Cys4 Zinc Finger Research Articles

The Transcriptional Repressor PerR Senses Sulfane Sulfur by Cysteine Persulfidation at the Structural Zn2+ Site in Synechococcus sp. PCC7002.

Cyanobacteria can perform both anoxygenic and oxygenic photosynthesis, a characteristic which ensured that these organisms were crucial in the evolution of the early Earth and the biosphere. Reactive oxygen species (ROS) produced in oxygenic photosynthesis and reactive sulfur species (RSS) produced in anoxygenic photosynthesis are closely related to intracellular redox equilibrium. ROS comprise superoxide anion (O2●-), hydrogen peroxide (H2O2), and hydroxyl radicals (●OH). RSS comprise H2S and sulfane sulfur (persulfide, polysulfide, and S8). Although the sensing mechanism for ROS in cyanobacteria has been explored, that of RSS has not been elucidated. Here, we studied the function of the transcriptional repressor PerR in RSS sensing in Synechococcus sp. PCC7002 (PCC7002). PerR was previously reported to sense ROS; however, our results revealed that it also participated in RSS sensing. PerR repressed the expression of prxI and downregulated the tolerance of PCC7002 to polysulfide (H2Sn). The reporter system indicated that PerR sensed H2Sn. Cys121 of the Cys4:Zn2+ site, which contains four cysteines (Cys121, Cys124, Cys160, and Cys163) bound to one zinc atom, could be modified by H2Sn to Cys121-SSH, as a result of which the zinc atom was released from the site. Moreover, Cys19 could also be modified by polysulfide to Cys19-SSH. Thus, our results reveal that PerR, a representative of the Cys4 zinc finger proteins, senses H2Sn. Our findings provide a new perspective to explore the adaptation strategy of cyanobacteria in Proterozoic and contemporary sulfurization oceans.

Structural and functional characterization of Cys4 zinc finger motif in the recombination mediator protein RecR.

Zinc finger motif widely exists in protein structure, which can play different roles in different proteins. RecR is an important recombination mediator protein (RMP) in the RecFOR pathway and zinc finger motif is the most conserved domain in RecR protein. However, the function of this zinc finger motif in RecR is unclear. Here, we have studied the structures of the single cysteine and double cysteines mutation within the zinc finger motif in Thermoanaerobacter tengcongensis RecR (TTERecR). We have also studied the DNA binding ability as well as TTERecO protein binding ability of single, double and even triple cysteines mutation of the zinc finger motif, and the mutants do not alter DNA binding by RecR nor the interaction between RecR and RecO. The function of TTERecR zinc finger motif is to maintain the stability of the three-dimensional structure.

Physiological levels of glutathione enhance Zn(II) binding by a Cys4 zinc finger

Using fluorescence and UV–vis spectroscopies and mass spectrometry, we demonstrated that the presence of physiological levels of reduced glutathione enhances the binding of Zn(II) to XPAzf, a Cys4 zinc finger peptide derived from the XPA protein, by means of formation of a ternary complex of a general formula ZnXPAzf[GSH]. Similar complexes were also indicated by ESI-MS for isostructural Co(II)- and Cd(II)-substituted XPAzf. The observed enhancement of the Zn(II) binding to XPAzf by a factor of 50 over the physiological range of GSH concentrations of 1–20 mM corresponds to a dissociation constant of GSH from the ZnXPAzf[GSH] complex of 0.05 μM. This effect may account for an apparent discrepancy between relatively low Zn(II) binding constants measured in vitro for many zinc fingers, and the requirement of tight Zn(II) binding enforced by intracellular zinc buffering by the thionein/metallothionein couple.

Reaction of the XPA Zinc Finger with S-Nitrosoglutathione

S-Nitrosoglutathione (GSNO) is an intracellular redox signaling molecule, also implicated in nitrosative stress. GSNO actions include modifications of Cys thiols in proteins. In this study, we focused on a GSNO reaction with a Cys4 zinc finger (ZF) sequence of human protein XPA, crucial to the nucleotide excision repair pathway of DNA repair. By using a corresponding synthetic 37-residue peptide acetyl-DYVICEECGKEFMDSYLMNHFDLPTCDNCRDADDKHK-amide (XPAzf) and combining the detection of noncovalent and covalent complexes by ESI-MS with zinc release monitored by the zinc-sensitive chromophore 4-(2-pyridylazo)resorcinol (PAR), we demonstrated that the reaction of XPAzf with GSNO yielded S-nitrosylated intermediates, intrapeptide disulfides, and mixed glutathione disulfides. The reaction started with the formation of a complex of GSNO with ZnXPAzf followed by thiol transnitrosylation reactions and the final formation of disulfides. The results obtained suggest that at low levels/transient exposures, GSNO may act as a reversible regulator of Cys4 ZF activity, whereas transnitrosylation by GSNO, occurring at prolonged exposures, may cause deleterious effects to the functions of Cys 4 ZF proteins. In the case of XPA, this may lead to DNA repair inhibition.

Crosstalk between Primase Subunits Can Act to Regulate Primer Synthesis in trans

The coordination of primase function within the replisome is an essential but poorly understood feature of lagging strand synthesis. By using crystallography and small-angle X-ray scattering (SAXS), we show that functional elements of bacterial primase transition between two dominant conformations: an extended form that uncouples a regulatory domain from its associated RNA polymerase core and a compact state that sequesters the regulatory region from the site of primer synthesis. FRET studies and priming assays reveal that the regulatory domain of one primase subunit productively associates with nucleic acid that is bound to the polymerase domain of a second protomer in trans. This intersubunit interaction allows primase to select initiation sites on template DNA and implicates the regulatory domain as a "molecular brake" that restricts primer length. Our data suggest that the replisome may cooperatively use multiple primases and this conformational switch to control initiation frequency, processivity, and ultimately, Okazaki fragment synthesis.

Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair.

RecR, together with RecF and RecO, facilitates RecA loading in the RecF pathway of homologous recombinational DNA repair in procaryotes. The human Rad52 protein is a functional counterpart of RecFOR. We present here the crystal structure of RecR from Deinococcus radiodurans (DR RecR). A monomer of DR RecR has a two-domain structure: the N-terminal domain with a helix-hairpin-helix (HhH) motif and the C-terminal domain with a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif. Four such monomers form a ring-shaped tetramer of 222 symmetry with a central hole of 30-35 angstroms diameter. In the crystal, two tetramers are concatenated, implying that the RecR tetramer is capable of opening and closing. We also show that DR RecR binds to both dsDNA and ssDNA, and that its HhH motif is essential for DNA binding.

Metal Binding and Selectivity in Zinc Proteins

AbstractZinc is one of the most abundant metals in living organisms and is an essential co‐factor of many metabolic enzymes and transcription factors. In this review, based on a recent body of theoretical and experimental results, the physical bases are delineated for the following aspects of zinc binding and selectivity in proteins: (1) What is the most thermodynamically preferable coordination geometry of a bidentate ligand (such as carboxylate) or Zn in Zn‐binding sites? (2) What is the protonation state of the Cys side chain in Cys4 zinc‐finger cores? (3) How does a protein select Zn from the mixture of ions in the surrounding fluids? (4) What is the role of the second shell in metal binding and selectivity? The key results are summarized and the physical basis and/or implications of the findings are discussed.

Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations.

Molecular dynamics simulations (MD) have been performed on variant crystal and NMR-derived structures of the glucocorticoid receptor DNA-binding domain (GR DBD). A loop region five residues long, the so-called D-box, exhibits significant flexibility, and transient perturbations of the tetrahedral geometry of two structurally important Cys4 zinc finger are seen, coupled to conformational changes in the D-box. In some cases, one of the Cys ligands to zinc exchanges with water, although no global distortion of the protein structure is observed. Thus, from MD simulation, dynamics of the D-box could partly be explained by solvent effects in conjunction with structural reformation of the zinc finger.

Measure for measure: a zinc finger ruler

Intervening sequences encoding introns or inteins are transferred laterally between homologous alleles in a mechanism termed ‘homing’. Homing endonucleases are the class of enzymes that trigger homing by catalyzing double-strand DNA breaks at target sequences. Over 250 homing endonucleases have been identified; they are encoded by open reading frames (ORFs) within the mobile intervening sequences.In contrast to restriction endonucleases, which typically function as dimers and cleave palindromic DNA sequences of 4–8 bp, homing endonucleases are small monomeric proteins that recognize longer more variable sequences. For example, the homing endonuclease I-TevI, encoded by the td intron of phage T4, is a 28 kD protein that recognizes a target site of 37 bp. Double-strand cleavage occurs 23–25 bp upstream from this homing site. I-TevI contains two functionally distinct domains, an N-terminal catalytic domain and a C-terminal binding domain, joined by a long flexible linker. Limited insertions and deletions between the recognition sequence and cleavage site are tolerated, indicating that the linker extends and retracts to locate the cleavage site. A crystal structure of the DNA-binding domain bound to its target sequence revealed an unexpected Cys-4 zinc finger subdomain. As demonstrated by Marlene Belfort and colleagues, this zinc finger acts as a molecular ruler between the homing and cleavage sites on the target DNA [1xZinc finger as distance determinant in the flexible linker of intron endonuclease I-TevI. Dean, A.B. et al. Proc. Natl. Acad. Sci. U. S. A. 2002; 99: 8554–8561Crossref | PubMed | Scopus (37)See all References][1].Although previously classified as part of the C-terminal binding domain, the zinc finger is dispensable for binding. To determine its contribution to endonuclease function, Belfort et al. constructed mutants of I-TevI in which the zinc finger was deleted or zinc chelation impaired by substituting one or more cysteines with alanine. DNA variants were also constructed with insertions or deletions between the homing and cleavage sites. The wild-type protein compensates for small insertions or deletions, but primarily cleaves the DNA a fixed distance from the homing site. By contrast, protein variants lacking an intact zinc finger cleave at the wild-type DNA sequence with less regard for distance. The protein does not simply use linker length to determine cleavage position. A mutant lacking the entire zinc finger (a 19 aa deletion) cleaves at the wild-type sequence even when it is further from the binding site owing to nucleotide insertions; that is, the linker ‘stretches out’ to find the preferred cleavage sequence. In the presence of the zinc finger, distance dominates, but without this motif, sequence overrides distance. The authors present a model in which the zinc finger organizes the linker between the catalytic and binding domains of the endonuclease.Zinc fingers typically bind in the major groove of DNA, as in the sequential Cys-2/His-2 zinc fingers of Zif268. The zinc finger of I-TevI, however, does not contribute significantly to binding energy. Indeed, the major groove of T4 DNA is effectively blocked by glycosylation of 5-hydroxymethylcytosine. Zinc fingers also mediate protein–protein interactions, although, to date, there is no evidence that other proteins are required for endonuclease activity. This function of a zinc finger as a distance determinant appears novel even among closely related homing endonucleases; it will be interesting to see whether zinc fingers exist in such a role in other modular proteins.

Factors governing the protonation state of cysteines in proteins: an Ab initio/CDM study.

The detailed mechanism of metal-cysteine binding is still poorly understood. It is not clear if every metal cation can induce cysteine deprotonation, how the dielectric medium affects this process, and the extent to which other ligands from the metal's first and second coordination shell influence cysteine ionization. It is also not clear if the zinc cation, with its positive charge reduced by charge transfer from the first two bound cysteinates, could still assist deprotonation of the next one or two cysteines in Cys3His and Cys4 zinc-finger cores. Here, we elucidate the factors governing the cysteine protonation state in metal-binding sites, in particular in Zn.Cys4 complexes, using a combined ab initio and continuum dielectric approach. Transition metal dications such as Zn2+ and Cu2+ and trivalent cations such as Al3+ with pronounced ability to accept charge from negatively charged Cys- are predicted to induce cysteine deprotonation, but not "hard" divalent cations such as Mg2+. A high dielectric medium was found to favor cysteine deprotonation, while a low one favored the protonated state. Polarizable ligands in the metal's first shell that can competitively donate charge to the metal cation were found to lower the efficiency of the metal-assisted cysteine deprotonation. The calculations predict that the zinc cation could assist deprotonation of all the cysteines during the folding of Cys4 zinc-finger cores and the [Zn.(Cys-)4]2- state is likely to be preserved in the final folded conformation of the protein provided the binding site is tightly encapsulated by backbone peptide groups or lysine/arginine side chains, which stabilize the ionized cysteine core.

The Cys4 zinc finger of bacteriophage T7 primase in sequence-specific single-stranded DNA recognition.

Bacteriophage T7 DNA primase recognizes 5'-GTC-3' in single-stranded DNA. The primase contains a single Cys4 zinc-binding motif that is essential for recognition. Biochemical and mutagenic analyses suggest that the Cys4 motif contacts cytosine of 5'-GTC-3' and may also contribute to thymine recognition. Residues His33 and Asp31 are critical for these interactions. Biochemical analysis also reveals that T7 primase selectively binds CTP in the absence of DNA. We propose that bound CTP selects the remaining base G, of 5'-GTC-3', by base pairing. Our deduced mechanism for recognition of ssDNA by Cys4 motifs bears little resemblance to the recognition of trinucleotides of double-stranded DNA by Cys2His2 zinc fingers.

Conversion of the E1A Cys4 zinc finger to a nonfunctional His2,Cys2 zinc finger by a single point mutation.

Trans-activation by the adenovirus E1A 289R protein requires a zinc finger defined by Cys-154, Cys-157, Cys-171, and Cys-174. Whereas individually replacing the four cysteine residues with serines resulted in a loss of transactivation, only three of the Cys----Ser mutants (C157S, C171S, and C174S) lost the ability to bind Zn(II). X-ray absorption fine structure analysis revealed that, in the wild-type protein, Zn(II) is coordinated by four cysteine residues whereas in the C154S mutant, Zn(II) is coordinated by two histidines and two cysteines. The mutant protein probably retains, as ligands, two cysteines on the right side of the zinc finger (Cys-171 and Cys-174) and recruits two of the four histidines on the left side (His-149, His-152, His-158, and His-160), despite the presence of Cys-157. This finding may shed light on the general structural requirements of zinc fingers.