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At least 991 records · Page 55Linked to original sources
PubMed1990

Crystal structure of plakalbumin, a proteolytically nicked form of ovalbumin. Its relationship to the structure of cleaved alpha-1-proteinase inhibitor.

The crystal structure of plakalbumin, a proteolytically nicked form of ovalbumin, has been determined to a resolution of 2.8 A by the isomorphous replacement method and preliminary refinement. The structure closely resembles that of the cleaved form of alpha-1-proteinase inhibitor, with some important exceptions. The disposition of the new carboxyl chain terminus liberated by proteolysis is different with respect to the central beta-sheet A in the structures of these two molecules. In alpha-1-proteinase inhibitor, the new chain terminus inserts in beta-sheet A to add a middle strand to the sheet. In plakalbumin, this strand remains free near the site at which the cleavage occurs. A structural basis for this difference in behavior is proposed from the structures and sequences of these two molecules and other members of the serpin family. The structures and positions of the putative signal peptide of ovalbumin, the several post-translational modifications, and the relationship of the intron-exon patterns of plakalbumin and alpha-1-proteinase inhibitor to their protein structures are also described.

Amino Acid Sequence↗
PubMed2003

Sugar interaction with metal ion: crystal structure and spectroscopic study of SrCl2.galactitol.4H2O.

The crystal structure of SrCl(2).galactitol.4H(2)O has been determined. It belongs to monoclinic system, C2/c space group with unit cell dimensions: a=13.9849(3), b=14.1601(5), c=8.3026(3) A, beta=104.621(2) degrees, V=1590.9(9) A(3) and Z=4. Each Sr(2+) ion in the unit cell binds to two molecules of galactitol through O2 and O3 in one alditol and O2' and O3' in the other, as well as to four water molecules. Sr-O distances in SrCl(2).galactitol.4H(2)O complex range from 2.5420 to 2.6359 A. FT-IR, Raman and far-IR spectra of SrCl(2).galactitol.4H(2)O all show that SrCl(2) coordinates with galactitol through OH groups of the sugar molecule to form the new complex.

Carbohydrates↗
PubMed2000

CH/pi interactions in the crystal structure of TATA-box binding protein/DNA complexes.

Crystal structures of TATA box-binding proteins (TBP) of various sources bound to their promoter DNA (TATA box) were analyzed with use of our program CHPI. A number of short CH/Csp2 contacts have been unveiled in these complexes at the boundary of TBP and the TATA box minor groove. The result was discussed in the context of the CH/pi interaction. Thus, the nature of nonpolar forces, reported in the past at the interface of the two components, has been attributed to the CH/pi interaction. Furthermore, many CH/pi contacts have been disclosed within the same strand of the promoter DNA. The structure of the TATA element, partially unwound and severely bent on complexation, seems to be stabilized by CH/pi interactions; H2' of the deoxyribose moiety and the methyl group in the thymine nucleotide play the primary role.

Binding Sites↗
PubMed1994

Drug binding by calmodulin: crystal structure of a calmodulin-trifluoperazine complex.

The crystal structure of calmodulin (CaM) bound to trifluoperazine (TFP) has been determined and refined to a resolution of 2.45 A. Only one TFP is bound to CaM, but that is sufficient to cause distortion of the central alpha-helix and juxtaposition of the N- and C-terminal domains similar to that seen in CaM-polypeptide complexes. The drug makes extensive contacts with residues in the C-terminal domain of CaM but only a few contacts with one residue in the N-terminal domain. The structure suggests that substrate binding to the C-terminal domain is sufficient to cause the conformational changes in calmodulin that lead to activation of its targets.

Animals↗
PubMed1996

Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex.

The crystal structure is reported of a tris(benzimidazole) analogue of the minor-groove drug Hoechst 33258 bound to the sequence d(CGCAAATTTGCG)2. The structure has been refined to an R factor of 17.4% at a resolution of 2.2 A. The ligand covers approximately 7 1/2 base pairs, including the 5'-AAATTT central sequence. This has an exceptionally narrow minor-groove width, together with high propeller twists for individual base pairs. The ligand has a highly twisted structure, with an overall twist of 50 degrees between aromatic rings. All three benzimidazole subunits are in register with the DNA, and there is a symmetric group of six hydrogen bonds between ligand and A.T base-pair edges. By contrast, the ligand does not show an optimal isohelical fit to the DNA. The correct phasing of drug and DNA base pairs is ensured by a number of changes to the DNA such that the central 5'-AAATTT region is slightly unwound relative to the structures of other noncovalent minor-groove drug complexes.

Benzimidazoles↗
PubMed1997

Crystal structure of nucleotide-free diphtheria toxin.

The crystal structure of diphtheria toxin (DT) in the absence of nucleotide (nucleotide-free DT) has been determined at 2.3 A resolution to a crystallographic R factor and free R factor of 18.2 and 28.2%, respectively. A comparison of this structure to the previously determined structures of DT in complex with adenyly(3'-5')uridine monophosphate (ApUp) and DT in complex with nicotinamide adenine dinucleotide (NAD) reveals that there are no significant movements of the two subdomains of the catalytic (C) domain associated with dinucleotide binding. The side chains of six residues within the active-site cleft, including Tyr65, Pro38, Tyr27, Thr23, Glu148, and Tyr54, show movements of up to 3 A upon dinucleotide binding. In the structure of nucleotide-free DT, the active-site loop residues 39-47 of the C domain are well ordered and extend over the active-site cleft in approximately the same position as in the structure of DT in complex with ApUp. This is in contrast to the structure of the DT-NAD complex, in which the active-site loop is disordered. On the basis of a comparison of the nucleotide-free and NAD-bound DT structures, we suggest that the interaction of NAD with Pro38 and also possibly Tyr54 and Trp153 could disrupt the network of hydrogen bonds that stabilizes the position of the active-site loop over the active-site cleft, allowing this loop to become disordered. This may be an important step in binding of the C domain of DT to its substrate, elongation factor-2.

Binding Sites↗
PubMed1997

Crystal structure of DNA photolyase from Anacystis nidulans.

The crystal structure at 1.8 A resolution of 8-HDF type photolyase from A. nidulans shows a backbone structure similar to that of MTHF type E. coli photolyase but reveals a completely different binding site for the light-harvesting cofactor.

Amino Acid Sequence↗
PubMed1995

Crystal structure of NADH oxidase from Thermus thermophilus.

The crystal structures of the flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) containing isoforms of NADH oxidase from Thermus thermophilus have been determined by isomorphous and molecular replacement and refined to 2.3 A and 1.6 A resolution with R-values of 18.5% and 18.6% respectively. The structure of the homodimeric enzyme consists of a central 4-stranded antiparallel beta-sheet covered by helices, a more flexible domain formed by two helices, and a C-terminal excursion connecting the subunits. The active sites are located in a deep cleft between the subunits. The binding site of the flavin cofactor lacks the common nucleotide binding fold and is different from the FMN binding site found in flavodoxins.

Binding Sites↗
PubMed2002

Crystal structure of microbial transglutaminase from Streptoverticillium mobaraense.

The crystal structure of a microbial transglutaminase from Streptoverticillium mobaraense has been determined at 2.4 A resolution. The protein folds into a plate-like shape, and has one deep cleft at the edge of the molecule. Its overall structure is completely different from that of the factor XIII-like transglutaminase, which possesses a cysteine protease-like catalytic triad. The catalytic residue, Cys(64), exists at the bottom of the cleft. Asp(255) resides at the position nearest to Cys(64) and is also adjacent to His(274). Interestingly, Cys(64), Asp(255), and His(274) superimpose well on the catalytic triad "Cys-His-Asp" of the factor XIII-like transglutaminase, in this order. The secondary structure frameworks around these residues are also similar to each other. These results imply that both transglutaminases are related by convergent evolution; however, the microbial transglutaminase has developed a novel catalytic mechanism specialized for the cross-linking reaction. The structure accounts well for the catalytic mechanism, in which Asp(255) is considered to be enzymatically essential, as well as for the causes of the higher reaction rate, the broader substrate specificity, and the lower deamidation activity of this enzyme.

Amino Acid Sequence↗
PubMed2002

Non-nucleoside analogue inhibitors bind to an allosteric site on HCV NS5B polymerase. Crystal structures and mechanism of inhibition.

X-ray crystal structures of two non-nucleoside analogue inhibitors bound to hepatitis C virus NS5B RNA-dependent RNA polymerase have been determined to 2.0 and 2.9 A resolution. These noncompetitive inhibitors bind to the same site on the protein, approximately 35 A from the active site. The common features of binding include a large hydrophobic region and two hydrogen bonds between both oxygen atoms of a carboxylate group on the inhibitor and two main chain amide nitrogen atoms of Ser(476) and Tyr(477) on NS5B. The inhibitor-binding site lies at the base of the thumb domain, near its interface with the C-terminal extension of NS5B. The location of this inhibitor-binding site suggests that the binding of these inhibitors interferes with a conformational change essential for the activity of the polymerase.

Allosteric Site↗
PubMed1997

Crystal structure of chicken riboflavin-binding protein.

The crystal structure of chicken egg white riboflavin-binding protein, determined to a resolution of 2.5 A, is the prototype of a family that includes other riboflavin- and folate-binding proteins. An unusual characteristic of these molecules is their high degree of cross-linking by disulfide bridges and, in the case of the avian proteins, the presence of stretches of highly phosphorylated polypeptide chain. The structure of chicken egg white riboflavin-binding protein is characterized by a ligand-binding domain and a phosphorylated motif. The ligand-binding domain has a fold that appears to be strongly conditioned by the presence of the disulfide bridges. The phosphorylated motif, essential for vitamin uptake, is made up of two helices found before and after the flexible phosphorylated region. The riboflavin molecule binds to the protein with the isoalloxazine ring stacked in between the rings of Tyr75 and Trp156. This geometry and the proximity of other tryptophans explain the fluorescent quenching observed when riboflavin binds to the protein.

Amino Acid Sequence↗
PubMed2002

A comparative study of intermolecular interactions in the crystal structures of phenyl/phenyl end-capped oligoanilines.

Three crystal structures have been analysed from the point of view of intermolecular interactions: N,N'-diphenyl-1,4-benzoquinone diimine, C(18)H(14)N(2), (I), its reduced form N,N'-diphenyl-1,4-phenylenediamine, C(18)H(16)N(2), (II), and N,N'-diphenyl-1,4-phenylenediammonium bis(p-toluenesulfonate), C(18)H(18)N(2)(2+) x 2C(7)H(7)O(3)S(-), (III), which contains fully protonated (II) with p-toluenesulfonic acid. The local molecular C(i) symmetry is preserved in all three structures and the packing seems to be dominated by the mutual arrangement of the simple polyaniline oligomers in the different protonation states. In (I), the most significant molecular interactions are stacking forces, forming columns of molecules along [001]. Close packing of the columns results in C-centering of the structure. In (II), only van der Waals interactions can be observed. In the structure of (III), the p-toluenesulfonate ions serve as acceptors in relatively strong N[bond]H...O hydrogen bonds. The N,N'-diphenyl-1,4-phenylenediammonium cation intercalates between two anions related by a centre of symmetry.

Journal Article↗
PubMed1994

Refined crystal structure of Acinetobacter glutaminasificans glutaminase-asparaginase.

The crystal structure of glutaminase-asparaginase from Acinetobacter glutaminasificans has been reinterpreted and refined to an R factor of 0.171 at 2.9 A resolution, using the same X-ray diffraction data that were used to build a preliminary model of this enzyme [Ammon, Weber, Wlodawer, Harrison, Gilliland, Murphy, Sjölin & Roberts (1988). J. Biol. Chem. 263, 150-156]. The current model, which does not include solvent, is based in part on the related structure of Escherichia coli asparaginase and is significantly different from the structure of the enzyme from A. glutaminasificans described previously. The reason for the discrepancies has been traced to insufficient phasing power of the original heavy-atom derivative data, which could not be compensated for fully by electron-density modification techniques. The corrected structure of A. glutaminasificans glutaminase-asparaginase is presented and compared with the preliminary model and with the structure of E. coli asparaginase.

Journal Article↗
PubMed2005

The first crystal structure of an archaeal helical repeat protein.

The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 A resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19 kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten alpha-helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein.

Algorithms↗
PubMed1989

Crystal structure and conformation of glycyl-glycyl-sarcosine.

Crystals of the tripeptide, glycyl-glycyl-sarcosine (C7H13N3O4) from aqueous methanol are orthorhombic, space group Pbcn with cell parameters at 294 K of a = 8.279(1), b = 9.229(4), c = 24.447(5)A, V = 1868.0 A3, M.W. = 203.2, and Z = 8. The crystal structure was solved and refined using CAD-4 data (1171 reflections greater than or equal to 3 sigma) to a final R-value of 0.053. The first peptide linkage is trans and planar whereas the second peptide link between Gly and sarcosine is cis and appreciably non-planar (w = 7.4 degrees). The peptide backbone has an extended conformation at the N-terminal part but adopts a polyglycine-II type of conformation at the C-terminal part. The backbone torsion angles are: psi 1 = -173.9, w1 = -177.8, (phi 2, psi 2) = (-178.8, -170.8), w2 = 7.4, (phi 3, psi 3) = (-81.6, 165.6 degrees).

Crystallography↗
PubMed1998

Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase.

Crystal structures of bovine heart cytochrome c oxidase in the fully oxidized, fully reduced, azide-bound, and carbon monoxide-bound states were determined at 2.30, 2.35, 2.9, and 2.8 angstrom resolution, respectively. An aspartate residue apart from the O2 reduction site exchanges its effective accessibility to the matrix aqueous phase for one to the cytosolic phase concomitantly with a significant decrease in the pK of its carboxyl group, on reduction of the metal sites. The movement indicates the aspartate as the proton pumping site. A tyrosine acidified by a covalently linked imidazole nitrogen is a possible proton donor for the O2 reduction by the enzyme.

Animals↗
PubMed1997

Crystal structures of nucleic acid complexes of ribonuclease U2.

Crystal structures of adenine-specific Ustilago sphaerogena ribonuclease U2 complexed with the substrate analogues, d(ApG), d(ApGpG), and d(ApGpC), with the intermediate analogue, 2',3'-O-isopropylidene-adenosine, and with the product, 3'-AMP, have been determined. In each structure, the adenine base is recognized by the enzyme with four hydrogen-bonds. In the substrate analogue structures, the second base of guanine is sandwiched between His 101 and Tyr 107 side-chains, and forms two hydrogen-bonds with Tyr 107 O and Asp 108 O delta 1 atoms. The third base of the trinucleotides is in van der Waals interaction with the Tyr 78 side-chain. The phosphate group between the second and third nucleosides forms two hydrogen-bonds with the side chains of Asp 37 and Tyr 78. Oxygen atoms of the scissile phosphate group are involved in interactions with catalytic residues of Tyr 39, His 41, Glu 62, Arg 85, and His 101. These interactions indicate that either His 41 or Glu 62 acts as a general base and His 101 acts as a general acid in the first step of RNA hydrolysis.

Amino Acid Sequence↗