examples of the crystal structure of glycolipids

... on the hACMSD crystals using the same beamline, clearly indicated the presence of a Zn metal ion bound to the enzyme Analysis of the diffraction data set allowed us to assign the crystal 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 of the overall structure of hACMSD The ... as the amino acid numbers The alternative conformations of the Trp–Met couple can be observed; the arrows indicate the unidirectional movement of the two protein residues upon ligand binding The...

Ngày tải lên: 18/02/2014, 06:20

... the overall structure is shown in Fig 3A The enzyme exists as a dimer of the abc heterotrimer There is a noncrystallographic twofold axis around the center of Fig 3A The structure of an abc heterotrimer ... irradiation [59] Therefore, we believe that the structure reported in this paper is also that of the glycerol dehydrataseÆcob(II)alamin complex The dihedral angle of the northern and southern least-squares ... 4C indicates the comparison of the position of the a-acetamide side chain of pyrrole ring A of the corrin ring in the glycerol dehydratase-bound cobalamin (Fig 4Ca) with those in the diol dehydratase-bound...

Ngày tải lên: 21/02/2014, 03:20

... al Crystal structure of NlpI A B C D Fig Solubility of NlpI constructs and the structure of mature NlpI (A) 10–20% gradient SDS ⁄ PAGE of NlpI expression products, showing the insolubility of the ... FEBS Crystal structure of 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...

Ngày tải lên: 07/03/2014, 16:20

... crystal structure of 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 ... 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 of the 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 of the bell pepper annexin Fig The three-dimensional structure of Anx(Gh1) (A) The fold of Anx(Gh1)...

Ngày tải lên: 17/03/2014, 03:20

... loop because of deletion of those residues The loop structure is responsible for the exo-activity of OXG-RCBH, and the absence of the 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) The structure of XEG was compared with those of other ... sides of the cleft are open This result, and those of the previous experiment with loop-deleted OXGRCBH [10], strongly suggest that the basis for the endo activity of XEG is the absence of the...

Ngày tải lên: 23/03/2014, 05:22

... 2008 FEBS 2285 Structure of spliceosomal cyclophilin PPWD1 T L Davis et al Fig Structure of PPWD1 and comparison with other Cyp structures (A) The structure of the isomerase domain of PPWD1 is shown ... Acceleration of the cis–trans isomerization of the peptide results in the collapse of these resonances into a single set of peaks (D) Binding, but not isomerization, of the N-terminal peptide of PPWD1 ... that the homotypic interaction modeled in the crystal structure is supported by solution methods catalysis, explaining the capture of the trans conformer in the crystal [36] However, as the HIV...

Ngày tải lên: 23/03/2014, 07:20

... 20 A from the center of the funnel, they form the base of the b subunit (Fig 3) The last four residues in the C-terminal coil (residues 171–174) are deeply anchored inside the core of the conical ... catalytic domains of the a subunit In the heterohexamer, the Rieske domain interacts with the base of the adjacent b subunit and the catalytic domain of the adjacent a subunit Most of the ab interactions ... for each of the three a subunits LI, on the other hand, could only be partially modeled for one of the three a subunits, the high flexibility of the loop precluded modeling for the two other chains...

Ngày tải lên: 23/03/2014, 09:21

... Structure and thermal stability of T maritima 2852 In order to reveal possible determinants of the increased thermotolerance of TmIDH, we compared the structure of the dimeric form with the ... of the 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 of the large domain between the ... of the large domain in the active site This interaction mimics the phosphorylation of the equivalent serine in EcIDH which Structure and thermal stability of T maritima inhibits the binding of...

Ngày tải lên: 23/03/2014, 10:21

... estimated the position of Glc )3 of the a-1,4-glucan using the structure of TAA complexed with acarbose (Fig 5C) The positions of the 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 of the active cleft around the nonreducing region The substrate recognition of TVA II at the ... in the catalytic site The structure of the complex was determined by molecular replacement using the structure of unliganded TVA II (PDB code 1JI2) [12] as a search model In the final model, there...

Ngày tải lên: 23/03/2014, 12:20

... diphosphate (ThDP) is the deprotonation of the C2 atom of the thiazolium ring (marked by an asterisk) The resulting ylid of ThDP (I) can attack the carbon atom of the carbonyl group of the substrate ... basis of the crystal structure of pyruvamide-activated ScPDC compared to that of ScPDC crystallized in the absence of any effectors [9], which is assumed to be the nonactivated state of the enzyme ... dimers The open and the closed side of the tetramer resulting from the special dimer arrangement are indicated Here, we describe the crystal structure of PDC from the yeast K lactis and the structural...

Ngày tải lên: 30/03/2014, 10:20

... on the basis of its X-ray structure [17] In this report, the stabilization mechanism of the hyperthermophilc b2 subunit will be discussed on the basis of the crystal structures, compared with the ... Crystal structure of tryptophan synthase b2 subunit alone (Eur J Biochem 271) 2625 structures of the a or b2 subunits alone as well as that of the complex The three-dimensional structure of the ... flexible region than the structure of the a and/or b subunits in the complex form reported Discussion Structure of Pf b2 and mutual activation Fig Crystal structure of b2 subunit alone of tryptophan...

Ngày tải lên: 30/03/2014, 14:20

... of the crystal, the enzyme was probably damaged by the X-ray beam during data collection‡ This led to the observation of a mixture of two conformers in the crystal The ‡ The oxidation state of ... page) The Structure of the A vinosum [NiFe] Hydrogenase 435 Fig (a) Stereoview of the electron density omit map (Fobs − Fcalc, σ cutoff) including the refined model of the active site of the [NiFe] ... considered to be a result of “oxidative damage” related to the aerobic purification and crystallization of the enzyme The additional metal site The C-terminus of the large subunit of the D vulgaris MF...

Ngày tải lên: 21/12/2016, 10:50

... (Leu104–Pro111) Indicative of the tightness of the 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 ... our crystal structure The terminating carboxyl group of the peptide at Asn207 is well defined in the 2Fo ) Fc electron density map, despite making no interactions with importin-a The presence of ... competes for the importin-a binding site, reducing binding affinity for cargo proteins and helping to facilitate the release of the cargo within the nucleus [10,11] The removal of the autoinhibitory...

Ngày tải lên: 14/02/2014, 19:20

... because the tertiary structure of ApeSOD has not been elucidated In the present study, for the first time, we describe the crystal structure of ApeSOD In particular, we focus on the coordination of the ... 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 of the 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 of the peroxide product This may be one of the reasons...

Ngày tải lên: 14/02/2014, 22:20

... molecules of the asymmetric unit of the wild-type structure Neither the mutation nor the different crystallization conditions evoked structural differences The crystal 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 the crystal structure ... out of the catalytic pocket upon phytate binding Here, PhyK mimics the phytate-bound structure of AppA, even in the absence of sulfate ions The side chain of the corresponding Glu212 bends out of...

Ngày tải lên: 16/02/2014, 09:20

... to the residue in the midpoint of the respective loop, as shown in Fig To the east of the active site the 37- and 60-loops border the S2¢ pocket of the proteinase The observed differences in the ... that the most similar regions of these proteinases mediate interaction of the two b-barrels, formation of the catalytic machinery and structures required for binding of the main chain of the substrate ... below) The southern boundary of the 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...

Ngày tải lên: 19/02/2014, 00:20

... gray indicates the C-terminal part The dimer’s formation is established by the incorporation of the b8-strand of one monomer into a b-sheet of the other monomer The position of the zinc ion is ... the presence of acetate in the crystal structure The binding of acetate in the active site is a further indication that the enzyme may be involved in deacetylation because acetate is one of the ... and determines the shape of the active site entry (e) The structure of the active site is essentially identical with the active sites of the MshB and LpxC proteins The conservation of catalytically...

Ngày tải lên: 19/02/2014, 00:20

... arrangement, and the side chain of Ser97 in VPRK is too short One side of the loop is involved in the binding of the P2–P4 residues of a substrate The other side of the loop is close to Arg94 (Lys ... a residue forming a part of the S2 site of the enzyme The disulfide bridge restricts the flexibility of a tight loop which is part of the S2 site The tight loop is further stabilized by a tight ... the carbonyl oxygen atom of the scissile bond in other subtilase–inhibitor complexes (data not shown) The Ca positions of the tripeptide occupy almost the same positions as the Ca positions of...

Ngày tải lên: 19/02/2014, 07:20

... ScPDC on the other hand involving the C-terminal part of the polypeptide chain (Fig 7) In the latter, differences in the conformation of the loop between Fig Stereo picture of the model of the a-carbanion/enamine ... in all of the tetrameric PDCs of known three-dimensional structure Binding of the cofactors ThDP and Mg2+ The homo-tetrameric IPDC binds four molecules of the cofactors ThDP and Mg2+ The ThDP ... catalytic residues The active site cavity in IPDC extends from the thiazolium ring of the cofactor to the surface of the protein The entrance of the active site cleft is covered by the C-terminal...

Ngày tải lên: 20/02/2014, 11:20

... for the N structure The G and TG structures were solved using the N structure as a search model, and the TG structure was used in phasing of the T structure The structures were refined using the ... [10], we determined the F structure containing the truncated region of the C-terminal domain; however, we failed to determine the structure of the intact glutaminase because the crystals exhibited ... in the G and TG structures The electron density of l-glutamate became more pronounced upon the addition of Tris The location and orientation of l-glutamate were determined on the basis of the...

Ngày tải lên: 06/03/2014, 09:22