Zinc co‐ordination in the DNA‐binding domain of the yeast transcriptional activator PPR1

Ball, Linda; Diakun, G.P.; Gadhavi, Paresh L.; Young, Nigel A.; Armstrong, Elaine M.; Garner, C. David; Laue, Ernest D.

doi:10.1016/0014-5793(94)01448-a

Cited by 14 publications

(5 citation statements)

References 21 publications

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“…The zinc(II)-binding cluster lies in the DNA major groove and contacts three base pairs . The Zn(II)2Cys6 motif of the S. cerevisiae PPR1 protein coordinates two zinc(II) ions via the six cysteine residues and forms a structure nearly identical in conformation to that observed for GAL4 (Marmorstein and Harrison, 1994;Ball et al, 1995). Coordination of two zinc(II) ions and/or DNA binding has now been documented for a number of other Zn(II)2Cys6 proteins (Table 1).…”

Section: The Zn(ii)2cys6 Dna Binding Motifmentioning

confidence: 73%

“…Accession numbers for the Swissprot and PIR databases are available from the WWW at URL http://mendel.genetics.unimelb.edu.au/ C6. * Binuclear zinc(II) coordination has been demonstrated for GAL4 Gardner et al, 1991;Beleja et al, 1992;Kraulis et al, 1992;Marmorstein et al, 1992), HAP1 (Timmerman et al, 1994), PPR1 (Marmorstein and Harrison, 1994;Ball et al, 1995), UME6 (Anderson et al, 1995), LAC9 , AlcR (Sequeval and Felenbok, 1994), and QutA (Levesley et al, 1996). of an extended variable subregion, as in PRIB and AlcR, may overcome the requirement for a proline by permitting the turn required between the a-helical CX 2 CX 6 C units.…”

Section: Structure Of the Zn(ii)2cys6 Domainmentioning

confidence: 99%

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Evolution of a Fungal Regulatory Gene Family: The Zn(II)2Cys6 Binuclear Cluster DNA Binding Motif

Todd

Andrianopoulos

1997

Fungal Genetics and Biology

260

265

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Section: The Zn(ii)2cys6 Dna Binding Motifmentioning

confidence: 73%

Section: Structure Of the Zn(ii)2cys6 Domainmentioning

confidence: 99%

Evolution of a Fungal Regulatory Gene Family: The Zn(II)2Cys6 Binuclear Cluster DNA Binding Motif

Todd

Andrianopoulos

1997

Fungal Genetics and Biology

260

265

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“…However, a similar Zn‚‚‚Zn distance of 3.16 Å has been determined by EXAFS for a binuclear Zn 2 (CysS) 6 cluster in transcriptional activator PPR1. In this cluster, both Zn(II) ions are bridged by two CysS ligands (54). The proposed EXAFS model for the Zn 3 -cluster in GIF shows a binuclear cluster similar to that in PPR1, which is linked with a third tetrahedral tetrathiolate Zn-site (19).…”

Section: Discussionmentioning

confidence: 89%

Evidence for a Dynamic Structure of Human Neuronal Growth Inhibitory Factor and for Major Rearrangements of Its Metal−Thiolate Clusters

et al. 1999

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Human neuronal growth inhibitory factor (GIF), a metallothionein-like protein classified as metallothionein-3, impairs the survival and the neurite formation of cultured neurons. Despite its approximately 70% amino acid sequence identity with those of mammalian metallothioneins (MT-1 and MT-2 isoforms), only GIF exhibits growth inhibitory activity. In this study, structural features of the metal-thiolate clusters in recombinant Zn(7)- and Cd(7)-GIF, and in part also in synthetic GIF (68 amino acids), were investigated by using circular dichroism (CD) and (113)Cd NMR. The CD and (113)Cd NMR studies of recombinant Me(7)-GIF confirmed the existence of distinct Me(4)S(11)- and Me(3)S(9)-clusters located in the alpha- and beta-domains of the protein, respectively. Moreover, a mutual structural stabilization of both domains was demonstrated. The (113)Cd NMR studies of recombinant (113)Cd(7)-GIF were conducted at different magnetic fields (66.66 and 133.33 MHz) and temperatures (298 and 323 K). At 298 K the spectra revealed seven (113)Cd signals at 676, 664, 651, 644, 624, 622, and 595 ppm. A striking feature of all resonances is the absence of resolved homonuclear [(113)Cd-(113)Cd] couplings and large apparent line widths (between 140 and 350 Hz), which account for the absence of cross-peaks in [(113)Cd, (113)Cd] COSY. On the basis of a close correspondence in chemical shift positions of the (113)Cd signals at 676, 624, 622, and 595 ppm with those obtained in our previous studies of (113)Cd(4)-GIF(32-68) [Hasler, D. W., Faller, P., and Vasák, M. (1998) Biochemistry 37, 14966], these resonances can be assigned to a Cd(4)S(11)-cluster in the alpha-domain of (113)Cd(7)-GIF. Consequently, the remaining three (113)Cd signals at 664, 651, and 644 ppm originate from a Me(3)S(9) cluster in the beta-domain. However, the latter resonances show a markedly reduced and temperature-independent intensity (approximately 20%) when compared with those of the alpha-domain, indicating that the majority of the signal intensity remained undetected. To account for the observed NMR features of (113)Cd(7)-GIF, we suggest that dynamic processes acting on two different NMR time scales are present: (i) fast exchange processes among conformational cluster substates giving rise to broad, weight-averaged resonances and (ii) additional very slow exchange processes within the beta-domain associated with the formation of configurational cluster substates. The implications of the structure fluctuation for the biological activity of GIF are discussed.

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“…Refinement with two zinc ions resulted in a zinc–zinc distance of ∼3.3 Å. In other proteins, as for example in GAL4, the zinc–zinc distance is 3.5 Å (Vallee et al 1991); in yeast PPR1 it is 3.16 Å (Ball et al 1995); in human apoferritin H‐chain the distance is 3.32 Å (Ball et al 1995); and in E. coli ferritin, 3.43 Å (Stillman et al 2001). The additional zinc corresponds to the conserved Wat2001 in the Dps family members.…”

Section: Discussionmentioning

confidence: 99%

Structural basis of the zinc‐ and terbium‐mediated inhibition of ferroxidase activity in Dps ferritin‐like proteins

et al. 2008

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Streptococcus suis Dpr is an iron-binding protein involved in oxidative stress resistance. It belongs to the bacterial Dps protein family whose members form dodecameric assemblies. Previous studies have shown that zinc and terbium inhibit iron incorporation in Listeria innocua Dps protein. In order to gain structural insights into the inhibitory effect of zinc and terbium, the crystal structures of Streptococcus suis Dpr complexes with these ions were determined at 1.8 Å and 2.1 Å , respectively. Both ions were found to bind at the ferroxidase center and in the same location as iron. In addition, a novel zinc-binding site formed by His40 and His44 was identified. Both His residues were found to be present within all known Streptococcus suis Dpr variants and in Streptococcus pneumoniae, Streptococcus gordonii, and Streptococcus sanguinis Dpr proteins. Amino acid sequence alignment of Dpr with other Dps family members revealed that His44 is highly conserved, in contrast to His40. The inhibitory effect of zinc and terbium on iron oxidation in Dpr was studied in vitro, and it was found that both ions at concentrations >0.2 mM almost completely abolish iron binding. These results provide a structural basis for the inhibitory effect of zinc and terbium in the Dps family of proteins, and suggest a potential role of the Dps proteins in zinc detoxification mechanisms involving the second zinc-binding site. Dps proteins share many structural and functional similarities with ferritins, a large family of iron-storage proteins (Hintze and Theil 2006). However, Dps proteins form a globular dodecameric assembly that is able to store up to 500 iron atoms (Grant et al. 1998) in contrast to ferritins, which are 24-meric with a storage capacity of up to 4500 iron atoms (Harrison and Arosio 1996;Bozzi et al. 1997;Zhao et al. 2002). Moreover, the active site of Dps proteins is located between neighboring monomers and not within individual monomers as in ferritins (Grant et al. 1998;Ilari et al. 2000;Kauko et al. 2004). On the Reprint requests to: Anastassios C. Papageorgiou, Turku Centre for Biotechnology, University of Turku and Å bo Akademi University, PO Box 123, Turku 20521, Finland; e-mail: tassos.papageorgiou@btk.fi; fax: 358-2-333-8000.Abbreviations: Dpr, Dps-like peroxide resistance; Dps, DNA-binding protein from starved cells or DNA protection during starvation; RMSD, root-mean-square deviation.Article and publication are at

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Zinc co‐ordination in the DNA‐binding domain of the yeast transcriptional activator PPR1

Cited by 14 publications

References 21 publications

Evolution of a Fungal Regulatory Gene Family: The Zn(II)2Cys6 Binuclear Cluster DNA Binding Motif

Evolution of a Fungal Regulatory Gene Family: The Zn(II)2Cys6 Binuclear Cluster DNA Binding Motif

Evidence for a Dynamic Structure of Human Neuronal Growth Inhibitory Factor and for Major Rearrangements of Its Metal−Thiolate Clusters

Structural basis of the zinc‐ and terbium‐mediated inhibition of ferroxidase activity in Dps ferritin‐like proteins

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