Symmetry-related Sites Research Articles

The catalytic Mn2+ sites in the enolase-inhibitor complex: crystallography, single-crystal EPR, and DFT calculations.

Crystals of Zn2+/Mn2+ yeast enolase with the inhibitor PhAH (phosphonoacetohydroxamate) were grown under conditions with a slight preference for binding of Zn2+ at the higher affinity site, site I. The structure of the Zn2+/Mn2+-PhAH complex was solved at a resolution of 1.54 A, and the two catalytic metal binding sites, I and II, show only subtle displacement compared to that of the corresponding complex with the native Mg2+ ions. Low-temperature echo-detected high-field (W-band, 95 GHz) EPR (electron paramagnetic resonance) and 1H ENDOR (electron-nuclear double resonance) were carried out on a single crystal, and rotation patterns were acquired in two perpendicular planes. Analysis of the rotation patterns resolved a total of six Mn2+ sites, four symmetry-related sites of one type and two out of the four of the other type. The observation of two chemically inequivalent Mn2+ sites shows that Mn2+ ions populate both sites I and II and the zero-field splitting (ZFS) tensors of the Mn2+ in the two sites were determined. The Mn2+ site with the larger D value was assigned to site I based on the 1H ENDOR spectra, which identified the relevant water ligands. This assignment is consistent with the seemingly larger deviation of site I from octahedral symmetry, compared to that of site II. The ENDOR results gave the coordinates of the protons of two water ligands, and adding them to the crystal structure revealed their involvement in a network of H bonds stabilizing the binding of the metal ions and PhAH. Although specific hyperfine interactions with the inhibitor were not determined, the spectroscopic properties of the Mn2+ in the two sites were consistent with the crystal structure. Density functional theory (DFT) calculations carried out on a cluster representing the catalytic site, with Mn2+ in site I and Zn2+ in site II, and vice versa, gave overestimated D values on the order of the experimental ones, although the larger D value was found for Mn2+ in site II rather than in site I. This discrepancy was attributed to the high sensitivity of the ZFS parameters to the Mn-O bond lengths and orientations, such that small, but significant, differences between the optimized and crystal structures alter the ZFS considerably, well above the difference between the two sites.

Growth, EPR and optical absorption spectra of l-threonine single crystals doped with Cu 2+ ions

We investigated the crystal growth, electron paramagnetic resonance (EPR) and optical absorption spectra of l-threonine doped with Cu 2+. The quality, size and habit of the single crystals grown from aqueous solution by the slow solvent evaporation and by the cooling methods vary when the impurities are introduced during the growth process. The variations with the magnetic field orientation of the EPR spectra of single-crystal samples at room temperature and 9.77 GHz in three crystal planes ( ab, bc and ac) show the presence of copper impurities in four symmetry-related sites of the unit cell. These spectra display well resolved hyperfine couplings of the S = 1 2 of Cu 2+ with the I Cu= 3 2 of the copper nuclei. Additional hyperfine splittings, well-resolved only for specific orientations of the magnetic field, indicate that the copper impurity ions in the interstitial sites have two N ligands with similar hyperfine couplings. The principal values of the g and A Cu tensors calculated from the EPR data are g 1=2.051(1), g 2=2.062(2), g 3=2.260(2), A Cu,1=16.9(5)×10 −4 cm −1, A Cu,2=21.8(6)×10 −4 cm −1 , A Cu,3=180.0(5)×10 −4 cm −1. The principal directions corresponding to g 3 and to A Cu,3 are coincident within the experimental errors, reflecting the orientation of the bonding planes of the copper ions in the crystal. The values of the crystal field energies are evaluated from the optical absorption spectrum, and the crystal field and bonding parameters of the Cu impurities in the crystal are calculated and analyzed. The EPR and optical absorption results are discussed in terms of the crystal structure of l-threonine and the electronic structure of the Cu 2+ ions, and compared with data reported for other systems. The effects of the impurities in the growth and habit of the crystals are also discussed.

G-Anisotropy of the S2-State Manganese Cluster in Single Crystals of Cyanobacterial Photosystem II Studied by W-Band Electron Paramagnetic Resonance Spectroscopy

The multiline signal from the S2-state manganese cluster in the oxygen evolving complex of photosystem II (PSII) was observed in single crystals of a thermophilic cyanobacterium Thermosynechococcus vulcanus for the first time by W-band (94 GHz) electron paramagnetic resonance (EPR). At W-band, spectra were characterized by the g-anisotropy, which enabled the precise determination of the tensor. Distinct hyperfine splittings (hfs's) as seen in frozen solutions of PSII at X-band (9.5 GHz) were detected in most of the crystal orientations relative to the magnetic field. In some orientations, however, the hfs's disappeared due to overlapping of a large number of EPR lines from eight crystallographic symmetry-related sites of the manganese cluster within the unit cell of the crystal. Analysis of the orientation-dependent spectral features yielded the following g-tensor components: g(x) = 1.988, g(y) = 1.981, g(z) = 1.965. The principal values suggested an approximate axial symmetry around the Mn(III) ion in the cluster.

Motion of Aromatic Hydrocarbons in the Microporous Aluminum Methylphosphonates AlMePO-α and AlMePO-β

(2)H wide-line NMR has been used, in conjunction with molecular dynamics simulations where appropriate, to follow the reorientation of the monoaromatic compounds benzene, toluene, and p-xylene within the one-dimensional channels of the alpha- and beta-polymorphs of aluminum methylphosphonate, Al(2)(CH(3)PO(3))(3). Variable-temperature, static, (2)H NMR spectra of adsorbed d(6)-benzene, d(3)-, d(5)-, and d(8)-toluenes, and d(3),d(3)-p-xylene were matched by line shape simulation. The motion of p-xylene in both polymorphs is approximated by the long axis of the molecule describing a cone within the channels, the half-angle of which is greater for the slightly wider channels in AlMePO-beta (27-30 degrees cf. 18-19 degrees). The (2)H NMR of d(3)-toluene is simulated using a similar model, whereas the signal from aromatic deuterons in d(5)- and d(8)-toluenes is simulated by a ring undergoing 2pi/3 flips around the para axis. The reorientation of benzene shows the largest differences between the two pore structures. In AlMePO-beta it tumbles with little restriction, although at low temperatures the spectral details are better matched by allowing the molecule to spend a greater proportion of its time closer to the wall. In AlMePO-alpha the much broader line shape arises from constrained motion within the strongly triangular channels. Molecular dynamics simulations of benzene in the two structures confirm the differences. They support a model for benzene in AlMePO-alpha where its motion is restricted to rotations about its 6-fold axis and 2pi/3 jumps between symmetry-related sites in the pores, so that the plane of the aromatic ring remains approximately parallel to the c-axis.

Crystal structure refinement of palygorskite from neutron powder diffraction

Palygorskite is a Mg-rich fibrous clay, present in nature as a mixture of two intricately intertwined polymorphs – monoclinic ( C2/m ) and orthorhombic ( Pbmn ) – characterized by the presence of channels along Z -axis, filled by weakly bound zeolitic water. A neutron powder diffraction study was carried out by full Rietveld refinement on a deuterated sample, measured at ISIS on the HRPD beam-line. The positions of oxygen and deuterium atoms of the zeolitic water were located ab initio through cyclically repeated Difference Fourier maps, and their atomic coordinates and occupancy factors were refined. The frameworks of both monoclinic and orthorhombic palygorskite do not differ significantly from the models reported in the literature, although they are more distorted. The arrangement of the zeolitic water molecules is highly disordered and different in the two polymorphs. Given the coexistence of several deuterium sets, two different H-bonding schemes are proposed for each polymorph. Further H-bonding alternatives could be derived by considering the location of oxygen atoms in partially occupied symmetry related sites. The links between the zeolitic water and the clay framework appear to be weaker in orthorhombic than in monoclinic palygorskite, as shown by the lower number and different strength of H-bonds. The detailed knowledge of the zeolitic water arrangement may help in better understanding the structural features and production techniques of palygorskite-based compounds of great interest, such as the Maya Blue pigment.

Twelve receptor molecules attach per viral particle of human rhinovirus serotype 2 via multiple modules

The crystallographic T=1 (pseudo T=3) icosahedral symmetry of the human rhinovirus capsid dictates the presence of 60 identical, symmetry related surface structures that are available for antibody and receptor binding. X-ray crystallography has shown that 60 individual very-low density lipoprotein receptor (VLDLR) modules bind to HRV2. Their arrangement around the fivefold axes of the virion suggested that tandem oligomers of such modules could attach simultaneously to symmetry-related sites. By resolving virus particles carrying various numbers of artificial recombinant concatemers of VLDLR repeat 3 (V33333) by capillary electrophoresis and extrapolation of the measured mobilities to that at saturation of all binding sites, we present evidence for up to 12 molecules of the concatemer to bind one single virion.

Single Crystal133Cs NMR Study of Cs+(15-Crown-5)2I-

Cesium-133 NMR spectra of a single crystal of tetragonal <TEX>$Cs^+ (15-crown-5)_2I^-$</TEX> were obtained as a function of crystal orientation in an applied magnetic field of 9.40T and analyzed to provide the magnitudes and orientations of the <TEX>$^{133}Cs$</TEX> chemical shift and quadrupolar tensors for two magnetically nonequivalent and symmetry related sites. Chemical shift tensor components and parameters of quadrupolar interactions are obtained as <TEX>${\delta}_{11}=46(1),\;{\delta}_{22}=60(1),\;{\delta}_{33}=-30(1)$</TEX> ppm, quadrupole coupling constant QCC = 581(1) kHz, and asymmetry parameter <TEX>${\eta}$</TEX> = 0.481(1), respectively. The nonaxially symmetric NMR parameters imply that the local environment of the cesium nuclei is nonaxially symmetric. The DANTE experiment burned holes in the <TEX>$^{133}Cs$</TEX> NMR line of the title compound. The hole burning of the single crystal and powder <TEX>$^{133}Cs$</TEX> NMR lines showed that the NMR lines are not homogeneously broadened.

Symmetric K + and Mg 2+ Ion-binding Sites in the 5 S rRNA Loop E Inferred from Molecular Dynamics Simulations

Potassium binding to the 5 S rRNA loop E motif has been studied by molecular dynamics at high (1.0 M) and low (0.2 M) concentration of added KCl in the presence and absence of Mg 2+. A clear pattern of seven deep groove K + binding sites or regions, in all cases connected with guanine N7/O6 atoms belonging to GpG, GpA, and GpU steps, was identified, indicating that the LE deep groove is significantly more ionophilic than the equivalent groove of regular RNA duplexes. Among all, two symmetry-related sites (with respect to the central G·A pair) were found to accommodate K + ions with particularly long residence times. In a preceding molecular dynamics study by Auffinger et al. in the year 2003, these two sites were described as constituting important Mg 2+ binding locations. Altogether, the data suggest that these symmetric sites correspond to the loop E main ion binding regions. Indeed, they are located in the deep groove of an important ribosomal protein binding motif associated with a fragile pattern of non-Watson–Crick pairs that has certainly to be stabilized by specific Mg 2+ ions in order to be efficiently recognized by the protein. Besides, the other sites accommodate monovalent ions in a more diffuse way pointing out their lesser significance for the structure and function of this motif. Ion binding to the shallow groove and backbone atoms was generally found to be of minor importance since, at the low concentration, no well defined binding site could be characterized while high K + concentration promoted mostly unspecific potassium binding to the RNA backbone. In addition, several K + binding sites were located in positions equivalent to water molecules from the first hydration shell of divalent ions in simulations performed with magnesium, indicating that ion binding regions are able to accommodate both mono- and divalent ionic species. Overall, the simulations provide a more precise but, at the same time, a more intricate view of the relations of this motif with its ionic surrounding.

An X-ray diffraction study of partially ordered electron density in clathrates of Dianin's compound that include simple carboxylic acids.

The nature of the inclusions in ten clathrate complexes of Dianin's compound have been investigated by the use of electron-density difference maps. The guest species are the first eight straight-chain carboxylic acids, formic to octanoic, a branched-chain acid (dimethylacetic acid) and trifluoroacetic acid. The point-group symmetry of the clathrate cavity, 3, is satisfied by partial occupation of symmetry-related sites by two included molecules in the case of formic, acetic and trifluoroacetic acids and by a single molecule in the remainder. Hydrogen-bonding requirements in the case of formic and acetic acids are satisfied by dimer formation; in the trifluoroacetic acid complex the two acid molecules form hydrogen bonds to framework O atoms at either end of the cavity. The adoption of gauche conformations in heptanoic and octanoic acid chains shortens them sufficiently that they fit the cavity with only slight distortion.

Alternating translocation of protein substrates from both ends of ClpXP protease.

In ClpXP protease complexes, hexameric rings of the ATP-dependent ClpX chaperone stack on one or both faces of the double-heptameric rings of ClpP. We used electron microscopy to record the initial binding of protein substrates to ClpXP and their accumulation inside proteolytically inactive ClpP. Proteins with N- or C-terminal recognition motifs bound to complexes at the distal surface of ClpX and, upon addition of ATP, were translocated to ClpP. With a partially translocated substrate, the non-translocated portion remained on the surface of ClpX, aligned with the central axis of the complex, confirming that translocation proceeds through the axial channel of ClpXP. Starting with substrate bound on both ends, most complexes translocated substrate from only one end, and rarely (<5%) from both ends. We propose that translocation from one side is favored for two reasons: initiation of translocation is infrequent, making the probability of simultaneous initiation low; and, further, the presence of protein within the cis side translocation channel or within ClpP generates an inhibitory signal blocking translocation from the trans side.

Characterization of divalent cation localization in the minor groove of the A(n)T(n) and T(n)A(n) DNA sequence elements by (1)H NMR spectroscopy and manganese(II).

The localization of Mn(2+) in A-tract DNA has been studied by (1)H NMR spectroscopy using a series of self-complementary dodecamer oligonucleotides that contain the sequence motifs A(n)(n) and T(n)A(n), where n = 2, 3, or 4. Mn(2+) localization in the minor groove is observed for all the sequences that have been studied, with the position and degree of localization being highly sequence-dependent. The site most favored for Mn(2+) localization in the minor groove is near the 5'-most ApA step for both the T(n)A(n) and the A(n)T(n) series. For the T(n)A(n) series, this results in two closely spaced symmetry-related Mn(2+) localization sites near the center of each duplex, while for the A(n)T(n) series, the two symmetry-related sites are separated by as much as one half-helical turn. The degree of Mn(2+) localization in the minor groove of the T(n)A(n) series decreases substantially as the AT sequence element is shortened from T(4)A(4) to T(2)A(2). The A(n)T(n) series also exhibits length-dependent Mn(2+) localization; however, the degree of minor groove occupancy by Mn(2+) is significantly less than that observed for the T(n)A(n) series. For both A(n)T(n) and T(n)A(n) sequences, the 3'-most AH2 resonance is the least broadened of the AH2 resonances. This is consistent with the observation that the minor groove of A-tract DNA narrows in the 5' to 3' direction, apparently becoming too narrow after two base pairs for the entry of a fully hydrated divalent cation. The results that are reported illustrate the delicate interplay that exists between DNA nucleotide sequence, minor groove width, and divalent cation localization. The proposed role of cation localization in helical axis bending by A-tracts is also discussed.

Molecular Dynamics Study of Ca2+ Binding Loop Variants of Silver Hake Parvalbumin with Aspartic Acid at the “Gateway” Position

The helix-loop-helix (i.e., EF-hand) Ca2+ ion binding motif is characteristic of a large family of high-affinity calcium ion binding proteins, including the parvalbumins, oncomodulins and calmodulins. In this work we describe a set of molecular dynamics computations on the major parvalbumin from the silver hake (SHPV-B) and on functional fragments of this protein, consisting of the first four helical regions (the ABCD fragment), and the internal helix- loop-helix region (the CD fragment). In both whole protein and protein fragments (i.e., ABCD and CD fragments), the 9th loop residue in the calcium ion binding site in the CD helix-loop-helix region (the so-called “gateway” position) has been mutated from glutamic acid to aspartic acid. Aspartic acid is one of the most common residues found at the gateway position in other (non-parvalbumin) EF-hand proteins, but has never been found at the gateway position of any parvalbumin. (Interestingly, aspartic acid does occur at the gateway position in the closely related rat and human oncomodulins.) Consistent with experimental observations, the results of our molecular dynamics simulations show that incorporation of aspartic acid at the gateway position is very disruptive to the structural integrity of the calcium ion coordination site in the whole protein. The aspartic acid mutation is somewhat less disruptive to the calcium ion coordination sites in the two parvalbumin fragments (i.e., the ABCD and CD fragments), presumably due to the higher degree of motional freedom allowable in these protein fragments. One problem associated with the E59D whole protein variant is a prohibitively close approach of the aspartate carboxyl group to the CD calcium ion observed in the energy-minimized (pre-molecular dynamics) structure. This steric situation does not emerge during energy-minimization of the wild-type protein. The damage to the structural integrity of the calcium ion coordination site in the whole protein E59D variant is not relieved during the molecular dynamics simulation. In fact, during the course of the 300 picosecond simulation, all of the calcium ion ligands leave the primary coordination sphere. In addition, the conserved hydrogen-bonds (in the short β-sheet structure) that links the CD site to the symmetry-related EF site (in the non-mutated whole protein) is also somewhat disrupted in the E59D whole protein variant. These results suggest that the Ca2+ ion binding deficiencies in the CD loop are related, at least in part, to the unique interaction that exists between the paired CD and EF hands in the whole protein. Our theoretical results correlate well with previous studies on engineered EF-hand proteins and with all of our experimental evidence on whole silver hake parvalbumin and enzymatically-generated parvalbumin fragments.

Electron spin resonance of Cu2+ impurities in l-arginine phosphate monohydrate single crystals

Using electron paramagnetic resonance spectroscopy we studied single crystals of l-arginine phosphate monohydrate doped with copper. The angular dependence of the spectrum in three orthogonal planes shows that the Cu2+ ions occupy two symmetry related sites in the structure. The Zeeman and hyperfine coupling tensors were determined. The principal values are: g1=2.053, g2=2.054, g3=2.251, A1≈0, A2=24×10−4cm−1 and A3=177×10−4cm−1. Superhyperfine interactions with 14N ligands, well resolved for certain orientations of the magnetic field, suggest that Cu impurities have three N ligands. In terms of the molecular structure and based in similar systems, our findings are discussed and suggestions are made.

Electrostatic Interactions between Charged Amino Acid Residues and the Bacteriochlorophyll Dimer in Reaction Centers from Rhodobacter sphaeroides

The extent of electrostatic contributions from the protein environment was assessed by the introduction of ionizable residues near the bacteriochlorophyll dimer in reaction centers from Rhodobacter sphaeroides. Two mutations at symmetry-related sites, M199 Asn to Asp and L170 Asn to Asp, resulted in a 48 and 44 mV lowering of the midpoint potential, respectively, compared to the wild type at pH 8, while a 75 mV decrease in the midpoint potential was observed for the mutation L168 His to Glu. The decrease relative to wild type was found to be approximately additive, up to 147 mV, for various combinations of the mutations. As the pH was lowered from 9.5 to 6.0, the relative decrease in the midpoint potential became smaller for each of these three mutations. Titration of the pH dependence of the change in midpoint potential of the M199 Asn to Asp mutant compared to wild type yielded a pK(a) value of 7.9 and a change in midpoint potential from low to high pH of 59 mV. The major effect of the mutation on the midpoint potential of the dimer is interpreted as stemming from a negative charge on the residue. An average dielectric constant of approximately 20 was estimated for the local protein environment, consistent with a relatively hydrophobic environment for residue M199. The rate of charge recombination between the primary quinone acceptor and the bacteriochlorophyll dimer decreased in the M199 Asn to Asp mutant at high pH, reflecting the decrease in midpoint potential.

Identification of a small-molecule binding site at the dimer interface of the HIV integrase catalytic domain.

Integration of the reverse-transcribed HIV cDNA into the host DNA is a required step in viral replication. The virus-encoded integrase protein catalyzes the initial DNA breaking and joining reactions that mediate cDNA integration. Here, the identification by X-ray crystallography of a small-molecule binding site on the integrase catalytic domain is reported. The small-molecule family studied consists of a core of arsenic or phosphorus surrounded by four aromatic groups. Two arsenic derivatives were visualized bound to integrase. In each case, two molecules bound at symmetry-related sites on the catalytic domain dimer interface. The first compound studied, tetraphenyl arsonium, did not inhibit integrase. However, a synthetic compound substituting a catechol for one of the phenyl rings, dihydroxyphenyltriphenylarsonium, bound to the same site and did inhibit the enzyme. Changes in the vicinity of the catalytic site were seen with the inhibitory compound only, potentially explaining its mechanism of action. Further substituting phosphonium for arsonium yielded a compound with an IC(50) in the low micromolar range. These findings may be useful in designing new inhibitors of integrase, which is at present the only one of the three HIV enzymes for which clinically useful inhibitors are not available.

Structure of uranium(VI) oxide dihydrate, UO3.2H2O; synthetic meta-schoepite (UO2)4O(OH)6.5H2O.

Structure of uranium(VI) oxide dihydrate, P03.2H20; synthetic meta-schoepite (UO2)40(OH)6.5H20 f The structure of uranium oxide dihydrate, also known as meta-schoepite (UO2)4O(OH)6.5H2O, has been determined from a synthetic single crystal. The structure, at 150 K, space group Pbcn, lattice constants a = 14.6861 (4), b = 13.9799 (3) and c = 16.7063 (5) A, consists of layers of stoichiometry (UO2)4O(OH)6, formed from edge-sharing UO7 pentagonal bipyramids, interleaved with hydrogen-bonded water molecules. Three of the layer hydroxyl groups are linked through hydrogen bonding to single water molecules and the three remaining OH units form interactions with water molecules that each act as acceptors in two hydrogen bonds. One of the water molecules in the inter-layer region is disordered over two symmetry-related sites and forms hydrogen-bonded interactions only within the layer and with the uranyl O atoms. The relationship of the structure of meta-schoepite to that of schoepite is discussed in detail.

Ammonium hydrogen squarate-water (3/2)

In the title compound, NH4+·C4HO4−·2\over 3H2O, the hydrogen squarate anions and water molecules are arranged to form planes almost parallel to bc. The ammonium cations are located between these planes and cross-link them in the a direction by means of an extensive network of hydrogen bonds. There are two symmetry-independent sets of cations and anions. One of the hydrogen squarate anions and one of the ammonium cations are situated on a twofold axis and the H atoms of these moieties are disordered over the symmetry-related sites.

Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex

Guanine quartets are readily formed by guanine nucleotides and guanine-rich oligonucleotides in the presence of certain monovalent and divalent cations. The quadruplexes composed of these quartets are of interest for their potential roles in vivo, their relatively frequent appearance in oligonucleotides derived from in vitro selection, and their inhibition of template directed RNA polymerization under proposed prebiotic conditions. The requirement of cation coordination for the stabilization of G quartets makes understanding cation-quadruplex interactions an essential step towards a complete understanding of G quadruplex formation. We have used15NH4+ as a probe of cation coordination by the four G quartets of the DNA bimolecular quadruplex [d(G4T4G4)]2, formed from oligonucleotides with the repeat sequence found in Oxytricha nova telomeres.1H and 15N heteronuclear NMR spectroscopy has allowed the direct localization of monovalent cation binding sites in the solution state and the analysis of cation movement between the binding sites. These experiments show that [d(G4T4G4)]2 coordinates three ammonium ions, one in each of two symmetry related sites and one on the axis of symmetry of the dimeric molecule. The NH4+ move along the central axis of the quadruplex between these sites and the solution, reminiscent of an ion channel. The residence time of the central ion is determined to be 250 ms. The15NH4+ is shown to be a valuable probe of monovalent cation binding sites and dynamics.

Stereochemistry and transformations of NH:N hydrogen bonds Part II. Proton stability in the monosalts of 1,4-diazabicyclo[2.2.2]octane

Crystal structures of three monosalts of 1,4-diazabicyclo[2.2.2]octane, perchlorate, tetrafluoroborate and bromide, have been studied by X-ray diffraction. The orthorhombic perchlorate and tetrafluoroborate salts are isostructural, while the bromide salt crystallizes in the hexagonal system. Varying stabilities of the acidic proton in the NH:N hydrogen bonds, linking the cations into chains, have been observed: in the perchlorate salt the H-atom is ordered, in the tetrafluoroborate it is 0.75:0.25 disordered at two N-sites, and in the hydrobromide the H-atom is 50:50 disordered between the symmetry-related sites. Possible mechanisms leading to the disorder of the protons and their stabilizing factors are discussed.

A glutamine 67--> histidine mutation in homotetrameric R67 dihydrofolate reductase results in four mutations per single active site pore and causes substantial substrate and cofactor inhibition.

R67 dihydrofolate reductase (DHFR) is a type II DHFR produced by bacteria as a resistance mechanism to increasing clinical use of the antibacterial drug trimethoprim. Type II DHFRs are not homologous in either sequence or structure with chromosomal DHFRs. The crystal structure of R67 DHFR shows a single active site pore that spans the length of the homotetramer. Related sites (due to a 222 symmetry element at the center of the pore) are used to bind ligands, i.e. each half of the pore can accommodate either the substrate, dihydrofolate (DHF), or the cofactor, NADPH, although DHF and NADPH are bound differently. To evaluate the role of glutamine 67 (and its symmetry-related Q167, Q267 and Q367 residues which occur at the center of the active site pore), a Q67H mutation was constructed. Binary binding of dihydrofolate (DHF; monitored by isothermal titration calorimetry) displays two identical sites with a Kd value of 0.04 microM, while binding of NADPH shows two sites possessing negative cooperativity with Kd values of 0.027 and 0.62 microM. A comparison of ligand binding in Q67H versus wild-type (wt) R67 DHFR indicates both ligands bind more tightly (80-6000-fold) and DHF binding in Q67H R67 DHFR no longer displays positive cooperativity as seen in wt R67 DHFR. Ternary complex binding in the Q67H mutant indicates a total of two ligands can bind per pore. Substantial substrate and cofactor inhibition are observed during catalysis, consistent with non-productive binding of either two DHF or two NADPH molecules in Q67H R67 DHFR. Because of the symmetry-related binding sites in the active site pore, the accumulation of potentially positive mutations in R67 DHFR is limited by the balance between tighter binding of ligands (and thus potentially increased catalytic efficiency) and inhibition that arises upon tighter binding of two identical ligands at symmetry-related sites.