Helical Stack Research Articles

Chirality Engineering of Nanostructured Copper Oxide for Enhancing Oxygen Evolution from Water Electrolysis.

The exploration of a new conceptual strategy for improving the oxygen evolution reaction (OER) of earth-abundant electrocatalysts is critical. In this study, chiral copper oxide nanoflower is explored by a self-assembly method. The characterization suggests the chiral structure originates from the crystal plane-level helical stack of the secondary nanosheets. Of note, the assembly illustrates a record-high degree of spin polarization of 96%, indicating the ideal alignment of electron spin. Moreover, density function theory calculations show the chiral structure reducing the reaction energy barrier (REB) while switching the potential-determining step from *O→*OOH to *OH→*O. Together with the enhanced electrochemical active surface area and accelerated charge transfer, the production of ground-state triplet O2 is improved via a spin-forbidden route that involves the singlet H2O/OH•. Consequently, the chiral nanoflower shows a overpotential of 308mV at 10mA cm-2 and a Tafel slope of 93.5mV dec-1, which is even superior to the commercial RuO2 (310mV, 101mV dec-1). This study presents a new strategy for improving the OER activity by simultaneously enhancing electronic properties and lowering the REB of an non-noble electrocatalyst via chirality engineering.

A type VII-secreted lipase toxin with reverse domain arrangement

The type VII protein secretion system (T7SS) is found in many Gram-positive bacteria and in pathogenic mycobacteria. All T7SS substrate proteins described to date share a common helical domain architecture at the N-terminus that typically interacts with other helical partner proteins, forming a composite signal sequence for targeting to the T7SS. The C-terminal domains are functionally diverse and in Gram-positive bacteria such as Staphylococcus aureus often specify toxic anti-bacterial activity. Here we describe the first example of a class of T7 substrate, TslA, that has a reverse domain organisation. TslA is widely found across Bacillota including Staphylococcus, Enterococcus and Listeria. We show that the S. aureus TslA N-terminal domain is a phospholipase A with anti-staphylococcal activity that is neutralised by the immunity lipoprotein TilA. Two small helical partner proteins, TlaA1 and TlaA2 are essential for T7-dependent secretion of TslA and at least one of these interacts with the TslA C-terminal domain to form a helical stack. Cryo-EM analysis of purified TslA complexes indicate that they share structural similarity with canonical T7 substrates. Our findings suggest that the T7SS has the capacity to recognise a secretion signal present at either end of a substrate.

Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond.

Damaged or mismatched DNA bases are normally thought to be able to flip out of the helical stack, providing enzymes with access to the faulty genetic information otherwise hidden inside the helix. Thymine glycol (Tg) is one of the most common products of nucleic acid damage. However, the static and dynamic structures of DNA duplexes affected by 5R-Tg epimers are still not clearly understood, including the ability of these to undergo spontaneous base flipping. Structural effects of the 5R-Tg epimers on the duplex DNA are herein studied using molecular dynamics together with reliable DFT based calculations. In comparison with the corresponding intact DNA, the cis-5R,6S-Tg epimer base causes little perturbation to the duplex DNA, and a barrier of 4.9 kcal mol–1 is obtained by meta-eABF for cis-5R,6S-Tg base flipping out of the duplex DNA, comparable to the 5.4 kcal mol–1 obtained for the corresponding thymine flipping in intact DNA. For the trans-5R,6R-Tg epimer, three stable local structures were identified, of which the most stable disrupts the Watson–Crick hydrogen-bonded G5/C20 base pair, leading to conformational distortion of the duplex. Interestingly, the relative barrier height of the 5R-Tg flipping is only 1.0 kcal mol–1 for one of these trans-5R,6R-Tg epimers. Water bridge interactions were identified to be essential for 5R-Tg flipping. The study clearly demonstrates the occurrence of partial trans-5R,6R-Tg epimer flipping in solution.

Twist to Boost: Circumventing Quantum Yield and Dissymmetry Factor Trade-Off in Circularly Polarized Luminescence.

Circularly polarized luminescence (CPL) enables promising applications in asymmetric photonics. However, the performances of CPL molecules do not yet meet the requirements of these applications. The shortcoming originates from the trade-off in CPL between the photoluminescence quantum yield (PLQY) and the photoluminescence dissymmetry factor (gPL). In this study, we developed a molecular strategy to circumvent this trade-off. Our approach takes advantage of the strong propensity of [Pt(N^C^N)Cl], where the N^C^N ligand is 1-(2-oxazoline)-3-(2-pyridyl)phenylate, to form face-to-face stacks. We introduced chiral substituents, including (S)-methyl, (R)- and (S)-isopropyl, and (S)-indanyl groups, into the ligand framework. This asymmetric control induces torsional displacements that give homohelical stacks of the Pt(II) complexes. X-ray single-crystal structure analyses for the (S)-isopropyl Pt(II) complex reveal the formation of a homohelical dimer with a Pt···Pt distance of 3.48 Å, which is less than the sum of the van der Waals radii of Pt. This helical stack elicits the metal-metal-to-ligand charge-transfer (MMLCT) transition that exhibits strong chiroptical activity due to the electric transition moment making an acute angle to the magnetic transition moment. The PLQY and gPL values of the MMLCT phosphorescence emission of the (S)-isopropyl Pt(II) complex are 0.49 and 8.4 × 10-4, which are improved by factors of ca. 6 and 4, respectively, relative to the values of the unimolecular emission (PLQY, 0.078; gPL, 2.4 × 10-4). Our photophysical measurements for the systematically controlled Pt(II) complexes reveal that the CPL amplifications depend on the chiral substituent. Our investigations also indicate that excimers are not responsible for the enhanced chiroptical activity. To demonstrate the effectiveness of our approach, organic electroluminescence devices were fabricated. The MMLCT emission devices were found to exhibit simultaneous enhancements in the external quantum efficiency (EQE, 9.7%) and the electroluminescence dissymmetry factor (gEL, 1.2 × 10-4) over the unimolecular emission devices (EQE, 5.8%; gEL, 0.3 × 10-4). These results demonstrate the usefulness of using the chiroptically active MMLCT emission for achieving an amplified CPL.

Impact of Molecular Size and Shape on the Supramolecular Co-Assembly of Chiral Tricarboxamides: A Comparative Study.

A comparative investigation of the chiral amplification features of a series of three families of C3 -symmetric tricarboxamides, 1,3,5-triphenylbenzenetricarboxamides (TPBAs), benzenetricarboxamides (BTAs) and oligo(phenylene ethynylene) tricarboxamides (OPE-TAs), is here reported. As previously observed for BTAs and OPE-TAs, a similar dichroic response is obtained for TPBAs decorated with one, two or three chiral side chains bearing stereogenic centers, thus confirming the efficient transfer of point chirality to the supramolecular helical aggregates. Unlike BTAs and OPE-TAs, the chiral amplification ability of TPBAs in majority rules experiments shows a negligible dependence on the number of chiral centers per monomeric unit, and stands the largest among the series of tricarboxamides. Detailed experimental and theoretical studies demonstrate that the rotation angle between the TPBA units in the helical stack is intermediate to that observed for BTAs and OPE-TAs. This feature strongly conditions the steric interactions between vicinal molecules in the stack and the final chiral amplification outcome. Furthermore, theoretical calculations show that achiral side chains favor the interdigitation of the helical aggregates and thereby the formation of bundle superstructures.

The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase

Efficient search for DNA damage embedded in vast expanses of the DNA genome presents one of the greatest challenges to DNA repair enzymes. We report here crystal structures of human 8-oxoguanine (oxoG) DNA glycosylase, hOGG1, that interact with the DNA containing the damaged base oxoG and the normal base G while they are nested in the DNA helical stack. The structures reveal that hOGG1 engages the DNA using different protein-DNA contacts from those observed in the previously determined lesion recognition complex and other hOGG1-DNA complexes. By applying molecular dynamics simulations, we have determined the pathways taken by the lesion and normal bases when extruded from the DNA helix and their associated free energy profiles. These results reveal how the human oxoG DNA glycosylase hOGG1 locates the lesions inside the DNA helix and facilitates their extrusion for repair.

Protein Subdomain Enrichment of NUP155 Variants Identify a Novel Predicted Pathogenic Hotspot.

Functional variants in nuclear envelope genes are implicated as underlying causes of cardiopathology. To examine the potential association of single nucleotide variants of nucleoporin genes with cardiac disease, we employed a prognostic scoring approach to investigate variants of NUP155, a nucleoporin gene clinically linked with atrial fibrillation. Here we implemented bioinformatic profiling and predictive scoring, based on the gnomAD, National Heart Lung and Blood Institute-Exome Sequencing Project (NHLBI-ESP) Exome Variant Server, and dbNSFP databases to identify rare single nucleotide variants (SNVs) of NUP155 potentially associated with cardiopathology. This predictive scoring revealed 24 SNVs of NUP155 as potentially cardiopathogenic variants located primarily in the N-terminal crescent-shaped domain of NUP155. In addition, a predicted NUP155 R672G variant prioritized in our study was mapped to a region within the alpha helical stack of the crescent domain of NUP155. Bioinformatic analysis of inferred protein-protein interactions of NUP155 revealed over representation of top functions related to molecular transport, RNA trafficking, and RNA post-transcriptional modification. Topology analysis revealed prioritized hubs critical for maintaining network integrity and informational flow that included FN1, SIRT7, and CUL7 with nodal enrichment of RNA helicases in the topmost enriched subnetwork. Furthermore, integration of the top 5 subnetworks to capture network topology of an expanded framework revealed that FN1 maintained its hub status, with elevation of EED, CUL3, and EFTUD2. This is the first study to report novel discovery of a NUP155 subdomain hotspot that enriches for allelic variants of NUP155 predicted to be clinically damaging, and supports a role for RNA metabolism in cardiac disease and development.

Coherent acoustic phonon dynamics in chiral copolymers.

Coherent phonon oscillations in the UV-Vis transient absorption and circular dichroism response of two chiral polyfluorene-based copolymer thin films are investigated. A slow oscillation in the hundred picosecond regime indicates the propagation of a longitudinal acoustic phonon with a frequency in the gigahertz range through cholesteric films of PFPh and PFBT, which allow for the optical determination of the longitudinal sound velocity in these polymers, with values of (2550 ± 140) and (2490 ± 150) m s−1, respectively. The oscillation is induced by a strain wave, resulting in a pressure-induced periodic shift of the electronic absorption bands, as extracted from a Fourier analysis of the transient spectra. The acoustic phonon oscillation is also clearly detected in the transient circular dichroism (TrCD) response of PFPh, indicating a transient pressure-induced shift of the CD spectrum and possibly also phonon-induced chirality changes via pitch length modulation of the cholesteric helical polymer stack.

Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process.

Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby the interrogated nt is extruded from the DNA helical stack and binds into the TDG active site. The dynamic mechanism of the base-flipping process at an atomistic resolution, however, remains elusive. Here, we employ the Markov State Model (MSM) constructed from extensive all-atom molecular dynamics (MD) simulations to reveal the complete base-flipping process for a G.T mispair at a tens of microsecond timescale. Our studies identify critical intermediates of the mispaired dT during its extrusion process and reveal the key TDG residues involved in the inter-state transitions. Notably, we find an active role of TDG in promoting the intrahelical nt eversion, sculpturing the DNA backbone, and penetrating into the DNA minor groove. Three additional TDG substrates, namely dU, 5fC, and 5caC, are further tested to evaluate the substituent effects of various chemical modifications of the pyrimidine ring on base-flipping dynamics.

Binding Kinetics of DNA Intercalation by Small Rhodium Complexes

We characterize the kinetics and DNA binding properties of the small rhodium based molecules, [Rh(bpy)2(chrysi)]3+ (chrysi) and [Rh(bpy)2(phi)]3+ (phi). Both motifs bind to DNA. Phi contains an aromatic ring system known to intercalate between adjacent bases in a fairly sequence-neutral manner. Intercalation is weaker for chrysi due to the presence of an additional aromatic ring. Instead, chrysi has been shown to bind to DNA mismatches preferentially, ejecting and replacing the bases along the helical stack. We used optical tweezers on single DNA hairpin and long DNA molecules. Hairpin unfolding experiments on mismatch-containing sequences show that chrysi binds preferentially to sequences containing mismatches, stabilizing the hairpin. Long double stranded DNA was stretched at a constant external force in the presence of the ligand and a change in DNA extension was observed to be driven directly by ligand intercalation. Under the influence of increasing force, intercalation of the phi ligand into matched DNA is observed as expected. Surprisingly this intercalation into matched DNA was also observed for the chrysi ligand. Further analysis revealed the dissociation constants (Kd) of the chrysi and phi complexes to be on the order of 1 μM, though phi showed a significantly stronger intercalating affinity than chrysi.

The crystal structure of the 5΄ functional domain of the transcription riboregulator 7SK.

In vertebrates, the 7SK RNA forms the scaffold of a complex, which regulates transcription pausing of RNA-polymerase II. By binding to the HEXIM protein, the complex comprising proteins LARP7 and MePCE captures the positive transcription elongation factor P-TEFb and prevents phosphorylation of pausing factors. The HEXIM-binding site embedded in the 5΄-hairpin of 7SK (HP1) encompasses a short signature sequence, a GAUC repeat framed by single-stranded uridines. The present crystal structure of HP1 shows a remarkably straight helical stack involving several unexpected triples formed at a central region. Surprisingly, two uridines of the signature sequence make triple interactions in the major groove of the (GAUC)2. The third uridine is turned outwards or inward, wedging between the other uridines, thus filling the major groove. A molecular dynamics simulation indicates that these two conformations of the signature sequence represent stable alternatives. Analyses of the interaction with the HEXIM protein confirm the importance of the triple interactions at the signature sequence. Altogether, the present structural analysis of 7SK HP1 highlights an original mechanism of swapping bases, which could represent a possible ‘7SK signature’ and provides new insight into the functional importance of the plasticity of RNA.

The essential activities of the bacterial sigma factor

Transcription is the first and most heavily regulated step in gene expression. Sigma (σ) factors are general transcription factors that reversibly bind RNA polymerase (RNAP) and mediate transcription of all genes in bacteria. σ Factors play 3 major roles in the RNA synthesis initiation process: they (i) target RNAP holoenzyme to specific promoters, (ii) melt a region of double-stranded promoter DNA and stabilize it as a single-stranded open complex, and (iii) interact with other DNA-binding transcription factors to contribute complexity to gene expression regulation schemes. Recent structural studies have demonstrated that when σ factors bind promoter DNA, they capture 1 or more nucleotides that are flipped out of the helical DNA stack and this stabilizes the promoter open-complex intermediate that is required for the initiation of RNA synthesis. This review describes the structure and function of the σ70 family of σ proteins and the essential roles they play in the transcription process.

Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin.

Unique, two-state modulating current signatures are observed when a cytosine-cytosine mismatch pair is confined at the 2.4 nm latch constriction of the α-hemolysin (αHL) nanopore. We have previously speculated that the modulation is due to base flipping at the mismatch site. Base flipping is a biologically significant mechanism in which a single base is rotated out of the DNA helical stack by 180°. It is the mechanism by which enzymes are able to access bases for repair operations without disturbing the global structure of the helix. Here, temperature dependent ion channel recordings of individual double-stranded DNA duplexes inside αHL are used to derive thermodynamic (ΔH, ΔS) and kinetic (EA) parameters for base flipping of a cytosine at an unstable cytosine-cytosine mismatch site. The measured activation energy for flipping a cytosine located at the latch of αHL out of the helix (18 ± 1 kcal mol-1) is comparable to that previously reported for base flipping at mismatch sites from NMR measurements and potential mean force calculations. We propose that the αHL nanopore is a useful tool for measuring conformational changes in dsDNA at the single molecule level.

Structural insights into the interaction of blood coagulation co-factor VIIIa with factor IXa: A computational protein–protein docking and molecular dynamics refinement study

Coagulation factor X (FX) zymogen activation by factor IXa (FIXa) enzyme plays a critical role in the middle-phase of coagulation cascade. The activation process is catalytically inert and requires FIXa binding and complex formation with co-factor VIIIa (FVIIIa). In order to understand the structural details of the FVIIIa:FIXa complex, we employed knowledge-driven protein–protein docking and aqueous-phase MD refinement methods to develop a stable structural complex between FVIIIa and FIXa. The model shows that all four domains of FIXa wrap across FVIIIa that spans the co-factor binding surface of A2, A3 and C1 domains. The region surrounding the 558-helix of the A2-domain of FVIIIa is predicted to be the key interaction site with the helical segments of Lys293–Lys301 and Asp332–Arg338 residues of the serine-protease domain of FIXa. The hydrophobic helical stack between the GLA and EGF1 domains of FIXa is predicted to be primary interacting region with the A3–C2 domain interface of FVIIIa.

Two different one-dimensional supramolecular chains formed from the reaction of 2-[1-(pyridin-4-ylmethyl)-1H-benzimidazol-2-yl]quinoline with two different precursors, Co(NO3)2 and CoCl2.

Two different one-dimensional supramolecular chains with Co(II) cations have been synthesized based on the semi-rigid ligand 2-[1-(pyridin-4-ylmethyl)-1H-benzimidazol-2-yl]quinoline (L), obtained by condensation of 2-(1H-benzimidazol-2-yl)quinoline and 4-(chloromethyl)pyridine hydrochloride. Starting from different Co(II) salts, two new compounds have been obtained, viz. catena-poly[[[dinitratocobalt(II)]-μ-2-[1-(pyridin-4-ylmethyl)-1H-benzimidazol-2-yl]quinoline] dichloromethane monosolvate acetonitrile monosolvate], {[Co(NO3)2(C22H16N4)]·CH2Cl2·CH3CN}n, (I) and catena-poly[[[dichloridocobalt(II)]-μ-2-[1-(pyridin-4-ylmethyl)-1H-benzimidazol-2-yl]quinoline] methanol disolvate], {[CoCl2(C22H16N4)]·2CH3OH}n, (II). In (I), the Co(II) centres lie in a distorted octahedral [CoN3O3] coordination environment. {Co(NO3)2L}n units form one-dimensional helical chains, where the L ligand has different directions of twist. The helical chains stack together via interchain π-π interactions to form a two-dimensional sheet, and another type of π-π interaction further connects neighbouring sheets into a three-dimensional framework with hexagonal channels, in which the acetonitrile molecules and disordered dichloromethane molecules are located. In (II), the Co(II) centres lie in a distorted trigonal-bipyramidal [CoCl2N3] coordination environment. {CoCl2L}n units form one-dimensional chains. The chains interact via C-H···π and C-H···Cl interactions. The result is that two-dimensional sheets are generated, which are further linked into a three-dimensional framework via interlayer C-H···Cl interactions. When viewed down the crystallographic b axis, the methanol solvent molecules are located in an orderly manner in wave-like channels.

The structural basis for recognition and modification of the 30S ribosomal subunit by an antibiotic resistance methyltransferase (569.3)

Ribosomal RNA contains modifications at specific nucleotides in all organisms, some of which control resistance to antibiotics. However, the mechanisms are not well understood controlling how modification enzymes recognize their specific target nucleotide and position it within the active site. We report the crystal structure of the pathogen‐derived aminoglycoside‐resistance rRNA methyltransferase NpmA bound to the 30S ribosomal subunit in a pre‐catalytic state. The structure reveals that NpmA recognizes conserved rRNA tertiary structure rather than RNA sequence. Additionally, the structure shows NpmA flips the target nucleotide from its position within the helical base stack to position it within the active site. The structure provides a general framework for investigating the mechanisms of other rRNA modification enzymes.Grant Funding Source: Supported by National Institutes of Health

Metadynamics simulation study on the conformational transformation of HhaI methyltransferase: an induced-fit base-flipping hypothesis.

DNA methyltransferases play crucial roles in establishing and maintenance of DNA methylation, which is an important epigenetic mark. Flipping the target cytosine out of the DNA helical stack and into the active site of protein provides DNA methyltransferases with an opportunity to access and modify the genetic information hidden in DNA. To investigate the conversion process of base flipping in the HhaI methyltransferase (M.HhaI), we performed different molecular simulation approaches on M.HhaI-DNA-S-adenosylhomocysteine ternary complex. The results demonstrate that the nonspecific binding of DNA to M.HhaI is initially induced by electrostatic interactions. Differences in chemical environment between the major and minor grooves determine the orientation of DNA. Gln237 at the target recognition loop recognizes the GCGC base pair from the major groove side by hydrogen bonds. In addition, catalytic loop motion is a key factor during this process. Our study indicates that base flipping is likely to be an “induced-fit” process. This study provides a solid foundation for future studies on the discovery and development of mechanism-based DNA methyltransferases regulators.

2,5-Bis[4-methyl-3-(pyridin-3-yl)phenyl]-1,3,4-oxadiazole and its one-dimensional polymeric complex with ZnCl2

2,5-Bis[4-methyl-3-(pyridin-3-yl)phenyl]-1,3,4-oxadiazole (L), C26H20N4O, forms one-dimensional chains via two types of intermolecular π-π interactions. In catena-poly[[dichloridozinc(II)]-μ-2,5-bis[4-methyl-3-(pyridin-3-yl)phenyl]-1,3,4-oxadiazole], [ZnCl2(C26H20N4O)]n, synthesized by the combination of L with ZnCl2, the Zn(II) centres are coordinated by two Cl atoms and two N atoms from two L ligands. [ZnCl2L]n forms one-dimensional P (plus) and M (minus) helical chains, where the L ligand has different directions of twist. The helical chains stack together via interchain π-π and C-H···π interactions.

Coordination-directed one-dimensional coordination polymers generated from a new oxadiazole bridging ligand and HgX2(X= Cl, Br and I)

A new 1,3,4-oxadiazole bridging bent organic ligand, 2,5-bis{5-methyl-2-[(4-pyridyl)methoxy]phenyl}-1,3,4-oxadiazole, C(28)H(24)N(4)O(3), L, has been used to create three novel one-dimensional isomorphic coordination polymers, viz. catena-poly[[[dichloridomercury(II)]-μ-2,5-bis{5-methyl-2-[(4-pyridyl)methoxy]phenyl}-1,3,4-oxadiazole] methanol monosolvate], {[HgCl(2)(C(28)H(24)N(4)O(3))]·CH(3)OH}(n), catena-poly[[[dibromidomercury(II)]-μ-2,5-bis{5-methyl-2-[(4-pyridyl)methoxy]phenyl}-1,3,4-oxadiazole] methanol monosolvate], {[HgBr(2)(C(28)H(24)N(4)O(3))]·CH(3)OH}(n), and catena-poly[[[diiodidomercury(II)]-μ-2,5-bis{5-methyl-2-[(4-pyridyl)methoxy]phenyl}-1,3,4-oxadiazole] methanol monosolvate], {[HgI(2)(C(28)H(24)N(4)O(3))]·CH(3)OH}(n). The free L ligand itself adopts a cis conformation, with the two terminal pyridine rings and the central oxadiazole ring almost coplanar [dihedral angles = 5.994 (7) and 9.560 (6)°]. In the Hg(II) complexes, however, one of the flexible pyridylmethyl arms of ligand L is markedly bent and helical chains are obtained. The Hg(II) atom lies in a distorted tetrahedral geometry defined by two pyridine N-atom donors from two L ligands and two halide ligands. The helical chains stack together via interchain π-π interactions that expand the dimensionality of the structure from one to two. The methanol solvent molecules link to the complex polymers through O-H···N and O-H···O hydrogen bonds.

Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA

The reliable repair of pre-mutagenic U/G mismatches that originated from hydrolytic cytosine deamination is crucial for the maintenance of the correct genomic information. In most organisms, any uracil base in DNA is attacked by uracil DNA glycosylases (UDGs), but at least in Methanothermobacter thermautotrophicus Δ H, an alternative strategy has evolved. The exonuclease III homologue Mth212 from the thermophilic archaeon M. thermautotrophicus Δ H exhibits a DNA uridine endonuclease activity in addition to the apyrimidinic/apurinic site endonuclease and 3′ → 5′exonuclease functions. Mth212 alone compensates for the lack of a UDG in a single-step reaction thus substituting the two-step pathway that requires the consecutive action of UDG and apyrimidinic/apurinic site endonuclease. In order to gain deeper insight into the structural basis required for the specific uridine recognition by Mth212, we have characterized the enzyme by means of X-ray crystallography. Structures of Mth212 wild-type or mutant proteins either alone or in complex with DNA substrates and products have been determined to a resolution of up to 1.2 Å, suggesting key residues for the uridine endonuclease activity. The insertion of the side chain of Arg209 into the DNA helical base stack resembles interactions observed in human UDG and seems to be crucial for the uridine recognition. In addition, Ser171, Asn153, and Lys125 in the substrate binding pocket appear to have important functions in the discrimination of aberrant uridine against naturally occurring thymidine and cytosine residues in double-stranded DNA.