 of the Xenopus protein Xfin adopts a compact, folded conformation in the presence of zinc. Complete 1H resonance assignments have been made. The peptide contains a helix, beginning as an alpha-helix and ending as a 3(10)-helix, that extends from residue 12 to 23. Several positively charged and polar residues located on this helix are likely to be involved in interactions with DNA. Residues 1-10 appear to adopt a hairpin-like structure.
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Affiliation(s)
- M S Lee
- Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA
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225
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Abstract
NMR studies of dynamics within structure have revealed that a quite new approach to protein structure and its relation to function is necessary. This approach requires the consideration in detail of the following: 1. Local movements of groups and small segments to allow fast recognition and fitting. The motion concerns on/off rates as well as binding. The observations affect surface/surface recognition, e.g. of antigen/antibody as well as of substrate and protein. 2. Somewhat larger interdomain or N- and C-terminal segments which allow rearrangement. Cases in point are the movement of segments in blood-clotting proteins or in histones. 3. Relative motion of helices in hinges. These actions are likely in such enzymes as kinases and P-450 cytochromes. 4. Relative motion of helices within domains (relative to other helices or sheets) in mechanical devices (triggers) e.g. in calmodulin. 5. General motion in random proteins. Examples extend from rubber-like proteins (entropy sensors), some glycoproteins, to proteins carrying peptide hormones to be generated only after hydrolysis. 6. Order----disorder transitions locally as in osteocalcin and metallothionine. 7. Swinging arm motions associated with special sequences such as (Ala-Pro)n. 8. Of great interest is the power of NMR to look at proteins which are relatively large, up to 50 kDa proteins, and to isolate certain zones of interest. This needs careful temperature dependent studies and analysis of separated domains [72] as well as the use of a great variety of pulse sequences [15] and of nuclei other than protons. 9. In this article I have illustrated the different possibilities using work in my own group. This is done to lessen the burden of extensive review. I fully realise that the range of examples is now large. I would stress though that the production of the necessary technology was the endeavour of several of us within the Oxford Enzyme Group from 1970 to 1985, i.e. from 270-600 MHz Fourier-transform NMR spectroscopy. 10. While all of these features have been demonstrated by NMR methods there are parallel developments both using X-ray diffraction methods and theoretical approaches. All these procedures are changing the view of protein structure to one which incorporates dynamics all the way from conventional vibronic/rotational coupling to the disordered motions characteristic of random polymers. It is the understanding of dynamics that leads to an appreciation of function.
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Affiliation(s)
- R J Williams
- Inorganic Chemistry Laboratory, University of Oxford
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226
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Lee MS, Gippert GP, Soman KV, Case DA, Wright PE. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science 1989; 245:635-7. [PMID: 2503871 DOI: 10.1126/science.2503871] [Citation(s) in RCA: 469] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The three-dimensional solution structure of a zinc finger nucleic acid binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. Spectra of a synthetic peptide corresponding to a single zinc finger from the Xenopus protein Xfin yielded distance and dihedral angle constraints that were used to generate structures from distance geometry and restrained molecular dynamics calculations. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding.
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Affiliation(s)
- M S Lee
- Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, CA 92037
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227
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Schroth GP, Cook GR, Bradbury EM, Gottesfeld JM. Transcription factor IIIA induced bending of the Xenopus somatic 5S gene promoter. Nature 1989; 340:487-8. [PMID: 2755511 DOI: 10.1038/340487a0] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Transcription factor IIIA (TFIIIA), the canonical zinc-finger protein, is a protein of relative molecular mass 39,000 (39K) that is required for transcription of 5S-ribosomal subunit genes in Xenopus. It binds in a sequence-specific manner to the internal control region of the 5S gene (see Fig. 1) and facilitates transcription of the gene by RNA polymerase III. It also binds to the 5S gene product to form a 7S ribonucleoprotein particle. In oocytes the 7S particle acts as a storage form of the RNA to be utilized later in development. TFIIIA binds to DNA through its 30 K N-terminal domain, which contains nine zinc-fingers. TFIIIA was the first protein described to have this type of DNA binding motif, but numerous other proteins have now been shown to have zinc-finger domains. A structure for a single zinc-finger from the yeast protein ADR1, was recently proposed based on two-dimensional NMR data (ref. 8), and a similar structure was proposed based on comparison with crystal structures of other metalloproteins. Although models for the interaction of TFIIIA with the 5S-ribosomal gene DNA have been proposed, based on nuclease digestion and methylation interference data, little precise structural information is available for TFIIIA and the physical basis for the interaction of zinc-fingers with DNA is not understood. Using both circular permutation and circularization assays we provide convincing biochemical evidence that TFIIIA bends the DNA at the internal promoter of the 5S gene.
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Affiliation(s)
- G P Schroth
- Department of Biological Chemistry, School of Medicine, University of California, Davis 95616
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228
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Mitchell PJ, Tjian R. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science 1989; 245:371-8. [PMID: 2667136 DOI: 10.1126/science.2667136] [Citation(s) in RCA: 2510] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The cloning of genes encoding mammalian DNA binding transcription factors for RNA polymerase II has provided the opportunity to analyze the structure and function of these proteins. This review summarizes recent studies that define structural domains for DNA binding and transcriptional activation functions in sequence-specific transcription factors. The mechanisms by which these factors may activate transcriptional initiation and by which they may be regulated to achieve differential gene expression are also discussed.
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Affiliation(s)
- P J Mitchell
- Howard Hughes Medical Institute, Department of Biochemistry, University of California, Berkeley 94720
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229
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Bellefroid EJ, Lecocq PJ, Benhida A, Poncelet DA, Belayew A, Martial JA. The human genome contains hundreds of genes coding for finger proteins of the Krüppel type. DNA (MARY ANN LIEBERT, INC.) 1989; 8:377-87. [PMID: 2505992 DOI: 10.1089/dna.1.1989.8.377] [Citation(s) in RCA: 152] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Our aim was to identify new human proteins with potential DNA binding activity, related to the Krüppel protein which regulates Drosophila segmentation. We screened a human placenta cDNA library and a human genomic DNA library with a synthetic oligonucleotide probe corresponding to the H/C link region that connects finger loops in the multifingered Krüppel protein. We found more than 100 different mRNAs encoding Krüppel multifingered proteins in the human placenta. In the whole human genome, the number of genes encoding such proteins reaches about 300. Sequence analysis of 14 cloned cDNAs indicated that they code for at least nine undescribed human finger proteins. The sequences of the 106 finger repeats present in these nine proteins are highly homologous. Most of the variability lies in a limited number of positions located in their postulated alpha-helical structure, and therefore could be implicated in their DNA-binding specificity.
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Affiliation(s)
- E J Bellefroid
- Laboratoire Central de Génie Génétique, Université de Liége, SartTilman, Belgium
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230
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Affiliation(s)
- J M Berg
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
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231
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Green LM, Berg JM. A retroviral Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys peptide binds metal ions: spectroscopic studies and a proposed three-dimensional structure. Proc Natl Acad Sci U S A 1989; 86:4047-51. [PMID: 2786206 PMCID: PMC287385 DOI: 10.1073/pnas.86.11.4047] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Retroviral gag gene-encoded core nucleic acid binding proteins contain either one or two sequences of the form Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys. Previously, one of us has proposed that these sequences form metal-binding domains in analogy with the "zinc finger" domains first observed in transcription factor IIIA. We report that an 18-amino acid peptide derived from the core nucleic acid binding protein from Rauscher murine leukemia virus binds metal ions such as Co2+ and Zn2+. The absorption spectrum of the peptide-Co2+ complex is highly suggestive of tetrahedral coordination involving three cysteinates and one histidine. Titration experiments indicate that the dissociation constant for the peptide-Co2+ complex is 1.0 microM and that Zn2+ binds more tightly than Co2+. A detailed three-dimensional structure for this domain based on conserved substructures in other crystallographically characterized metalloproteins and on a detailed analysis of the Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys sequences from retroviruses and other related sources is proposed.
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Affiliation(s)
- L M Green
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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232
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Thukral SK, Tavianini MA, Blumberg H, Young ET. Localization of a minimal binding domain and activation regions in yeast regulatory protein ADR1. Mol Cell Biol 1989; 9:2360-9. [PMID: 2503705 PMCID: PMC362309 DOI: 10.1128/mcb.9.6.2360-2369.1989] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
ADR1 is a transcription factor required for activation of the glucose-repressible alcohol dehydrogenase 2 (ADH2) gene in Saccharomyces cerevisiae. ADR1 has two zinc finger domains between amino acids 102 and 159, and it binds to an upstream activation sequence (UAS1) in the ADH2 promoter. A functional dissection of ADR1 was performed by using a series of amino- and carboxy-terminal deletion mutants of ADR1, most of which were fused to the Escherichia coli beta-galactosidase. These deletion mutants were assayed for binding to UAS1 in vitro, for the ability to activate ADH2 transcription in vivo, and for level of expression. Deletion of ADR1 amino acids 150 to 172 and 76 to 98 eliminated DNA binding in vitro, which accounted for the loss of transcriptional activation in vivo. Results with the former deletion mutant indicated that both of the ADR1 zinc fingers are necessary for sequence-specific DNA binding. Results with the latter deletion mutant suggested that at least part of the sequence between amino acids 76 to 98, in addition to the two finger domains, is required for high-affinity DNA binding. The smallest fusion protein able to activate ADH2 transcription, containing ADR1 amino acids 76 to 172, was much less active in vivo than was the longest fusion protein containing amino acids 1 to 642 of ADR1. In addition, multiple regions of the ADR1 polypeptide (including amino acids 40 to 76, 260 to 302, and 302 to 505), which are required for full activation of ADH2, were identified. An ADR1-beta-galactosidase fusion protein containing only the amino-terminal 16 amino acids of ADR1 was present at a much higher level than were larger fusion proteins, which suggested that the sequences within ADR1 influence the expression of the gene fusion.
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Affiliation(s)
- S K Thukral
- Department of Biochemistry, University of Washington, Seattle 98195
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233
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Millstein LS, Gottesfeld JM. Control of gene expression in eukaryotic cells: lessons from class III genes. Curr Opin Cell Biol 1989; 1:497-502. [PMID: 2697269 DOI: 10.1016/0955-0674(89)90011-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- L S Millstein
- Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, California
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