... and discussion Description of the structures There is one molecule in the asymmetric unit of both structures composed of a single domain consisting of 14 helices, 12 of them forming an (a ⁄ a6) ... side-chains The structureof the starch binding domain of A niger glucoamylase was solved by NMR in its native state [10] and in a complex with b-cyclodextrin [11] Crystal structures of an intact ... suspension of 37.5 mg of starch in 1.25 mL of 1.5 m TrisHCl buffer, pH 8.8, and mL of water was boiled for and after cooling to room temperature, 1.65 mL of acrylamide solution (30%), 60 lL of 10%...
... assist the structure- based rational design of enzyme inhibitors with potential medical interest Crystal structureof human ACMSD C-ter N-ter Results and Discussion Overall quality of the model ... three-dimensional structureof hACMSD in complex with DHAP was solved by molecular replacement ˚ and refined at a resolution of 2.0 A The monomer present in the asymmetric unit contains 332 residues out of 336, ... other members of the amidohydrolase superfamily [24,25] However, as no structureof complexes with either the substrate, product or inhibitors had been reported, precise identification of the protein...
... core of the protein Mononucleotides binding into the active site of RNase Sa2 not affect the overall fold of the protein Superposition of 88 corresponding CA atoms of all 16 molecules (structures ... Bauerova-Hlinkova et al Structures of RNase Sa2–mononucleotide complexes A B Fig Stereoview of the A ⁄ C crystallographic dimer (A, green; C, pink) in structures 3D5G, 3GDY, 3D5I, and 3D4A (A), and in structure ... et al Structures of RNase Sa2–mononucleotide complexes molecules A and B of 3DH2) Unlike the anti-conformation found in the complex with RNase Sa [24], exo2¢,3¢-GCPT in the active site of RNase...
... complexof GmHO-1 at pH 7.0 (0.1 M, KPB) a-1, Expansion of the gxy region of (A) (solid line) and of the corresponding part of the spectrum of ferric heme–rHO-1 (dotted line) a-2, Expansion of ... pocket structure As shown in Table 2, the hyperfine splitting constants of the 15N nucleus of the distal NO and of the 14N nucleus of the proximal His of the GmHO-1 complex are closer to those of ... that, in spite of the low homology of the amino acid sequence with those of known HOs, the heme– GmHO-1 complex has similar spectroscopic characteristics to those of the heme complexes of cyanobacterial,...
... deviation of ± 4% T brucei T cruzi 2000 2000 350 800 65 2000 150 900 200 700 HOP Inhibition and site-directed mutagenesis of T brucei gGAPDH In the absence of a 3D structureof a complexof T brucei ... brucei gGAPDH modelling studies Results 3D structureof the T cruzi gGAPDH–HOP complex Quality of the structure (RCSB PDB accession No 1QXS) Despite the lack of NCS restraints during the refinement ... that improved activity of this compound may be a result of hydrogen bonding between the hydroxyl of Thr167 of the protein and the amino group of compound No other inhibitor offered such an interaction...
... inhibitors of PETN reductase (Fig 6) ˚ The overall structureof the 1.05 A reduced PETNprogesterone complex is virtually identical to the oxidized complex (PDB code 1H60) Two molecules of isopropanol ... form of the enzyme-steroid complex We conjectured that the reduced form of the enzyme might direct binding of the steroid in the flipped conformation, thus facilitating catalysis Our structureof ... between the postulated structureof the catalytically active reduced enzyme-substrate complex and the observed crystallographic structures of the oxidized enzyme-substrate complex However, in some...
... a dimer of the abc heterotrimer There is a noncrystallographic twofold axis around the center of Fig 3A The structureof an abc heterotrimer unit is shown in Fig 3B The central region of the a ... 24 25 26 27 28 29 Structureof B12-dependent glycerol dehydratase (Eur J Biochem 269) 4493 coenzyme B12: X-ray structureof diol dehydratase-adeninylpentylcobalamin complexStructure 8, 775–788 ... crystal structureof glycerol dehydratase in complex with cobalamin and propane-1,2-diol was determined at ˚ 2.1 A resolution by the molecular replacement method The schematic view of the overall structure...
... loop of helix 22 and to the tetraloop of helix 23a stabilize the tertiary fold of the upper three-helix junction The tertiary structureof the upper three-helix junction forms Fig Details of S15–Tth ... Trp; and Y, Tyr (B) Sequence of the Tth T4 RNA from the central domain of T thermophilus 16S rRNA The secondary structure and the general topology of the tertiary structure are shown Helical domains ... magnetic resonance structureof the free protein (19) but unlike the crystal structureof the free protein (20), in which ␣1 lies distal to the core (21) There are three principal regions of S15 that...
... loop L6 of chagasin and S21e of Chagasin–papain complexstructure papain providing an illustrative example A comparison of the present chagasin–papain complex with the structureof papain in complex ... superposition of the Ca atoms of papain from the crystal structures of its complexes with cystatin B (PDB code 1STF) and chagasin (this work) The upper panel emphasizes the different angle of approach of ... the interactions of papain with loop L6 of chagasin and loop L2 of cystatin B (C) Zoom-in view of the interactions of papain with loop L4 of chagasin and the N-terminal segment of cystatin B (D)...
... nicotinamide ring of NAD Based on the structureof citrate, we modeled the l-aspartate molecule into the active site of A fulgidus l-aspDH (Fig 4B) and then minimized the energy of the complex using ... bonds Fig Comparison of the structures of A fulgidus L-aspDH and T maritima L-aspDHs (A) The superimposed Ca-traces of A fulgidus L-aspDH and T maritima L-aspDH; the structures of the two enzymes ... structure [22,23] A pair of aromatic Ion-pair interaction Recent studies of the structures of hyperthermophilic proteins have shown that the number of ion pairs and the formation of ion networks contribute...
... observation) Maintenance of the open C-shape of the base of the clamp-loader complex is also consistent with crystal structures determined recently in our group, of a nucleotide-loaded c complex (S L Kazmirski, ... determined the 3D structureof a : complexof the E coli v and w subunits in order to explore the function of these two proteins Subunits v and w interact to form an elongated heterodimer, of comparable ... of the replication factor C (RFC) clamp-loader subunits of eukaryotes and archaebacteria [16] Crystal structures of a functional E coli clamp-loader complex, cdd¢ (stoichiometry : : 1), and of...
... for this residue in the crystal structureof Anx24(Ca32) In the current structure, the conformation of the AB loop in the first domain differs from that of molecule of Anx24(Ca32) only around residues ... crystal structureof Anx(Gh1) from cotton emphasizes the high conservation of the unique annexin fold even among the members of the plant subfamily of annexin proteins The fold is comprised of the ... side of the plant proteins, which is not observed with non-plant annexins since the modules are packed much tighter A comparison of the current structureof Anx(Gh1) with the structures of Anx24(Ca32)...
... FEBS 1003 Structureof B subtilis c-glutamyltranspeptidase A K Wada et al B C Fig Comparison of the structures of GGTs from (A) B subtilis, (B) E coli and (C) H pylori The structureof each GGT ... Elucidation of the structural factors related to the salt tolerance of B subtilis GGT may help in the development of better-engineered GGT Here, we report the crystal structureof B subtilis GGT in complex ... envelope [20] When the structureof CapD in complex with di-a-l-glutamate peptide, a nonhydrolyzable analog of the substrate, is compared with that of the B subtilis GGT–glutamate complex, it is apparent...
... Least-squares superimposition of domain of all of the GBP structures is shown in Fig 5B, illustrating the ‘fan’ of A B related conformations observed The GGal complex is the most closed structure found to ... importance of GGal as a bacterial carbon source Results and Discussion Overall structure The structureof GBP in complex with GGal was determined by molecular replacement using the Salmonella GBP–Gal structure ... because of the significantly larger number of hydrogen bonds compared with the structures with simple sugars The other structures represent a series of conformations that ‘link’ the GGal complex...
... method of Somogyi-Nelson [26] was followed Ó FEBS 2004 Structureof T vulgaris a-amylase II complex (Eur J Biochem 271) 2533 Results Carbohydrate in the catalytic site The structureof the complex ... Ó FEBS 2004 Structureof T vulgaris a-amylase II complex (Eur J Biochem 271) 2531 Fig Ribbon representation of the fold of TVA II in complex with 42-P2 (A) Dimeric form ... 42-P2 binding The complexed structure enables a detailed analysis of the interactions of the active site with 42-P2 To facilitate description of these interactions, the active cleft of TVA II is separated...
... (2003) Crystal structureof rat heme oxygenase-1 in complex with biliverdin-iron chelate: conformational change of Ó FEBS 2004 39 40 41 42 43 44 Structureof cyanobacterium heme–HO complex (Eur ... S.Y., Shiro, Y & Ikeda-Saito, M (2004) The crystal structures of the ferric and ferrous forms of the heme complexof Hmu O, a heme oxygenase of Corynebacterium diphtheriae J Biol Chem 279, 11937–11947 ... bond partner of the carbonyl group of Gly139 is the amide group of Gly144, and the amide group of Gly143 is hydrogen-bonded to the distal ligand of the heme iron (the residue numbers of the three...
... differences between the two structures Structureof individual CTPR390 molecules Considering the individual 3-TPR units, the structureof CTPR390 is almost identical to the structureof the parent protein, ... Cortajarena et al A C Structureof designed TPR module–ligand complex B D CTPR390–peptide complex CTPR390 binds specifically and with moderate affinity (Kd of 200 lm) to the C-terminal peptide of Hsp90 [5] ... and Structureof designed TPR module–ligand complex a = b = 90°, c = 120° The CTPR390 structure was solved by molecular replacement using molrep [16] in the ccp4i suite [17] The structureof the...
... unliganded PDZ domain structures Figure shows a superposition of SAP97PDZ2 C378S structure with the NMR structureof PSD-95PDZ2 and the crystal structureof SAP102 The backbone structures are highly ... The structureof the C378G variant of SAP97PDZ2 was practically identical to that of C378S variant, except for the mutated residue, and because of its better resolution, only the structureof ... related PDZ domain structures The solution structureof the second PDZ domain of PSD-95 has been determined by NMR [21], and, quite recently, coordinates of the PDZ2 domain of SAP102 crystallized...
... analogues Fig (A) The structureof one subunit of Uu-TK (yellow) with conformations of the flexible loop as found in Uu-TK in complex with dT in subunit A (orange, A), Uu-TK in complex with dTTP (green, ... determined the first structureof a member of the TK1 family in complex with the substrate dT The possibilities for drug design have been investigated by enzyme kinetics and analyzed in view of substrate ... further advances Results and discussion Overall structure The overall tetrameric structureof Uu-TK in the substrate complex is very similar to that in the complex with the feedback inhibitor dTTP Each...
... University on behalf of the U.S Department of Energy, Office of Basic Energy Sciences The SSRL Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and ... (Table 1) As a result, the structureof the complex is an average of the two half-sites Similarly, TL3 was bound in the active site of the 12X FIV PR with its C2 axis of symmetry coincident with ... Schiffer CA: "Substrate Shape Determines Specificity of Recognition for HIV-1 Protease: Analysis of Crystal Structures of Six Substrate Complexex" Structure 2002, 10:369-381 Ozer N, Haliloglu T, Schiffer...