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PubMed1995

Crystal structure of piperazinium oleate at -150 degrees C.

The crystal structure of piperazinium oleate ([C4H12N2]2+.2[C18H34O2]-) has been determined from X-ray diffraction data at -150 degrees C in order to study the oleate chain conformation and molecular packing. Differential scanning calorimetry shows three reversible crystalline state phase transitions (54.5, -34.8, and -54.8 degrees C) in the range from the melting point (84.8 degrees C) to -160 degrees C. The cell constants for a flash-frozen crystal at -150 degrees C are a = 5.630(2), b = 14.900(2), c = 24.825(4) A, alpha = 88.77(2), beta = 88.12(2), gamma = 80.38(2) degrees; Z = 2, space group P1; Dc = 1.05 g cm-3, m.p. = 84.8 degrees C. The cell constants are similar at room temperature except for a doubling of b at -150 degrees C. The crystal structure at -150 degrees C has been refined to R(F2) = 0.116 for 8410 independent reflections. There are two independent oleate anions (A and B), both having an overall extended conformation except for kinks that are different at the cis olefin group. The oleate A chain is ordered while the oleate B chain is disordered in two regions. Because of different torsion angles at bonds adjacent to the double bond, the B-chain olefin group adopts two configurations, one of which is predominant. From the olefin group to the terminal methyl group, the B-chain adopts one of two all-trans configurations with equal probability. It cannot be determined whether the two kinds of disorder are correlated. Taking into account the centrosymmetrically related oleate chains, the crystal structure contains at least six and possibly eight extended chain conformers with different kinks at the olefin group. Third and fourth order displacement parameters have been determined for the partially resolved atomic sites in the oleate B chain and these have been used to map probability density functions for the disordered atoms. The piperazinium cations are in a chair conformation. Each is hydrogen bonded to four oleate anions, forming an infinite ribbon parallel to (025). These ribbons are stacked upon each other to form a monolayer 24.8 A thick parallel to (001).

Calorimetry↗
PubMed2005

Crystal structure of human pFGE, the paralog of the Calpha-formylglycine-generating enzyme.

In eukaryotes, sulfate esters are degraded by sulfatases, which possess a unique Calpha-formylglycine residue in their active site. The defect in post-translational formation of the Calpha-formylglycine residue causes a severe lysosomal storage disorder in humans. Recently, FGE (formylglycine-generating enzyme) has been identified as the protein required for this specific modification. Using sequence comparisons, a protein homologous to FGE was found and denoted pFGE (paralog of FGE). pFGE binds a sulfatase-derived peptide bearing the FGE recognition motif, but it lacks formylglycine-generating activity. Both proteins belong to a large family of pro- and eukaryotic proteins containing the DUF323 domain, a formylglycine-generating enzyme domain of unknown three-dimensional structure. We have crystallized the glycosylated human pFGE and determined its crystal structure at a resolution of 1.86 A. The structure reveals a novel fold, which we denote the FGE fold and which therefore serves as a paradigm for the DUF323 domain. It is characterized by an asymmetric partitioning of secondary structure elements and is stabilized by two calcium cations. A deep cleft on the surface of pFGE most likely represents the sulfatase polypeptide binding site. The asymmetric unit of the pFGE crystal contains a homodimer. The putative peptide binding site is buried between the monomers, indicating a biological significance of the dimer. The structure suggests the capability of pFGE to form a heterodimer with FGE.

Amino Acid Motifs↗
PubMed2006

The first crystal structure of phosphofructokinase from a eukaryote: Trypanosoma brucei.

The crystal structure of the ATP-dependent phosphofructokinase (PFK) from Trypanosoma brucei provides the first detailed description of a eukaryotic PFK, and enables comparisons to be made with the crystal structures of bacterial ATP-dependent and PPi-dependent PFKs. The structure reveals that two insertions (the 17-20 and 329-348 loops) that are characteristic of trypanosomatid PFKs, but absent from bacterial and mammalian ATP-dependent PFKs, are located within and adjacent to the active site, and are in positions to play important roles in the enzyme's mechanism. The 90 residue N-terminal extension forms a novel domain that includes an "embracing arm" across the subunit boundary to the symmetry-related subunit in the tetrameric enzyme. Comparisons with the PPi-dependent PFK from Borrelia burgdorferi show that several features thought to be characteristic of PPi-dependent PFKs are present in the trypanosome ATP-dependent PFK. These two enzymes are generally more similar to each other than to the bacterial or mammalian ATP-dependent PFKs. However, there are critical differences at the active site of PPi-dependent PFKs that are sufficient to prevent the binding of ATP. This crystal structure of a eukaryotic PFK has enabled us to propose a detailed model of human muscle PFK that shows active site and other differences that offer opportunities for structure-based drug discovery for the treatment of sleeping sickness and other diseases caused by the trypanosomatid family of protozoan parasites.

Adenosine Triphosphate↗
PubMed1985

Intercalation of water molecules between nucleic acid bases in the crystal structures of 6-azathymine hemihydrate and 5-amino-2-thiocytosine dihydrochloride dihydrate.

The crystal structure of 6-azathymine hemihydrate (6AzTH) exhibits a novel intercalation of water molecules interposed half-way between the modified bases 6.3 to 6.7 A apart. The crystal contains four molecules of 6-azathymine (6AzT) and two water molecules as the independent repeating unit. These two water molecules together with the four bases form two separate water sandwiches. In the crystal structure these sandwiches form two sets of local clusters. The anhydrous crystalline form of 6AzT, on the other hand, is stabilized by base stacking interactions. Both the water molecules in 6AzTH that are involved in sandwich formation have trigonal coordination around them. A reexamination of the crystal structure of 5-amino-2-thiocytosine (5A2TC) revealed that one of the water molecules in this structure also forms a water sandwich and has trigonal coordination whereas the other water molecule with tetrahedral coordination does not form a sandwich. The environment and the characteristics of the intercalated water molecule in these structures suggest a possible role for such water intercalations in the dynamics of DNA. Crystals of 6AzTH are monoclinic, space group P21/n, with unit cell parameters a = 8.861 (1), b = 13.177 (3), c = 20.662 (2) A, beta = 93.35 (1) degrees, and Z = 16. From diffractometer data (2503 reflections, greater than or equal to 3 sigma), the crystal structure was solved and refined to an R of 0.056.

Base Sequence↗
PubMed2002

The use of restraints in Rietveld refinement of molecular compounds; a case study using the crystal structure determination of tryptamine free base.

The previously unknown crystal structure of the biogenic compound tryptamine, in the form of a free base (C(10)H(12)N(2)), has been solved from X-ray powder diffraction data using simulated annealing followed by restrained Rietveld refinement [space group P2(1)2(1)2(1), a = 12.28593 (6), b = 8.53351 (4), c = 8.49385 (4) A, Z = 4, final reduced-chi(2) = 5.255]. A restrained Rietveld refinement was carried out in which the global weight factor, f, of the stereochemical restraints was gradually lowered. The effect of the relaxation of restraints on the crystal structure and on chi(2) was studied and a criterion for the final choice of f is reported. The crystal structure reported here shows efficient packing involving weak intermolecular hydrogen bonding and a herringbone-type packing pattern.

Journal Article↗
PubMed2005

Effect of the semirigid capping ligand on the structure formation of cyano-bridged bimetallic assemblies: syntheses, crystal structures, and magnetic properties.

The syntheses, crystal structures, and magnetic properties of three novel cyano-bridged bimetallic assemblies, [Ni(bpm)(2)](3)[Co(CN)(6)](2)x3.5H(2)O (1), [Co(bpm)(2)][Fe(CN)(5)NO]x2H(2)O (2), and [Co(bpm)(2)][Ni(CN)(4)] (3) (bpm = bis(1-pyrazolyl)methane), are reported. Complex 1 crystallizes in the tetragonal space group P4(3)2(1)2 with a = 12.800(5) A, b = 12.800(5) A, c = 42.80(3) A, V = 7012(6) A(3), and Z = 8. Complex 2 crystallizes in the chiral trigonal space group P3(2)21 with a = 11.9961(19) A, b = 11.9961(19) A, c = 16.062(5) A, gamma = 120 degrees , V = 2001.7(8) A(3), and Z = 3. Complex 1 is a trigonal bipyramidal complex in which three [Ni(bpm)(2)](2+) units are situated in the equatorial plane and are connected to the two apical [Co(CN)(6)](3)(-) units via three N ends of the cyanide groups. Complex 2 possesses a triangular left-handed helical chain structure composed of [Co(bpm)(2)](2+) linked by [Fe(CN)(5)NO](2)(-); the shortest intramolecular Co...Fe distance is 5.162 A. To the best of our knowledge, this is the first observation of a heteronuclear helical chain structure based on pentacyanonitrosylferrate(II). The structure of complex 3 is roughly determined by X-ray crystallograhy analysis to be a 1D zigzag chain. These structure variations, from a discrete cluster to a 1D helical chain and a 1D zigzag chain, rely on the semirigidity of the capping ligand bpm. Magnetic susceptibility measurements indicate that complex 1 has an intramolecular ferromagnetic interaction (J = 4.06 cm(-)(1)) between the nickel(II) ions; this is further confirmed by the magnetization measurements. In complexes 2 and 3, the cobalt(II) ions are located in a moderately strong field.

Journal Article↗
PubMed1999

Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD.

The structural basis for the extreme discrimination achieved by malate dehydrogenases between a variety of closely related substrates encountered within the cell has been difficult to assess because of the lack of an appropriate catalytically competent structure of the enzyme. Here, we have determined the crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase with the alternative substrate alpha-ketomalonate and the coenzyme analogue 1,4,5,6-tetrahydronicotinamide. Both subunits of the dimeric porcine heart, and from the prokaryotes Escherichia coli and Thermus flavus. However, large changes are noted around the active site, where a mobile loop now closes to bring key residues into contact with the substrate. This observation substantiates a postulated mechanism in which the enzyme achieves high levels of substrate discrimination through charge balancing in the active site. As the activated cofactor/substrate complex has a net negative charge, a positive counter-charge is provided by a conserved arginine in the active site loop. The enzyme must, however, also discriminate against smaller substrates, such as pyruvate. The structure shows in the closed (loop down) catalytically competent complex two arginine residues (91 and 97) are driven into close proximity. Without the complimentary, negative charge of the substrate side-chain of oxaloacetate or alpha-ketomalonate, charge repulsion would resist formation production of this catalytically productive conformation, hence minimising the effectiveness of pyruvate as a substrate. By this mechanism, malate dehydrogenase uses charge balancing to achieve fivefold orders of magnitude in discrimination between potential substrates.

Amino Acid Sequence↗
PubMed1995

Solution structure of the B-chain of insulin as determined by 1H NMR spectroscopy. Comparison with the crystal structure of the insulin hexamer and with the solution structure of the insulin monomer.

The solution structure of the isolated B-chain of bovine insulin has been determined by 1H NMR spectroscopy combined with simulated annealing calculations. Complete sequence-specific assignments for the proton resonances are reported together with a set of 309 NOEs used in the structure calculations. Chemical-shift variations from random coil values provide support for the existence of helical regions in the polypeptide chain, as do a characteristic series of d alpha beta(i, i + 3) NOEs from residues B8 to B17. While there is some evidence for a limited degree of conformational averaging over the helical region, in general the helix is relatively well defined and corresponds closely to the helical region seen in the X-ray crystal structure of the insulin hexamer. Other similarities with the crystal structure include turn-like conformations at the carboxy terminal end of the helix and extended strands at both the amino and carboxy termini of the peptide. These similarities between the crystal structure and the isolated B-chain suggest that this peptide has intrinsic folding properties, which allow it to adopt its characteristic structure in intact insulin without the need for extensive cooperative interactions with the A-chain. Despite these general similarities, an important difference between the isolated B-chain and the intact protein occurs in the carboxy terminal region. This region appears significantly more mobile in the isolated B-chain. As a conformational change involving the carboxy terminus has been implicated in receptor binding, the current study of the isolated B-chain provides valuable information on the extent of this region's intrinsic mobility.

Amino Acid Sequence↗
PubMed2006

Crystal structure of ferric-yersiniabactin, a virulence factor of Yersinia pestis.

Yersiniabactin (Ybt), the siderophore produced by Yersinia pestis, has been crystallized successfully in the ferric complex form and the crystal structure has been determined. The crystals are orthorhombic with a space group of P2(1)2(1)2(1) and four distinct molecules per unit cell with cell dimensions of a=11.3271(+/-0.0003)A, b=22.3556(+/-0.0006)A, and c=39.8991(+/-0.0011)A. The crystal structure of ferric Ybt shows that the ferric ion is coordinated as a 1:1 complex by three nitrogen electron pairs and three negatively charged oxygen atoms with a distorted octahedral coordination. The molecule displays a Delta absolute configuration with chiral centers at N2, C9, C10, C12, C13, and C19 in R, R, R, R, S, S configurations, respectively. Few of the crystal structures of siderophores have been solved, and those which have been are of simple hydroxamate and catechol types such as ferrioxamine B and agrobactin. To our knowledge this is the first report of the ferric crystal structure of 5-member heterocycle siderophore.

Crystallization↗
PubMed2003

The crystal structure of Echinococcus granulosus fatty-acid-binding protein 1.

We describe the 1.6 A crystal structure of the fatty-acid-binding protein EgFABP1 from the parasitic platyhelminth Echinococcus granulosus. E. granulosus causes hydatid disease, which is a major zoonosis. EgFABP1 has been implicated in the acquisition, storage, and transport of lipids, and may be important to the organism since it is incapable of synthesising most of its lipids de novo. Moreover, EgFABP1 is a promising candidate for a vaccine against hydatid disease. The crystal structure reveals that EgFABP1 has the expected 10-stranded beta-barrel fold typical of the family of intracellular lipid-binding proteins, and that it is structurally most similar to P2 myelin protein. We describe the comparison of the crystal structure of EgFABP1 with these proteins and with an older homology model for EgFABP1. The electron density reveals the presence of a bound ligand inside the cavity, which we have interpreted as palmitic acid. The carboxylate group of the fatty acid interacts with the protein's P2 motif, consisting of a conserved triad R em leader R-x-Y. The hydrophobic tail of the ligand assumes a fairly flat, U-shaped conformation and has relatively few interactions with the protein.We discuss some of the structural implications of the crystal structure of EgFABP1 for related platyhelminthic FABPs.

Amino Acid Motifs↗
PubMed2004

Correlation between crystal structure and mobility in organic field-effect transistors based on single crystals of tetrathiafulvalene derivatives.

Recently, it was reported that crystals of the organic material dithiophene-tetrathiafulvalene (DT-TTF) have a high field-effect charge carrier mobility of 1.4 cm(2)/(V x s). These crystals were formed by a simple drop-casting method, making this material interesting to investigate for possible applications in low-cost electronics. Here, organic single-crystal field-effect transistors based on materials related to DT-TTF are presented and a clear correlation between the crystal structure and the electrical characteristics is observed. The observed relationship between the mobilities in the different crystal structures is strongly corroborated by calculations of both the molecular reorganization energies and the maximum intermolecular transfer integrals. The most suitable materials described here exhibit mobilities that are among the highest reported for organic field-effect transistors and that are the highest reported for solution-processed materials.

Journal Article↗
PubMed2002

The elusive vanadate (V(3)O(9))(3-): isolation, crystal structure, and nonaqueous solution behavior.

The isolation, crystal structure, and nonaqueous solution characteristics of the first trinuclear vanadate are presented. The crystal structure reveals a six-membered cyclic arrangement of alternating vanadium and oxygen atoms for the anion of [(C(4)H(9))(4)N](3)(V(3)O(9)). The (51)V NMR spectrum of this compound in CD(3)CN exhibits multiple peaks. The relative intensities of each resonance can be altered by concentration and temperature changes, the later of which are reversible. Addition of [(C(4)H(9))(4)N]Br and NaClO(4) also perturbs the equilibria between species observed. Conductivity data for [(C(4)H(9))(4)N](3)(V(3)O(9)) in CH(3)CN as a function of concentration display pronounced curvature and indicate formation of a neutral species in solution at the highest concentrations studied. Stoichiometric mixtures of [(C(4)H(9))(4)N](3)(V(3)O(9)) with the known vanadates [(C(4)H(9))(4)N](3)(HV(4)O(12)), [(C(4)H(9))(4)N](3)(V(5)O(14)), and [(C(4)H(9))(4)N](3)(H(3)V(10)O(28)) are prepared and examined by (51)V NMR. Equilibration between the various vanadates is observed and characterized. Resonances for these known vanadates, however, cannot be used to identify the peaks found for [(C(4)H(9))(4)N](3)(V(3)O(9)), alone, in solution. The existence of ion pairs in acetonitrile is the only interpretation for the solution behavior of [(C(4)H(9))(4)N](3)(V(3)O(9)) consistent with all data. As such, we can directly observe each possible ion pairing state by (51)V NMR: (V(3)O(9))(3-) at -555 ppm, [[(C(4)H(9))(4)N](V(3)O(9))] (2-) at -569 ppm, [[(C(4)H(9))(4)N](2)(V(3)O(9))](-) at -576 ppm, and [(C(4)H(9))(4)N](3)(V(3)O(9)) at -628 ppm. To the best of our knowledge, [(C(4)H(9))(4)N](3)(V(3)O(9)) presents the first case in which every possible ion paired state can be observed directly from a parent polyion. Isolation and characterization of this simple metal oxo moiety may now facilitate efforts to design functional polyoxometalates.

Journal Article↗
PubMed2005

ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis.

The amino terminal Cu(II)- and Ni(II)-binding (ATCUN) motif is a small metal-binding site found in the N-terminus of many naturally occurring proteins. The ATCUN motif has been implicated in DNA cleavage and has been shown to have antitumor activity. In proteins, the ATCUN motif is formed from a histidine in the third position, its preceding residue and the free N-terminus. Four nitrogen atoms from these three residues act as metal ligands. Knowledge of metal-binding geometry helps in the design of metal-binding peptides and in understanding of the mechanisms of metal-mediated functions. Since the N-terminus region of ATCUN-containing proteins is highly disordered, no geometrical features can be derived from the protein structures. However, the crystal structure of a small metal-bound ATCUN peptide shows that the nitrogen ligands form a distorted square planar geometry. Distance constraints derived from this designed peptide were used to search 1949 polypeptide chains to find ATCUN-like motifs in any position along the polypeptide chain. Only approximately 1.9% and approximately 0.3% of histidines are involved in partial and full ATCUN-like geometric features, respectively. These two datasets were compared with the dataset of all histidines. None of the ATCUN-like motifs occur in the middle of an alpha-helix or a beta-strand. Further sequence analysis revealed total conservation of ATCUN histidines in four proteins including the transcription factor TBX3, implicated in Ulnar-Mammary Syndrome. Our analysis suggests that the ATCUN-like motif in TBX3 is a potential metal-binding site, although a structural role was not completely ruled out. Metal-binding activity in TBX3, if confirmed, will help us to understand the role of metals in transcriptional regulation and is likely to cast light on the causes of some serious genetic disorders. A conformational role is suggested for ATCUN-like motifs in other proteins.

Binding Sites↗
PubMed2001

Structural basis for a change in substrate specificity: crystal structure of S113E isocitrate dehydrogenase in a complex with isopropylmalate, Mg2+, and NADP.

Isocitrate dehydrogenase (IDH) catalyzes the oxidative decarboxylation of isocitrate and has negligible activity toward other (R)-malate-type substrates. The S113E mutant of IDH significantly improves its ability to utilize isopropylmalate as a substrate and switches the substrate specificity (k(cat)/K(M)) from isocitrate to isopropylmalate. To understand the structural basis for this switch in substrate specificity, we have determined the crystal structure of IDH S113E in a complex with isopropylmalate, NADP, and Mg(2+) to 2.0 A resolution. On the basis of a comparison with previously determined structures, we identify distinct changes caused by the amino acid substitution and by the binding of substrates. The S113E complex exhibits alterations in global and active site conformations compared with other IDH structures that include loop and helix conformational changes near the active site. In addition, the angle of the hinge that relates the two domains was altered in this structure, which suggests that the S113E substitution and the binding of substrates act together to promote catalysis of isopropylmalate. Ligand binding results in reorientation of the active site helix that contains residues 113 through 116. E113 exhibits new interactions, including van der Waals contacts with the isopropyl group of isopropylmalate and a hydrogen bond with N115, which in turn forms a hydrogen bond with NADP. In addition, the loop and helix regions that bind NADP are altered, as is the loop that connects the NADP binding region to the active site helix, changing the relationship between substrates and enzyme. In combination, these interactions appear to provide the basis for the switch in substrate specificity.

Amino Acid Substitution↗
PubMed2001

Crystal structure analysis and chiral recognition study of Delta-[Ru(bpy)2(py)2][(+)-O,O'-dibenzoylD-tartrate].12H2O and Lambda-[Ru(bpy)2(py)2][(-)-O,O'-dibenzoyl-L-tartrate].12H2O.

The molecular structure and crystal-packing mode of the enantiopure chiral building blocks Delta-[Ru(bpy)(2)(py)(2)][(+)-O,O'-dibenzoyl-D-tartrate].12H(2)O (I) and Lambda-[Ru(bpy)(2)(py)(2)][(-)-O,O'-dibenzoyl-L-tartrate].12H(2)O (II) have been determined by single-crystal X-ray diffraction data. This study proposes a model of how the L- and D-dibenzoyltartrate anions recognize the chirality of the hydrophobic [Ru(bpy)(2)(py)(2)](2+) complex. The monoclinic unit cell contains four complex cations, four tartrate anions, and 48 water molecules. Since there are no possibilities to form hydrogen bonds between the cations and anions, chiral recognition is due to crystal packing. Two benzoyl rings of two different tartrate anions are gripping the two bpy-planes of the Ru-complex. Further a third benzoyl ring from a tartrate anion is packed between the two pyridine rings, favoring one enantiomeric form to crystallize from aqueous solution. Crystal structure data for I at 153 K: a = 15.342(3) A, b = 19.200(4) A, c = 18.872(4) A, beta = 104.841(3) degrees, monoclinic space group C(2), R(1)= 0.0239 (I > 2sigma(I)), R(2) = 0.0606, Flack parameter = 0.0115 (with esd 0.0166). For II at 293 K: a = 15.376(4) A, b = 19.388(11) A, c = 19.085(7) A, beta = 105.11(2) degrees, monoclinic space group C121, R(1)= 0.0686 (I > 2sigma(I)), R(2) = 0.1819, Flack parameter = -0.0100 (with esd 0.0521).

Journal Article↗
PubMed2003

Aromatic-aromatic interactions in crystal structures of helical peptide scaffolds containing projecting phenylalanine residues.

Aromatic-aromatic interactions between phenylalanine side chains in peptides have been probed by the structure determination in crystals of three peptides: Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, I; Boc-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-Val-Ala-Phe-Aib-OMe, II; Boc-Aib-Ala-Phe-Aib-Phe-Ala-Val-Aib-OMe, III. X-ray diffraction studies reveal that all three peptides adopt helical conformations in the solid state with the Phe side chains projecting outward. Interhelix association in the crystals is promoted by Phe-Phe interactions. A total of 15 unique aromatic pairs have been characterized in the three independent crystal structures. In peptides I and II, the aromatic side chains lie on the same face of the helix at i/i + 4 positions resulting in both intrahelix and interhelix aromatic interactions. In peptide III, the Phe side chains are placed on the opposite faces of the helix, resulting in exclusive intermolecular aromatic interactions. The distances between the centroids of aromatic pair ranges from 5.11 to 6.86 A, while the distance of closest approach of ring carbon atoms ranges from 3.27 to 4.59 A. Examples of T-shaped and parallel-displaced arrangements of aromatic pairs are observed, in addition to several examples of inclined arrangements. The results support the view that the interaction potential for a pair of aromatic rings is relatively broad and rugged with several minima of similar energies, separated by small activation barriers.

Crystallography, X-Ray↗
PubMed2005

Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits.

Phosphoglycerate dehydrogenases exist in at least three different structural motifs. The first D-3-phosphoglycerate dehydrogenase structure to be determined was from Escherichia coli and is a tetramer composed of identical subunits that contain three discernable structural domains. The crystal structure of D-3-phosphoglycerate dehydrogenase from Mycobacterium tuberculosis has been determined at 2.3 A. This enzyme represents a second structural motif of the D-3-phosphoglycerate dehydrogenase family, one that contains an extended C-terminal region. This structure is also a tetramer of identical subunits, and the extended motif of 135 amino acids exists as a fourth structural domain. This intervening domain exerts quite a surprising characteristic to the structure by introducing significant asymmetry in the tetramer. The asymmetric unit is composed of two identical subunits that exist in two different conformations characterized by rotation of approximately 180 degrees around a hinge connecting two of the four domains. This asymmetric arrangement results in the formation of two different and distinct domain interfaces between identical domains in the asymmetric unit. As a result, the surface of the intervening domain that is exposed to solvent in one subunit is turned inward in the other subunit toward the center of the structure where it makes contact with other structural elements. Significant asymmetry is also seen at the subunit level where different conformations exist at the NAD-binding site and the putative serine-binding site in the two unique subunits.

Amino Acid Motifs↗
PubMed1999

Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol.

Multiple-solvent crystal structure determination (MSCS) allows the position and orientation of bound solvent fragments to be identified by determining the structure of protein crystals soaked in organic solvents. We have extended this technique by the determination of high-resolution crystal structures of thermolysin (TLN), generated from crystals soaked in 2% to 100% isopropanol. The procedure causes only minor changes to the conformation of the protein, and an increasing number of isopropanol interaction sites could be identified as the solvent concentration is increased. Isopropanol occupies all four of the main subsites in the active site, although this was only observed at very high concentrations of isopropanol for three of the four subsites. Analysis of the isopropanol positions shows little correlation with interaction energy computed using a molecular mechanics force field, but the experimentally determined positions of isopropanol are consistent with the structures of known protein-ligand complexes of TLN.

2-Propanol↗