... on the hACMSD crystals using the same beamline, clearly indicated the presence of a Zn metal ion bound to the enzyme Analysis ofthe diffraction data set allowed us to assign thecrystal to the ... in the crystal, and a mixture of monomeric and dimeric forms in solution [18] Therefore, the available structural data suggest Fig Ribbon representation ofthe overall structureof hACMSD The ... as the amino acid numbers The alternative conformations ofthe Trp–Met couple can be observed; the arrows indicate the unidirectional movement ofthe two protein residues upon ligand binding The...
... the overall structure is shown in Fig 3A The enzyme exists as a dimer ofthe abc heterotrimer There is a noncrystallographic twofold axis around the center of Fig 3A Thestructureof an abc heterotrimer ... irradiation [59] Therefore, we believe that thestructure reported in this paper is also that ofthe glycerol dehydrataseÆcob(II)alamin complex The dihedral angle ofthe northern and southern least-squares ... 4C indicates the comparison ofthe position ofthe a-acetamide side chain of pyrrole ring A ofthe corrin ring in the glycerol dehydratase-bound cobalamin (Fig 4Ca) with those in the diol dehydratase-bound...
... al Crystalstructureof NlpI A B C D Fig Solubility of NlpI constructs and thestructureof mature NlpI (A) 10–20% gradient SDS ⁄ PAGE of NlpI expression products, showing the insolubility ofthe ... FEBS Crystalstructureof NlpI natural TPRs in the PDB (13 TPR-containing coordinate sets) consist of nonglobular, extended arrays of helices [9,10,13–21] Second, the majority of these (11 structures) ... matches to the consensus the full-length HOP, they act to facilitate the assembly of multichaperone regulatory complexes The structural independence of these TPR domains, and the presence of independent...
... crystalstructureof Anx(Gh1) from cotton emphasizes the high conservation ofthe unique annexin fold even among the members ofthe plant subfamily of annexin proteins The fold is comprised of ... are either distorted or the access of a cation to the site is blocked by the presence of a side chain of a basic residue In case ofthe IIAB site (Fig 2), the acidic residue acting as the bidentate ... residue in the present structure is somehow halfway between the loop-in and the loop-out position ofthe bell pepper annexin Fig The three-dimensional structureof Anx(Gh1) (A) The fold of Anx(Gh1)...
... loop because of deletion of those residues The loop structure is responsible for the exo-activity of OXG-RCBH, and the absence ofthe loop is associated with endo-activity in XEG Therefore, it ... to the exo-loop of OXG-RCBH The coordinates and structure factors have been deposited in the Protein Data Bank (PDB) (accession code 3A0F) Thestructureof XEG was compared with those of other ... sides ofthe cleft are open This result, and those ofthe previous experiment with loop-deleted OXGRCBH [10], strongly suggest that the basis for the endo activity of XEG is the absence of the...
... 2008 FEBS 2285 Structureof spliceosomal cyclophilin PPWD1 T L Davis et al Fig Structureof PPWD1 and comparison with other Cyp structures (A) Thestructureofthe isomerase domain of PPWD1 is shown ... Acceleration ofthe cis–trans isomerization ofthe peptide results in the collapse of these resonances into a single set of peaks (D) Binding, but not isomerization, ofthe N-terminal peptide of PPWD1 ... that the homotypic interaction modeled in thecrystalstructure is supported by solution methods catalysis, explaining the capture ofthe trans conformer in thecrystal [36] However, as the HIV...
... 20 A from the center ofthe funnel, they form the base ofthe b subunit (Fig 3) The last four residues in the C-terminal coil (residues 171–174) are deeply anchored inside the core ofthe conical ... catalytic domains ofthe a subunit In the heterohexamer, the Rieske domain interacts with the base ofthe adjacent b subunit and the catalytic domain ofthe adjacent a subunit Most ofthe ab interactions ... for each ofthe three a subunits LI, on the other hand, could only be partially modeled for one ofthe three a subunits, the high flexibility ofthe loop precluded modeling for the two other chains...
... Structure and thermal stability of T maritima 2852 In order to reveal possible determinants ofthe increased thermotolerance of TmIDH, we compared thestructureofthe dimeric form with the ... ofthe small domains showed an rmsd of ˚ 0.27 A for the Ca-atoms, whereas the rmsd between ˚ the large domains was 0.32 A The relative difference in the rotation ofthe large domain between the ... ofthe large domain in the active site This interaction mimics the phosphorylation ofthe equivalent serine in EcIDH which Structure and thermal stability of T maritima inhibits the binding of...
... estimated the position of Glc )3 ofthe a-1,4-glucan using thestructureof TAA complexed with acarbose (Fig 5C) The positions ofthe maltose unit, Glc )1 and )2, are almost the same in the two ... Thus, the hydrolysis of pullulan by TVA II appears to be the result of effective binding due to the shape ofthe active cleft around the nonreducing region The substrate recognition of TVA II at the ... in the catalytic site Thestructureofthe complex was determined by molecular replacement using thestructureof unliganded TVA II (PDB code 1JI2) [12] as a search model In the final model, there...
... diphosphate (ThDP) is the deprotonation ofthe C2 atom ofthe thiazolium ring (marked by an asterisk) The resulting ylid of ThDP (I) can attack the carbon atom ofthe carbonyl group ofthe substrate ... basis ofthecrystalstructureof pyruvamide-activated ScPDC compared to that of ScPDC crystallized in the absence of any effectors [9], which is assumed to be the nonactivated state ofthe enzyme ... dimers The open and the closed side ofthe tetramer resulting from the special dimer arrangement are indicated Here, we describe thecrystalstructureof PDC from the yeast K lactis and the structural...
... on the basis of its X-ray structure [17] In this report, the stabilization mechanism ofthe hyperthermophilc b2 subunit will be discussed on the basis ofthecrystal structures, compared with the ... Crystalstructureof tryptophan synthase b2 subunit alone (Eur J Biochem 271) 2625 structures ofthe a or b2 subunits alone as well as that ofthe complex The three-dimensional structureofthe ... flexible region than thestructureofthe a and/or b subunits in the complex form reported Discussion Structureof Pf b2 and mutual activation Fig Crystalstructureof b2 subunit alone of tryptophan...
... groups The one exception to this is the location ofthe amide group of Lys204 at P3, where there is a break in the main-chain density at the 2.8r map level The corresponding position in the apo structure ... (Leu104–Pro111) Indicative ofthe tightness ofthe fit, there are a large number (30) of atom-to-atom van der Waals’ contacts between the Tyr205 side chain and importin-a (Table 2) The numbers of contacts are ... competes for the importin-a binding site, reducing binding affinity for cargo proteins and helping to facilitate the release ofthe cargo within the nucleus [10,11] The removal ofthe autoinhibitory...
... because the tertiary structureof ApeSOD has not been elucidated In the present study, for the first time, we describe thecrystalstructureof ApeSOD In particular, we focus on the coordination ofthe ... NE2 of His31, bound to the metal, in the company of a water oxygen, from the apical positions The manga˚ nese was only 0.06 A out ofthe equatorial plane (Table 3) The angles around the metal cofactor ... [26] These findings lead to the hypothesis that Fe-bound ApeSOD mimics the product-inhibited form and the shift of Tyr39 suppresses the release ofthe peroxide product This may be one ofthe reasons...
... molecules ofthe asymmetric unit ofthe wild-type structure Neither the mutation nor the different crystallization conditions evoked structural differences Thecrystal was grown in the presence of phytate, ... is the only direct contact between the protein backbone and the substrate The side chain of Thr292 is found to recognize the 2-phosphate in both the binding model of PhyK and thecrystalstructure ... out ofthe catalytic pocket upon phytate binding Here, PhyK mimics the phytate-bound structureof AppA, even in the absence of sulfate ions The side chain ofthe corresponding Glu212 bends out of...
... to the residue in the midpoint ofthe respective loop, as shown in Fig To the east ofthe active site the 37- and 60-loops border the S2¢ pocket ofthe proteinase The observed differences in the ... that the most similar regions of these proteinases mediate interaction ofthe two b-barrels, formation ofthe catalytic machinery and structures required for binding ofthe main chain ofthe substrate ... below) The southern boundary ofthe active site cleft of DESC1 is formed by the 145 autolysis loop The backbone of this loop differs markedly from the other serine proteinases, making the active...
... gray indicates the C-terminal part The dimer’s formation is established by the incorporation ofthe b8-strand of one monomer into a b-sheet ofthe other monomer The position ofthe zinc ion is ... the presence of acetate in thecrystalstructureThe binding of acetate in the active site is a further indication that the enzyme may be involved in deacetylation because acetate is one ofthe ... and determines the shape ofthe active site entry (e) Thestructureofthe active site is essentially identical with the active sites ofthe MshB and LpxC proteins The conservation of catalytically...
... arrangement, and the side chain of Ser97 in VPRK is too short One side ofthe loop is involved in the binding ofthe P2–P4 residues of a substrate The other side ofthe loop is close to Arg94 (Lys ... a residue forming a part ofthe S2 site ofthe enzyme The disulfide bridge restricts the flexibility of a tight loop which is part ofthe S2 site The tight loop is further stabilized by a tight ... the carbonyl oxygen atom ofthe scissile bond in other subtilase–inhibitor complexes (data not shown) The Ca positions ofthe tripeptide occupy almost the same positions as the Ca positions of...
... ScPDC on the other hand involving the C-terminal part ofthe polypeptide chain (Fig 7) In the latter, differences in the conformation ofthe loop between Fig Stereo picture ofthe model ofthe a-carbanion/enamine ... in all ofthe tetrameric PDCs of known three-dimensional structure Binding ofthe cofactors ThDP and Mg2+ The homo-tetrameric IPDC binds four molecules ofthe cofactors ThDP and Mg2+ The ThDP ... catalytic residues The active site cavity in IPDC extends from the thiazolium ring ofthe cofactor to the surface ofthe protein The entrance ofthe active site cleft is covered by the C-terminal...
... for the N structureThe G and TG structures were solved using the N structure as a search model, and the TG structure was used in phasing ofthe T structureThe structures were refined using the ... structures, those ofthe N and G structures were slightly poor [38, 39] For the N structure, the extensive disordered regions in its structure might be responsible for these values For the G structure, ... report thecrystalstructureofthe intact glutaminase under four different conditions: in the absence ofthe additives (referred to as N); in the presence of Tris (referred to as T); in the presence...
... for the compactness and stability ofthe active site The H-bond length between the carbonyl oxygen of Cys34 and the amide ˚ nitrogen of Leu38 is 2.99 A in this structure, as compared ˚ in the ... Backbone superpositions ofthe six structures of hTRXL-N and other thioredoxin related proteins or domains 1GH2 (crystal structureof hTRXL-N, 2–108), 2TRX (crystal structureof E coli thioredoxin, ... Among the three types of thioredoxin proteins, least is known about hTRXL Here, we report our work on the isolation ofthe gene, hTRXL, the functional identification ofthe gene product and the structure...