Nucleic Acids Research Advance Access originally published online on November 5, 2007
Nucleic Acids Research 2007 35(22):7714-7720; doi:10.1093/nar/gkm748
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2007, Vol. 35, No. 22 7714-7720
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Molecular Biology |
Characterization of DNA-binding activity of Z
domains from poxviruses and the importance of the β-wing regions in converting B-DNA to Z-DNA
1Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea, 2Department of Biology, Massachusetts Institute of technology, Cambridge, MA 02139, USA and 3Department of Chemistry, School of Natural Sciences, Sungkyunkwan University, Suwon 440-746, Korea
*To whom correspondence should be addressed. Tel: +82 31 299 4563; Fax: +82 31 299 4575; Email: ygkimmit{at}skku.edu Correspondence may also be addressed to Kyeong Kyu Kim. Tel: 82 31 299 6136; Fax: 82 31 299 6159; Email: kkim{at}med.skku.ac.kr
Received July 5, 2007. Revised September 9, 2007. Accepted September 10, 2007.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONSUPPLEMENTARY DATAREFERENCES |
|---|
The E3L gene is essential for pathogenesis in vaccinia virus. The E3L gene product consists of an N-terminal Z
domain and a C-terminal double-stranded RNA (dsRNA) binding domain; the left-handed Z-DNA-binding activity of the Z domain of E3L is required for viral pathogenicity in mice. E3L is highly conserved among poxviruses, including the smallpox virus, and it is likely that the orthologous Z domains play similar roles. To better understand the biological function of E3L proteins, we have investigated the Z-DNA-binding behavior of five representative Z domains from poxviruses. Using surface plasmon resonance (SPR), we have demonstrated that these viral Z domains bind Z-DNA tightly. Ability of ZE3L converting B-DNA to Z-DNA was measured by circular dichroism (CD). The extents to which these Zs can stabilize Z-DNA vary considerably. Mutational studies demonstrate that residues in the loop of the β-wing play an important role in this stabilization. Notably the Z domain of vaccinia E3L acquires ability to convert B-DNA to Z-DNA by mutating amino acid residues in this region. Differences in the host cells of the various poxviruses may require different abilities to stabilize Z-DNA; this may be reflected in the observed differences in behavior in these Z proteins. |
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONSUPPLEMENTARY DATAREFERENCES |
|---|
Poxviruses are the largest, most complex, double-stranded DNA viruses that have been observed to replicate in the cytoplasm of infected cells (1,2). Each poxvirus exhibits a different host range; some are extremely species specific, for example, swinepox virus, while others exhibit a broad host range (3,4). Vaccinia virus is the best-characterized member of this large family, due to its long established role in vaccination against smallpox as well as its importance as a gene transfer vehicles (1).
The E3L protein of vaccinia virus is composed of two distinct domains associated with two different nucleic acid-binding properties. The N-terminal domain (Z) binds tightly and specifically to left-handed Z-DNA (5–8), while the C-terminal domain comprises a well-characterized double-stranded RNA (dsRNA) binding domain (9–12). The dsRNA-binding domain allows the virus to overcome host defense systems mediated by the dsRNA activated protein kinase PKR (9). Vaccinia virus lacking the dsRNA-binding domain of E3L has an increased sensitivity to IFN and restricted host range (13). The Z-DNA-binding domain is a member of the Z family of Z-DNA-binding proteins, whose other members include the vertebrate dsRNA editing enzyme ADAR1 and the mammalian Z-DNA-binding protein ZBP1 (previously known as DLM-1).
The molecular structures of several Z domains have been determined. Z:Z-DNA co-crystal structures have been solved for the Z domains of human ADAR1 (14), mouse ZBP1 (15) and yaba-like disease virus E3L (16). In each case, the protein adopts a helix-turn-helix with β-sheet (winged helix-turn-helix) fold, with the left-handed DNA backbone grasped between the recognition helix and the β-sheet by numerous hydrogen bonds. Both the precise shape of the fold and the interaction with DNA are extremely similar among these proteins. The DNA-contacting residues are highly conserved, both between species within a given protein and between different members of the Z family (15,16), however, different members of the Z family are not otherwise similar. The solution structure of free vaccinia virus ZE3L shows the same overall fold and supports the concept that E3L proteins share their Z-DNA-binding mode (17). There is one provocative difference between the different Z structures: although the contacts between the β-sheet and the DNA are nearly the same, the shape and position of the β-sheet is variable, differing in each or the determined structures (16,17).
In previous studies, the Z-DNA-binding domain of E3L protein from vaccinia virus (vZE3L) was shown to play a key role in viral pathogenesis in mice (18,19). Furthermore, it was shown that the ability to bind Z-DNA is the essential characteristic required for the biological activity of this domain; vZE3L can be replaced with the Z domain of either ADAR1 or ZBP1 with no loss of viral pathogenicity. Mutations that decrease or abolish Z-DNA-binding activity proportionately decrease or abolish pathogenicity (19). It has been demonstrated that the Z-DNA-binding activity of vZE3L is responsible for the anti-apoptotic activity of vaccinia E3L when expressed in cultured cells and can activate expression of a battery of genes (20). Therefore, it is of interest to characterize the binding activity of viral Z domains in order to better understand poxvirus infection.
In this study, we have expressed the ZE3L domains from a representative group of five poxviruses: vaccinia virus (vZE3L), swinepox virus (spZE3L), yaba-like disease virus (yabZE3L), orf virus (orfZE3L) and lumpy skin disease virus (lsZE3L) (Figure 1).We show that these proteins bind strongly to Z-DNA and alter the equilibrium between B-DNA and Z-DNA. In addition, we have modified the β-sheets of several of these proteins using site-directed mutagenesis. These modified proteins display altered Z-DNA-binding activity, showing that changes in this region can modulate the interaction between protein and Z-DNA. These modulations are similar in magnitude to differences between the E3Ls of several poxviruses. It remains to be determined whether such changes in binding activity would alter the biology of the virus.
|
|
MATERIALS AND METHODS |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONSUPPLEMENTARY DATAREFERENCES |
|---|
Protein expression and purification
The sequences encoding viral Z
domains were either amplified from viral genomic DNAs (orfZE3L and vZE3L) by PCR or assembled from synthesized oligonucleotides (lsZE3L, spZE3L and yabZE3L) and cloned into the expression vector pET28a (Novagen), to be expressed as N-terminal-(His)6-tagged fusion proteins. Expression clones were confirmed by restriction enzyme analysis and DNA sequencing. Resulting vectors were transformed into Escherichia coli strain BL21(DE3). Expression and purification of viral Zs were carried out essentially as described elsewhere (16,21). Briefly, cells were grown at 37°C in LB medium supplemented with 30 µg/ml kanamycin until they reached a final concentration of OD600 = 0.5–0.7, at which time IPTG was added to 0.5 mM. Protein was expressed for 4 h at 37°C with the exception of yabZE3L, which was induced at 18°C (16). Cells were harvested by centrifugation at 4000g for 10 min at 4°C. Proteins were purified a metal-chelating column (AP biotech), followed by removal of the N-terminal (His)6-tag with thrombin (Boehringer Mannheim). Z was further purified by ion exchange chromatography (GE), and dialyzed against 5 mM HEPES, pH 7.5, 10 mM NaCl, except yabZE3L and its mutants, which have limited solubility in low salt, for which 100 mM NaCl was used (16). The purified protein was adjusted to >2 mM final concentration, as determined by UV absorbance at 280 nm, using extinction coefficients deduced from amino acid sequence. The purified proteins were stored frozen at –70°C until use.
Surface plasmon resonance analysis
The binding affinities of viral Zs for Z-DNA were determined by surface plasmon resonance (SPR) using a BIAcore 2000 as described previously (5). Briefly, ca. 300 response units (RU) of biotinylated poly (dG–dC) stabilized in the Z conformation (22) were immobilized on a SA chip (Biacore). Protein solutions at concentrations between 75 nM and 2000 nM were passed over the chip surface at 20 µl/min. All experiments were carried out at 25°C in HBS buffer (10 mM HEPES, pH 7.4, 150 mM NaCl, 0.01 mM EDTA). Regeneration was performed with a pulse of 0.05% SDS. The association and dissociation times were 180 and 200 s, respectively. For analysis, binding curves were fitted using BIA evaluation 3.0 and the 1:1 binding drifting baseline model.
Circular dichroism (CD)
Poly (dG–dC) (AP biotech) was rehydrated with 10 mM Tris–Cl, pH 7.4, 100 mM NaCl prior to use. The conversion of poly (dG–dC) from the B to the Z conformation was monitored by circular dichroism (CD). CD spectra were taken at 25°C using a Jasco J-810 CD spectrophotometer. Measurements were carried out on 150 µg/ml (225 µM base pair) DNA in CD buffer (10 mM HEPES, pH 7.4, 10 mM NaCl and 0.1 mM EDTA) in a 2 mm quartz cell for all proteins except yabZE3L and its mutants, which included 100 mM NaCl. To the DNA, 90 µM (final concentration) protein was added. The maximum volume of protein added to the sample did not exceed 5% of the total. Wavelength spectra were recorded at 1 nm interval averaged over 3 s. For kinetic measurements, CD signal changes at 255 nm were recorded at 1 s intervals for 1 h.
Mutagenesis of viral Zs
Mutant proteins were constructed using the QuikChange® site-directed mutagenesis kit (Stratagene), according to the instructions provided by the supplier. After PCR and cloning, the sequence of each construct was verified.
|
RESULTS AND DISCUSSION |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONSUPPLEMENTARY DATAREFERENCES |
|---|
We chose five representative viral Z
s from several subfamilies of poxvirus for careful examination. The amino acid sequences of these Z domains show relatively little sequence identity (between 19% and 39%); in contrast to the proteins as a whole, the residues that make contact with DNA are highly conserved (Figure 1) (14–16). Many, including the asparagine and tyrosine in the recognition helix -3, and the first proline and tryptophan in the wing β-3 are invariant in proteins that bind Z-DNA, while the rest show mostly conservative changes. An exception is the Thr-191 of hZADAR1; this residue makes contact with the DNA in the hZADAR1 co-crystal structure, but is not well conserved in other Zs. Even between poxvirus proteins there is no observable conservation of residues that do not contact DNA. In order to determine the effect on DNA binding of sequence variability in the Z domains from E3L proteins, the activity of these domains was examined, with a focus on the effect of the residues preceding the invariant proline. We will henceforth refer to the two residues preceding the conserved proline as ‘P-2’ and ‘P-1’ (Figure 1).
Characterization of the interaction between the ZE3L poxviruses and Z-DNA by SPR
The viral Z domains shown in Figure 1 were purified from E. coli. Z-DNA-binding activities of these viral Zs were determined using SPR. The equilibrium-binding constant (KD) values were calculated from association (kon) and dissociation (koff) rate constants determined by fitting real-time kinetic data. As shown in Table 1, the binding constants ranging from 60 to 177 nM. This is comparable to the binding affinity of hZADAR1, 57 nM (Table 1). Data from a typical SPR experiment is shown in supporting information (Figure S1).
|
Conversion of B to Z-DNA by poxviral Z
proteinsDNA with the sequence d(CG)n can be stabilized into Z-form by the binding of hZ
ADAR1; the B–Z transition has been observed by CD (5,6). Z domains from other proteins have been characterized by CD for their ability to induce the B–Z transition (15,16,23,24), and variability between proteins with comparable binding constants has been seen. For example, the two Z family domains from human ZBP1 produce a slower B to Z transition than hZADAR1 (23).
As shown in Figure 2, all the tested Z proteins were able to alter the equilibrium between B- and Z-DNA in these experiments, with the exception of vZE3L. Although, vZE3L is not able to change the B–Z equilibrium under these conditions, its binding to Z-DNA has been demonstrated previously, both in vitro and in vivo (8). On the other hand, the rate of B to Z conversion by yabZE3L and the equilibrium state are the same as that of hZADAR1 (16). The other Z proteins yield slower and less complete B–Z transitions than yabZE3L, but faster and more complete than vZE3L.
|
One way to quantify the results obtained by CD is to normalize the data with respect to hZ
ADAR1. hZADAR1 is the best characterized Z family protein and binds extremely tightly and specifically. Two comparisons can be made: (i) the extent of Z-DNA stabilization and (ii) the time required to reach equilibrium. By both of these criteria, the order of B to Z conversion was hZADAR1 
yabZE3L > lsZE3L > orfZE3L spZE3L. Proteins that produce a faster, more complete conversion from the B to the Z-form tend to have a faster kon as determined by SPR, however the correlation is not consistent. orfZE3L has a kon of 7.2 x 104, higher than spZE3Lor lsZE3L, but results in slower and less complete stabilization of Z-DNA than lsZE3L. It should be noted that the SPR experiments measure the binding of Z protein to preformed Z-DNA, while the CD experiments observe a conformational change in dsDNA induced by the protein. Factors including the off rate, the specific geometry and contacts between the protein and the Z-DNA are likely to affect the conversion of B-DNA to Z-DNA in a different way than the binding to pre-stabilized Z-DNA.
Gain of B to Z-DNA conversion activity in a vZE3L mutant
The Z domain from vaccinia virus E3L appears inert in the CD experiments shown above. However, tight and specific binding to Z-DNA has been shown previously (8), and SPR shows that it binds preformed Z-DNA more tightly than spZE3L, lsZE3L or orfZE3L. This apparent contradiction correlates with a low on rate, an order of magnitude less that that of yabZE3L (Table 1). The solution structure of vZE3L shows a considerable difference between the position and sequence of this wing and that of yabZE3L, which binds tightly and specifically in all assays [Figure 3 and (16,17)]. In order to assess the importance of residues in the β-wing (β-2, β-3 and the loop region in-between, Figure 1), Asp-60 (P-2) and Ile-61 (P-1) in vZE3L were both changed to threonines. For comparison, yabZE3L was also mutated to more closely resemble vZE3L in sequence: Ser-64 (P-2) and Asn-65 (P-1) were changed to Asp and Ile, respectively. Changing the residues at P-2 and P-1 in the β-wing can significantly affect the ability of a Z protein to convert DNA from the B to the Z conformation, as shown in Figure 4. The mutation yabZE3LSN6465TT has no effect—rate and equilibrium of the B-DNA to Z-DNA conversion are unchanged. In contrast, yabZE3LSN6465DI produces a decreased rate and lower equilibrium.
|
|
Examination of the structure of the β-wing (Figure 3) suggests an explanation for this effect. The wing from vZ
E3L is positioned parallel to the DNA, aligning the two prolines nearest to the backbone, while the wing from yabZE3L extends toward the backbone, providing DNA interactions not only with the prolines but also with the Asn at P-1. It is possible that both P-1 and P-2 amino acid residues can make DNA contacts, possibly with DNA in an intermediate state between B and Z. These residues would then play a larger role in the conversion of DNA from the B to the Z-form than in binding to pre-stabilized Z-DNA. If this is true, positively charged and polar residues at positions P-1 and P-2 should effect the B to Z-DNA transition better non-polar amino acids and much better than negatively charged amino acids. The yabZE3L mutants described above both satisfy this prediction. In the case of vZE3L, the negatively charged Asp at P-2 could decrease binding to DNA, and the neutral Ile at P-1 cannot form hydrogen binds. The mutations D60T and I61T, vZE3LDI6061TT, remove one negative charge and offer the possibility of hydrogen bonds at both sites.
Effect of changes in P-1 and P-2 in other viral Zs
To further test the hypothesis, mutations were made in other Z domains from E3L proteins. When both P-1 and P-2 were changed to threonine in orfZE3L, a pronounced increase in the proportion of Z-DNA at equilibrium and the rate of conversion were seen (Figure 5 and Table 2). In order to determine whether changes at both P-1 and P-2 were required for this effect, the single mutations orfZE3LGN5455TN and orfZE3LGN5455GT were tested. As shown in Figure 5, the orfZE3LGN5455TN mutation was sufficient to produce the increased binding. Changing Gly at P-2 to another amino acid acts to stiffen the β-turn; this will increase Z-DNA binding, except in the case of a negatively charged amino acid, which will destabilize binding due to electrostatic effects, as demonstrated by orfZE3LGN5455DI (Table 2).
|
|
Similar experiments with spZ
E3L verify that for these proteins, a change to threonine at position P-2 is sufficient to increase the stabilization of Z-DNA (Table 2). This result is unexpected because the residue at position P-1 contacts the Z-DNA in hZADAR1 and yabZE3L; therefore an effect of optimizing the residue at that position is more expected. The notable effect of sequence at P-2 supports the idea that this residue plays a role in either making a binding intermediate between protein and DNA, or, attractively, in shifting the equilibrium between B-DNA and Z-DNA by stabilizing an intermediate. This later possibility explains the discrepancy between KD values and CD data.
When positions P-2 and P-1 are changed to aspartic acid and isoleucine, respectively, in orfZE3L or spZE3L, the effect is the same as that seen in yabZE3LSN6465DI (Table 2). The mutant proteins bind Z-DNA less well. This supports the hypothesis that these residues are not optimized for DNA binding in vZE3L.
Although a single threonine at position P-2 increases the B- to Z-DNA conversion activity of orfZE3L and spZE3L as much as the double mutant, this is not true for vZE3L (Table 2). In the case of the vaccinia protein, neither vZE3LDI6061TI nor vZE3LDI6061DT shows any activity in the CD assay. This suggests that the position of the β-wing of vZE3L remains different for that of yabZE3L, even in the presence of a single mutation. It is likely that other residues also play a role in positioning the wing.
Effect of a charged amino acid in position P-2
It has been hypothesized that the presence of a positively charged amino acid at position P-2 could increase the ability of a Z protein to alter the equilibrium between B-DNA and Z-DNA. This was tested by making mutants of vZE3L, orfZE3L and spZE3L, in each of which P-2 and P-1 were changed to lysine and threonine, respectively. As predicted, the presence of the positively charged lysine improved the ability of the protein to stabilize Z-DNA (Table 2). In each case, the KT mutant performed better than the TT mutant. This supports the idea that residues P-1 and P-2 are close to or make contact with the DNA backbone, as part of a binding intermediate and/or in the final Z-DNA–protein complex. Binding to and stabilization of Z-DNA by a Z protein can be optimized if residue P-2 is positively charged and residue P-1 is able to form a hydrogen bind to a backbone phosphate.
Biological implications of modulation of Z-DNA binding by viral Zs
Although residues that are required for binding to Z-DNA are well conserved in Z domains from viral E3L gene products, we have shown that there are residues that modulate DNA binding, which are conserved poorly or not at all. On one hand, yabZE3L binds to Z-DNA extremely tightly, and is fully capable of stabilizing appropriate sequences in the Z conformation. On the other, vZE3L cannot stabilize Z-DNA in the absence of other factors such as cobalt hexamine or negative supercoiling. Nevertheless, it is in vaccinia virus that it has been shown that the ability of E3L to bind Z-DNA is essential for viral pathogenicity (19).
In vaccinia infections, it is essential for ZE3L to bind Z-DNA; mutations that decrease Z-DNA binding of vZE3L decrease the pathogenicity of the virus (19). However, it is possible that viral E3L proteins do not have to stabilize Z-DNA in the absence of other factors, but rather bind to Z-DNA stabilized by factors such as negative supercoiling. Perhaps certain viral Zs, e.g. vZE3L, do not need to stabilize Z-DNA on their own. Substitution of a stronger Z domain such as hZADAR1 or mZZBP1 for vZE3L in a chimeric E3L maintains pathogenicity but does not increase it (19).
Our study demonstrates that viral Zs from different poxviruses have different ability for Z-DNA stabilization. The variability in the sequence of the β-wing and the modulation in Z-DNA-binding activity may reflect the lifecycle of the virus. In each of viruses, different degrees of modulation of Z-DNA-binding activity may be essential. Too weak binding will inactivate the Z, but too much binding may result in binding to inappropriate targets or the activation of genes that will hamper viral activity.
The biological action of the different viral Z domains can only be the object of speculation at present. When transfected into a cultured cell, Z can prevent apoptosis, stopping one of the most powerful host defenses against viral infection. Expression of Z also regulates the expression of many genes (20), and may act thus in viral pathogenesis. Finally, viral Zs may compete with cellular Zs or other, as yet undiscovered, Z-DNA-binding proteins, much as the C-terminal dsRNA-binding domain acts by competing for substrate with PKR.
|
SUPPLEMENTARY DATA |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONSUPPLEMENTARY DATAREFERENCES |
|---|
Supplementary Data are available at NAR Online.
|
ACKNOWLEDGEMENTS |
|---|
This research was supported by the KOSEF grants from the National Research Laboratory Program (NRL-2006-02287), the Ubiquitome Research Program (M10533010002-06N3301-00210), and the 21C Frontier Functional Proteomics Program (FPR06B2-120) funded by the Korean government (MOST), and the grants from the National Institutes of Health and the Ellison Medical Foundation. Funding to pay the Open Access publication charges for this article was provided by the grant from National Laboratory program (NRL-2006-02287) of the Korean government (MOST).
Conflict of interest statement. None declared.
|
REFERENCES |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTS AND DISCUSSIONSUPPLEMENTARY DATAREFERENCES |
|---|
- Whitley RJ. Poxviridae: the viruses and their replication. In: Fields Virology—Fields B, Knipe D, Howley P, eds. (1996) Vol. 2, Chapter 83. 3rd. Philadelphia: Lippincott-Raven. 2637–2671.
- Yuwen H, Cox JH, Yewdell JW, Bennink JR, Moss B. Nuclear localization of a double-stranded RNA-binding protein encoded by the vaccinia virus E3L gene. Virology (1993) 195:732–744.[CrossRef][Web of Science][Medline]
- Afonso CL, Tulman ER, Lu Z, Zsak L, Osorio FA, Balinsky C, Kutish GF, Rock DL. The genome of swinepox virus. J. Virol. (2002) 76:783–790.
[Abstract/Free Full Text] - McFadden G. Poxvirus tropism. Nat. Rev. Microbiol. (2005) 3:201–213.[CrossRef][Web of Science][Medline]
- Herbert A, Alfken J, Kim YG, Mian IS, Nishikura K, Rich A. A Z-DNA binding domain present in the human editing enzyme, double-stranded RNA adenosine deaminase. Proc. Natl Acad. Sci. USA (1997) 94:8421–8426.
[Abstract/Free Full Text] - Berger I, Winston W, Manoharan R, Schwartz T, Alfken J, Kim YG, Lowenhaupt K, Herbert A, Rich A. Spectroscopic characterization of a DNA-binding domain, Z alpha, from the editing enzyme, dsRNA adenosine deaminase: evidence for left-handed Z-DNA in the Z alpha-DNA complex. Biochemistry (1998) 37:13313–13321.[CrossRef][Web of Science][Medline]
- Kim YG, Lowenhaupt K, Maas S, Herbert A, Schwartz T, Rich A. The zab domain of the human RNA editing enzyme ADAR1 recognizes Z-DNA when surrounded by B-DNA. J. Biol. Chem. (2000) 275:26828–26833.
[Abstract/Free Full Text] - Kim YG, Lowenhaupt K, Oh DB, Kim KK, Rich A. Evidence that vaccinia virulence factor E3L binds to Z-DNA in vivo: implications for development of a therapy for poxvirus infection. Proc. Natl Acad. Sci. USA (2004) 101:1514–1518.
[Abstract/Free Full Text] - Chang HW, Watson JC, Jacobs BL. The E3L gene of vaccinia virus encodes an inhibitor of the interferon-induced, double-stranded RNA-dependent protein kinase. Proc. Natl Acad. Sci. USA (1992) 89:4825–4829.
[Abstract/Free Full Text] - Chang HW, Jacobs BL. Identification of a conserved motif that is necessary for binding of the vaccinia virus E3L gene products to double-stranded RNA. Virology (1993) 194:537–547.[CrossRef][Web of Science][Medline]
- Romano PR, Zhang F, Tan SL, Garcia-Barrio MT, Katze MG, Dever TE, Hinnebusch AG. Inhibition of double-stranded RNA-dependent protein kinase PKR by vaccinia virus E3: role of complex formation and the E3 N-terminal domain. Mol. Cell. Biol. (1998) 18:7304–7316.
[Abstract/Free Full Text] - Sharp TV, Moonan F, Romashko A, Joshi B, Barber GN, Jagus R. The vaccinia virus E3L gene product interacts with both the regulatory and the substrate binding regions of PKR: implications for PKR autoregulation. Virology (1998) 250:302–315.[CrossRef][Web of Science][Medline]
- Shors T, Kibler KV, Perkins KB, Seidler-Wulff R, Banaszak MP, Jacobs BL. Complementation of vaccinia virus deleted of the E3L gene by mutants of E3L [In Process Citation]. Virology (1997) 239:269–276.[CrossRef][Web of Science][Medline]
- Schwartz T, Rould MA, Lowenhaupt K, Herbert A, Rich A. Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science (1999) 284:1841–1845.
[Abstract/Free Full Text] - Schwartz T, Behlke J, Lowenhaupt K, Heinemann U, Rich A. Structure of the DLM-1-Z-DNA complex reveals a conserved family of Z- DNA-binding proteins. Nat. Struct. Biol. (2001) 8:761–765.[CrossRef][Web of Science][Medline]
- Ha SC, Lokanath NK, Van Quyen D, Wu CA, Lowenhaupt K, Rich A, Kim YG, Kim KK. A poxvirus protein forms a complex with left-handed Z-DNA: crystal structure of a Yatapoxvirus Zalpha bound to DNA. Proc. Natl Acad. Sci. USA (2004) 101:14367–14372.
[Abstract/Free Full Text] - Kahmann JD, Wecking DA, Putter V, Lowenhaupt K, Kim YG, Schmieder P, Oschkinat H, Rich A, Schade M. The solution structure of the N-terminal domain of E3L shows a tyrosine conformation that may explain its reduced affinity to Z-DNA in vitro. Proc. Natl Acad. Sci. USA (2004) 101:2712–2717.
[Abstract/Free Full Text] - Brandt TA, Jacobs BL. Both carboxy- and amino-terminal domains of the vaccinia virus interferon resistance gene, E3L, are required for pathogenesis in a mouse model. J. Virol. (2001) 75:850–856.
[Abstract/Free Full Text] - Kim YG, Muralinath M, Brandt T, Pearcy M, Hauns K, Lowenhaupt K, Jacobs BL, Rich A. A role for Z-DNA binding in vaccinia virus pathogenesis. Proc. Natl Acad. Sci. USA (2003) 100:6974–6979.
[Abstract/Free Full Text] - Kwon JA, Rich A. Biological function of the vaccinia virus Z-DNA-binding protein E3L: gene transactivation and antiapoptotic activity in HeLa cells. Proc. Natl Acad. Sci. USA (2005) 102:12759–12764.
[Abstract/Free Full Text] - Schwartz T, Lowenhaupt K, Kim YG, Li L, Brown B.AII, Herbert A, Rich A. Proteolytic dissection of Zab, the Z-DNA-binding domain of human ADAR1. J. Biol. Chem. (1999) 274:2899–2906.
[Abstract/Free Full Text] - Kim DJ, Oh DB, Lee SM, Choi IS, Kim YG. Fluorescence detection of protein/Z-DNA interactions. Bull. Korean Chem. Soc. (2004) 25:1430–1432.
- Ha SC, Van Quyen D, Hwang HY, Oh DB, Brown B.AII, Lee SM, Park HJ, Ahn JH, Kim KK, et al. Biochemical characterization and preliminary X-ray crystallographic study of the domains of human ZBP1 bound to left-handed Z-DNA. Biochim. Biophys. Acta. (2006) 1764:320–323.[Medline]
- Rothenburg S, Deigendesch N, Dittmar K, Koch-Nolte F, Haag F, Lowenhaupt K, Rich A. A PKR-like eukaryotic initiation factor 2alpha kinase from zebrafish contains Z-DNA binding domains instead of dsRNA binding domains. Proc. Natl Acad. Sci. USA (2005) 102:1602–1607.
[Abstract/Free Full Text]
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  S. C. Ha, D. Kim, H.-Y. Hwang, A. Rich, Y.-G. Kim, and K. K. Kim The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA PNAS, December 30, 2008; 105(52): 20671 - 20676. [Abstract] [Full Text] [PDF]
|
|
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||