Ultrahigh-resolution centrosymmetric crystal structure of Z-DNA reveals the massive presence of alternate conformations

2016 ◽  
Vol 72 (11) ◽  
pp. 1203-1211 ◽  
Author(s):  
Pawel Drozdzal ◽  
Miroslaw Gilski ◽  
Mariusz Jaskolski
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Structural Disorder ◽  
Crystal Form ◽  
X Rays ◽  
Dna Duplexes ◽  
Dna Hydration ◽  
Dna Backbone ◽  
Z Dna ◽  
Natural Enantiomer

The self-complementary d(CGCGCG) hexanucleotide was synthesized with both D-2′-deoxyribose (the natural enantiomer) and L-2′-deoxyribose, and the two enantiomers were mixed in racemic (1:1) proportions and crystallized, producing a new crystal form withC2/csymmetry that diffracted X-rays to 0.78 Å resolution. The structure was solved by direct, dual-space and molecular-replacement methods and was refined to anRfactor of 13.86%. The asymmetric unit of the crystal contains one Z-DNA duplex and three Mg2+sites. The crystal structure is comprised of both left-handed (D-form) and right-handed (L-form) Z-DNA duplexes and shows an unexpectedly high degree of structural disorder, which is manifested by the presence of alternate conformations along the DNA backbone chains as well as at four nucleobases (including one base pair) modelled in double conformations. The crystal packing of the presented D/L-DNA–Mg2+structure exhibits novel DNA hydration patterns and an unusual arrangement of the DNA helices in the unit cell. The paper describes the structure in detail, concentrating on the mode of disorder, and compares the crystal packing of the racemic d(CGCGCG)2duplex with those of other homochiral and heterochiral Z-DNA structures.

scholarly journals Crystal structure of Z-DNA in complex with the polyamine putrescine and potassium cations at ultra-high resolution

2021 ◽  
Vol 77 (3) ◽  
Author(s):  
Pawel Drozdzal ◽  
Miroslaw Gilski ◽  
Mariusz Jaskolski
Keyword(s):  
Crystal Structure ◽  
High Resolution ◽  
Hydrogen Bonds ◽  
Structural Disorder ◽  
Potassium Cation ◽  
Water Molecules ◽  
Dna Duplexes ◽  
Dna Backbone ◽  
Z Dna ◽  
Phosphate Groups

The X-ray crystal structure of the d(CGCGCG)2/putrescine(2+)/K+ complex has been determined at 0.60 Å resolution. Stereochemical restraints were used only for the putrescinium dication, and 23 bonds and 18 angles of the Z-DNA nucleotides with dual conformation. The N atoms of the putrescine(2+) dication form three direct hydrogen bonds with the N7_G atoms of three different Z-DNA molecules, plus three water-mediated hydrogen bonds with cytosine, guanine and phosphate acceptors. A unique potassium cation was also unambiguously identified in the structure, albeit at a ∼0.5 occupation site shared with a water molecule, providing the first example of such a complex with Z-DNA. The K+ cation has coordination number of eight and an irregular coordination sphere, formed by four water molecules and four O atoms from two phosphate groups of the Z-DNA, including ligands present at fractional occupancy. The structural disorder of the Z-DNA duplex is manifested by the presence of alternate conformations along the DNA backbone. Comparison of the position and interactions of putrescine(2+) in the present structure with other ultra-high-resolution structures of Z-DNA in complexes with Mn2+ and Zn2+ ions shows that the dicationic putrescinium moiety can effectively substitute these metal ions for stabilization of Z-type DNA duplexes. Furthermore, this comparison also suggests that the spermine(4+) tetracation has a higher affinity for Z-DNA than K+.

scholarly journals Structure of d(TGCGCA)2 and a Comparison to Other DNA Hexamers

1998 ◽  
Vol 54 (6) ◽  
pp. 1273-1284 ◽  
Author(s):  
Anne Harper ◽  
James A. Brannigan ◽  
Martin Buck ◽  
Lorraine Hewitt ◽  
Richard J. Lewis ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Water Structure ◽  
Dna Conformation ◽  
Phosphate Binding ◽  
X Ray ◽  
Phosphate Backbone ◽  
Cell Dimensions ◽  
Z Dna ◽  
Close Contacts

The X-ray crystal structure of d(TGCGCA)2 has been determined at 120 K to a resolution of 1.3 Å. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the `pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388–11402] but with significantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA)2 with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na+, Mg2+ and Co3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure.

scholarly journals Chlamydia protein Pgp3 studied at high resolution in a new crystal form

IUCrJ ◽  
2018 ◽  
Vol 5 (4) ◽  
pp. 439-448 ◽  
Author(s):  
Sahir Khurshid ◽  
Lata Govada ◽  
Gillian Wills ◽  
Myra O. McClure ◽  
John R. Helliwell ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Transmitted Disease ◽  
Crystal Form ◽  
Potassium Bromide ◽  
Macromolecular Complex ◽  
Unique Challenge ◽  
Space Group ◽  
X Ray ◽  
Terminal Domain

The protein Pgp3 is implicated in the sexually transmitted disease chlamydia and comprises an extended complex arrangement of a C-terminal domain (CTD) and an N-terminal domain (NTD) linked by a triple-helix coiled coil (THCC). Here, the X-ray crystal structure of Pgp3 from an LGV1 strain is reported at the highest X-ray diffraction resolution obtained to date for the full protein. The protein was crystallized using a high concentration of potassium bromide, which resulted in a new crystal form with relatively low solvent content that diffracted to a resolution of 1.98 Å. The three-dimensional structure of this new crystal form is described and compared with those of other crystal forms, and the potassium bromide binding sites and the relevance to chlamydia isolates from around the globe are described. The crystal packing is apparently driven by the CTDs. Since the threefold axes of the THCC and NTD are not collinear with the threefold axis of a CTD, this naturally leads to disorder in the THCC and the portion of the NTD that does not directly interact with the CTDviacrystal packing. The key avenue to resolving these oddities in the crystal structure analysis was a complete new analysis in space groupP1 and determining the space group asP212121. This space-group assignment was that originally determined from the diffraction pattern but was perhaps complicated by translational noncrystallographic symmetry. This crystal structure of a three-domain multi-macromolecular complex with two misaligned threefold axes was a unique challenge and has not been encountered before. It is suggested that a specific intermolecular interaction, possibly of functional significance in receptor binding in chlamydia, might allow the design of a new chemotherapeutic agent against chlamydia.

Direct observation of arylnitrene formation in the photoreaction of arylazide crystals

2010 ◽  
Vol 66 (6) ◽  
pp. 639-646 ◽  
Author(s):  
Terufumi Takayama ◽  
Takahiro Mitsumori ◽  
Masaki Kawano ◽  
Akiko Sekine ◽  
Hidehiro Uekusa ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Uv Light ◽  
Crystal Form ◽  
The Other ◽  
Azido Group ◽  
X Rays ◽  
Butanoic Acid ◽  
Cell Dimensions ◽  
Triplet Nitrene

Seven crystal structures of arylazides, 2-azidobiphenyl (2), 4-(4-azidophenyl)butanoic acid (3), 3-azidobenzoic acid (4), N-(4-azidophenyl)acetamide (5), 2,4,6-trichlorophenyl azide (6), 2,5-dibromophenyl azide (7) and 2,4,6-tribromophenyl azide (8), have been analyzed by X-rays. When the crystals were irradiated with UV light at ≃ 80 K, only 2-azidobiphenyl gradually changed its cell dimensions with the retention of the single-crystal form. The crystal structure after photo-irradiation was analyzed by X-rays under the same conditions as those before photo-irradiation. Approximately 20% of the 2-azidobiphenyl molecule was converted to the triplet 2-biphenylnitrene and dinitrogen molecules. The existence of the triplet nitrene was confirmed by ESR and IR measurements. Although the structure of dinitrogen was clearly determined, the nitrene structure was obscure because the nitrene produced was almost superimposed on the original 2-azidobiphenyl. The other six crystals were non-reactive or easily broken when they were exposed to UV light. The different reactivity between 2-azidobiphenyl and the other compounds was successfully explained by the reaction cavity of the azido group.

scholarly journals A new crystal form of Lys48-linked diubiquitin

2010 ◽  
Vol 66 (9) ◽  
pp. 994-998 ◽  
Author(s):  
Jean-François Trempe ◽  
Nicholas R. Brown ◽  
Martin E. M. Noble ◽  
Jane A. Endicott
Keyword(s):  
Crystal Structure ◽  
Crystal Packing ◽  
Crystal Form ◽  
Asymmetric Unit ◽  
Polyubiquitin Chains ◽  
Isopeptide Bond ◽  
Closed Conformation ◽  
Crystallization Conditions

Lys48-linked polyubiquitin chains are recognized by the proteasome as a tag for the degradation of the attached substrates. Here, a new crystal form of Lys48-linked diubiquitin (Ub2) was obtained and the crystal structure was refined to 1.6 Å resolution. The structure reveals an ordered isopeptide bond in atransconfiguration. All three molecules in the asymmetric unit were in the same closed conformation, in which the hydrophobic patches of both the distal and the proximal moieties interact with each other. Despite the different crystallization conditions and different crystal packing, the new crystal structure of Ub2is similar to the previously published structure of diubiquitin, but differences are observed in the conformation of the flexible isopeptide linkage.

scholarly journals Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes

2021 ◽  
Vol 22 (2) ◽  
pp. 947
Author(s):  
Mitsuki Tsuruta ◽  
Yui Sugitani ◽  
Naoki Sugimoto ◽  
Daisuke Miyoshi
Keyword(s):  
Molecular Crowding ◽  
Dna Duplexes ◽  
Crowding Effect ◽  
Backbone Flexibility ◽  
Cpg Dinucleotides ◽  
Key Factor ◽  
Dna Backbone ◽  
A Cell ◽  
Stabilization Effect ◽  
And Function

Methylated cytosine within CpG dinucleotides is a key factor for epigenetic gene regulation. It has been revealed that methylated cytosine decreases DNA backbone flexibility and increases the thermal stability of DNA. Although the molecular environment is an important factor for the structure, thermodynamics, and function of biomolecules, there are few reports on the effects of methylated cytosine under a cell-mimicking molecular environment. Here, we systematically investigated the effects of methylated cytosine on the thermodynamics of DNA duplexes under molecular crowding conditions, which is a critical difference between the molecular environment in cells and test tubes. Thermodynamic parameters quantitatively demonstrated that the methylation effect and molecular crowding effect on DNA duplexes are independent and additive, in which the degree of the stabilization is the sum of the methylation effect and molecular crowding effect. Furthermore, the effects of methylation and molecular crowding correlate with the hydration states of DNA duplexes. The stabilization effect of methylation was due to the favorable enthalpic contribution, suggesting that direct interactions of the methyl group with adjacent bases and adjacent methyl groups play a role in determining the flexibility and thermodynamics of DNA duplexes. These results are useful to predict the properties of DNA duplexes with methylation in cell-mimicking conditions.

scholarly journals X-ray crystal structure of a malonate-semialdehyde dehydrogenase fromPseudomonassp. strain AAC

2017 ◽  
Vol 73 (1) ◽  
pp. 24-28 ◽  
Author(s):  
Matthew Wilding ◽  
Colin Scott ◽  
Thomas S. Peat ◽  
Janet Newman
Keyword(s):  
Crystal Structure ◽  
Search Model ◽  
Molecular Replacement ◽  
X Rays ◽  
X Ray Diffraction ◽  
Acetyl Coa ◽  
Space Group ◽  
X Ray ◽  
Semialdehyde Dehydrogenase

The NAD-dependent malonate-semialdehyde dehydrogenase KES23460 fromPseudomonassp. strain AAC makes up half of a bicistronic operon responsible for β-alanine catabolism to produce acetyl-CoA. The KES23460 protein has been heterologously expressed, purified and used to generate crystals suitable for X-ray diffraction studies. The crystals belonged to space groupP212121and diffracted X-rays to beyond 3 Å resolution using the microfocus beamline of the Australian Synchrotron. The structure was solved using molecular replacement, with a monomer from PDB entry 4zz7 as the search model.

Molecular and Crystal Structure of d(CGCGmo4CG): N4−Methoxy-cytosineguanine Base Pairs in Z-DNA

1990 ◽  
Vol 9 (3) ◽  
pp. 467-469 ◽  
Author(s):  
L. Van Meervelt ◽  
M. H. Moore ◽  
P. Kong Thoo Lin ◽  
D. M. Brown ◽  
O. Kennard
Keyword(s):  
Crystal Structure ◽  
Molecular And Crystal Structure ◽  
Base Pairs ◽  
Z Dna

scholarly journals Near-atomic resolution analysis of BipD, a component of the type III secretion system ofBurkholderia pseudomallei

2010 ◽  
Vol 66 (9) ◽  
pp. 990-993 ◽  
Author(s):  
M. Pal ◽  
P. T. Erskine ◽  
R. S. Gill ◽  
S. P. Wood ◽  
J. B. Cooper
Keyword(s):  
Crystal Form ◽  
Target Cells ◽  
X Rays ◽  
Secretion Systems ◽  
Monoclinic Crystal ◽  
Major Function ◽  
Type Iii ◽  
Associated Proteins ◽  
Target Cell Membrane ◽  
Type Iii Protein Secretion

Burkholderia pseudomallei, the causative agent of melioidosis, possesses a type III protein secretion apparatus that is similar to those found inSalmonellaandShigella. A major function of these secretion systems is to inject virulence-associated proteins into target cells of the host organism. ThebipDgene ofB. pseudomalleiencodes a secreted virulence factor that is similar in sequence and is most likely to be functionally analogous to IpaD fromShigellaand SipD fromSalmonella. Proteins in this family are thought to act as extracellular chaperones at the tip of the secretion needle to help the hydrophobic translocator proteins enter the target cell membrane, where they form a pore and may also link the translocon pore with the secretion needle. BipD has been crystallized in a monoclinic crystal form that diffracted X-rays to 1.5 Å resolution and the structure was refined to anRfactor of 16.1% and anRfreeof 19.8% at this resolution. The putative dimer interface that was observed in previous crystal structures was retained and a larger surface area was buried in the new crystal form.

Sign in / Sign up

Export Citation Format

Share Document