a crystal structure of l2

... atoms of Asp11 and Asn23 (Fig 3) in an arrangement similar to what is observed in VPRK Both PRK and VPRK have calcium bound at Ca3 SPRK also has an aspartic acid residue at position at 200, and ... initial comparative studies showed that the catalytic turnover was at least twice that of PRK, but substrate affinity was reduced SPRK was compared with PRK and was found to be remarkable stable against ... program for molecular replacement J Appl Crystallogr 30, 1022–1025 Perrakis A, Harkiolaki M, Wilson KS & Lamzin VS (2001) ARP ⁄ wARP and molecular replacement Acta Crystallogr Sect D Biol Crystallogr...

Ngày tải lên: 19/02/2014, 07:20

... (excluding water molecules and peptide atoms) and rj is the standard deviation of B factors The normalized B factors have a zero mean and unit variance All atoms that satisfy Bz ‡ are treated as outliers ... protein crystallography Acta Crystallogr D: Biol Crystallogr 50, 760–763 37 Evans P (2006) Scaling and assessment of data quality Acta Crystallogr D: Biol Crystallogr 62, 72–82 38 McCoy AJ, Grosse-Kunstleve ... with a contact area ˚ of 13.5 A2 and the Lys residue at P3 with a contact ˚ area of 10.2 A2 Residues outside the central binding area have significantly lower values These results are summarized...

Ngày tải lên: 14/02/2014, 19:20

... values increase from G1P over PhyK to AppA by a factor of  2200 The conformational changes of AppA upon substrate binding facilitate a faster turnover of phytate and are in line with a higher specificity ... site-directed mutagenesis kit (Stratagene, La Jolla, CA, USA) Plasmid pET-1TK was used as template and Kleb(HtoA)fw (5¢-GCTTAGCCGCGCCGGCATTCG) and Kleb(HtoA)rv (5¢-CGAATGCCGGCGCGGCTAAGC) as primers ... conserved active-site motifs, RHGXRXP and HD, and hydrolyze metal-free phytate with pH optima in the acidic range They consist of two domains, a large a ⁄ b domain and a small a domain with the catalytic...

Ngày tải lên: 16/02/2014, 09:20

... a- amino-b-carboxymuconate-e-semialdehyde decarboxylase J Am Chem Soc 129, 9278–9279 Fukuoka SI, Ishiguro K, Yanagihara K, Tanabe A, Egashira Y, Sanada H & Shibata K (2002) Identification and expression of a cDNA encoding human 6622 ... a- amino-b-carboxymuconate-e-semialdehyde decarboxylase (ACMSD) J Biol Chem 277, 35162–35167 Tanabe A, Egashira Y, Fukuoka SI, Shibata K & Sanada H (2002) Expression of rat hepatic 2-amino3-carboxymuconate-6-semialdehyde ... T, Yang K, Liu A & Zhang H (2006) Crystal structure of a- amino-b-carboxymuconic-e-semialdehyde decarboxylase: insight into the active site and catalytic mechanism of a novel decarboxylase reaction...

Ngày tải lên: 18/02/2014, 06:20

... growth factors and proteinase inhibitors Biol Chem 380, 473–483 Kataoka H, Uchino H, Asada Y, Hatakeyama K, Nabeshima K, Sumiyoshi A & Koono M (1997) Analy- Crystal structure of the catalytic domain ... Shimomura T, Denda K, Kitamura A, Kawaguchi T, Kito M, Kondo J, Kagaya S, Qin L, Takata H, Miyazawa K et al (1997) Hepatocyte growth factor activator inhibitor, a novel Kunitz-type serine protease ... al Crystal structure of the catalytic domain of DESC1 Fig Structure- based sequence alignment of the human DESC1 catalytic domain with human DESC2 [2], human DESC3 [2], HAT, HAT-like [6], human...

Ngày tải lên: 19/02/2014, 00:20

... References Ivanova N, Sorokin A, Anderson I, Galleron N, Candelon B, Kapatral V, Bhattacharyya A, Reznik G, Mikhailova N, Lapidus A et al (2003) Genome sequence of Bacillus cereus and comparative analysis ... consisting of two hydrogen-bonded antiparallel b-strands (b6–b7), an a- helical hairpin (helices a5 , a6 ) and a C-terminal strand (b8) Helix a5 and strand b7 partially cover one side of the Rossmann fold ... Tanaka T, Fukui T, Atomi H & Imanaka T (2003) Characterization of an exo-b-D-glucosaminidase involved in a novel chitinolytic pathway from the hyperthermophilic archaeon Thermococcus kodakaraensis...

Ngày tải lên: 19/02/2014, 00:20

... Number of ion pairsa Number of hydrogen bonds Main chain–main chain Main chain–side chain Side chain–side chain Total ˚ Exposed surface areab (A2 ) ˚ Apolarc (A2 ) ˚ Buried surface areab (A2 ) ˚ Apolarc ... uracil–DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features Acta Crystallogr Sect D 59, 1357–1365 10 Aghajari N, Van Petegem F, Villeret V, Chessa JP, Gerday C, Haser ... whereas the overall exposed surface areas of the psychro- and the mesophilic enzymes are larger than for the thermophile enzyme, mainly as a result of larger area of apolar atoms, the meso- and...

Ngày tải lên: 19/02/2014, 16:20

... 5¢-aataatccatggggagtaatacttcctggcgta aaagtgaagtcc-3¢ and 5¢-attattggatccctattgctggtccgattctgccag-3¢ 3-TPR NlpI primers (residues 62–197) were 5¢-aataatccatgg gggcacagcttttatatgagcgcggag-3¢ and ... hydrodynamic radius than a globular molecule of similar polypeptide length However, calculation of the Matthews coefficient from initial crystallographic data indicated that a dimer was most compatible ... (Finland) Data for this study were measured at beamline X12C of the National Synchrotron Light Source We are grateful for the assistance of Dr Anand Saxena in the use of this beamline The National...

Ngày tải lên: 07/03/2014, 16:20

... smoothly in alternating steps of automatic adjustment with CNS and manual adjustment with the program O [34] The final model has a final R-factor of 0.222 with a free R-factor of 0.253 Molecular graphics ... in length and contains an 867-bp ORF, which encodes for a protein with 289 amino acids and a calculated molecular mass of 32 kDa A search of the nonredundant protein sequence database was performed ... of thioredoxin and antioxidants on the activation of transcription factors NF-kappa B and AP-1 Proc Natl Acad Sci USA 91, 1672–1676 14 Spector, A. , Yan, G.Z., Huang, R.R., McDermott, M.J., Gascoyne,...

Ngày tải lên: 08/03/2014, 22:20

... The DASA of the AB dimer is defined as [(ASA of A) + (ASA of B) ) (ASA of AB dimer)] ⁄ The number of water molecules in the dimer interface was detected with ASV CALCULATOR [34] ASA was calculated ... was calculated (Table 1) It is conceivable that a dimer with larger DASA is more plausible We found that the DASAs of the AB and DA dimers were comparable Although the DASA of the CD dimer was ... beamline staff of PF and SPring-8 for data collection We also acknowledge the kind support of M Maeda (National Institute of Agrobiological Sciences, Japan) for calculation of DASA This work was...

Ngày tải lên: 14/03/2014, 23:20

... et al crystal structure of a cellulase was reported; it was a catalytic domain of Hypocrea jecorina Cel 6A (HjeCel 6A, formerly designated cellobiohydrolase II), a GH6 cellobiohydrolase from an ascomycete ... HinCel 6A and CcCel6C (Fig 2) indicated that Asp150 and Asp334 of CcCel6C are the potential catalytic residues and could act as a proton donor and a base, respectively Another aspartic acid residue ... CLUSTALW2 server, and manual adjustment was carried out based on the comparison of the crystal structures The numbering of amino acid residues and secondary structures (a1 a8 and b0–bVII) are given Residues...

Ngày tải lên: 15/03/2014, 10:20

... analysis of the aggregation state of PPL2 employing 3964 Table Amino acid composition [molÆ(mol protein))1] of PPL2 Asx, aspartic acid and asparagine; Glx, glutamic acid and glutamine Amino acid ... 4065–4070 15 Utarabhand P & Akkayanont P (1995) Purification of a lectin from Parkia javanica beans Phytochemistry 38, 281–285 16 Cavada BS, Madeira SVF, Calvete JJ, Sousa LAG, Bomfim LR, Dantas AR, Lopes ... FEBS B S Cavada et al PPL2, an endochitinase from Parkia platycephala Fig Structural features of PPL2 and the GH18 family (A) Multiple sequence alignment of PPL2, hevamine, XIP-I and ConB Absolutely...

Ngày tải lên: 16/03/2014, 13:20

... pharmacology of squill New York Acad Med Bull 50, 747–750 Narayanan S, Surolia A & Karande AA (2004) Ribosome-inactivating protein and apoptosis: abrin causes cell death via mitochondrial pathway ... characterization and crystallization of charybdin The yield of the purified protein was 150–200 mg protein per 100 g of bulbs Charybdin appeared as a single band with a molecular mass of 29 kDa ... ImageQuant software was used for quantification comparing the relative darkness 2690 Total plant DNA was extracted from the bulb Approximately 0.1 g of material cut from the inner part of the bulb was...

Ngày tải lên: 16/03/2014, 14:20

... 380 B Yan, et al.r Inorganic Chemistry Communications (2000) 379–382 Fig Packing view of ŽC H 10 N2 wW3 O10 x along the b-axis 2.4 X-ray Crystallographic Studies X-ray crystallographic data of were ... initially isolated from the hydrothermal reaction of WO , en, NaOH and H O in polycrystalline form Replacement of NaOH with LiOH produces the same crystalline phase with similar product quality and ... organicrinorganic hybrid phases are obtained and structurally identified using the single crystal X-ray diffraction method Brief crystal data of one of the phases, a mono- Results and Discussion The...

Ngày tải lên: 19/03/2014, 16:48

... soluble RI, was loaded onto an RNase A affinity column For affinity chromatography, RNase A was attached covalently to the resin of a 5-mL Crystal structure of RNase A tandem enzymes HiTrap NHS-ester ... reaction was started by addition of FAM-AUAA-TAMRA (final concentration 50 nm) After a distinct time interval, lL of trypsin (0.5 mgÆmL)1) was added The reaction was finalized by addition of lL of ... Growth media were from Difco Laboratories (Detroit, MI, USA) Escherichia coli strain BL21(DE3) was from Stratagene (Heidelberg, Germany) FAM-AUAA-TAMRA was from Metabion International AG (Martinsried,...

Ngày tải lên: 22/03/2014, 16:21

... was amplified by PCR from the plasmid pCY167 (Suzuki H & Yamada C, Unpublished), using forward primer 5¢-CATATGGATGAGTACAAACA AGTAGATG-3¢ and reverse primer 5¢-GGATCCTCGAG CTCATTTACGTTTTAAATTAATGCCGAT-3¢ ... article, the crystal structures of Bacillus anthracis CapD, a GGT-related enzyme, in the absence and presence of a glutamate dipeptide were reported [19] B anthracis CapD catalyzes the cleavage of the ... Boanca G, Sand A, Okada T, Suzuki H, Kumagai H, Fukuyama K & Barycki JJ (2007) Autoprocessing of Helicobacter pylori c-glutamyltranspeptidase leads to the formation of a threonine–threonine catalytic...

Ngày tải lên: 22/03/2014, 21:20

... precipitant Prior to data collection, a crystal was transferred into Analysis of substrate specificity Substrate specificity was analyzed using xyloglucan tetradecasaccharide, XXXGXXXG, prepared as ... crystallography Acta Crystallogr D 50, 760–763 18 Navaza J (1994) AMoRe: an automated package for molecular replacement Acta Crystallogr A 50, 157–163 19 Brunger AT, Adams PD, Clore GM, DeLano WL, ¨ Gros ... at various concentrations of the substrate, tamarind seed xyloglucan (Dainippon Sumitomo Pharma, Osaka, Japan), in 50 mm sodium acetate buffer (pH 5.5) at 45 °C for 15 The bicinchoninate assay...

Ngày tải lên: 23/03/2014, 05:22

... Glu272–Arg148 21 19 14 092 8248 5844 –1 6.5 No of hydrogen bonds (side chain–side chain) Aromatic stacking ˚ ASA total (A2 ) ˚ ASA apolar (A2 ) ˚ ASA polar (A2 ) Formal global charge Theoretical pIb ... activity: crystallographic structure at 2 -A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase Proc Natl Acad Sci USA 90, 11257–11261 ... hydrophobic contacts and aromatic interactions are similar in all enzymes Frequently, alterations of the accessible surface of nonpolar side chains and of the accessible charged surfaces are observed...

Ngày tải lên: 23/03/2014, 07:20

... proteins have been implicated in transcriptional activation and repression, regulation of alternative splicing, regulation of mRNA stability, translational activation or repression and RNA packaging ... A, Max KEA, Welfle H, Balbach J & Heinemann U (2004) Singlestranded DNA bound to bacterial cold-shock proteins: preliminary crystallographic and Raman analysis Acta Crystallogr D Biol Crystallogr ... bacteria are very similar and may be attributed to the same function, a finding that has already been demonstrated for the CSP paralogues of B subtilis and E coli [3,41] Apart from eubacteria,...

Ngày tải lên: 23/03/2014, 09:21

... 5’-AAAAGGTCGACATCTGGATGGCGACGAAAGACACGATC-3’ 5’-GATCGTGTCTTTCGTCGCCATCCAGATGTCGACCTTTT-3’ D36N-1 5’-CATCCTTCCCTATCTCAACATCCAGCTGGTTTACT-3’ D341N-1 5’-AAGGGGAGAACTCAACGGAACACCGGAGG-3’ 5’-CACTCTCGAAGAGTTCATAAACGAAGTGAAGAAGAATCTC-3’ ... performed as described previously [17] Table Primer sequences TmIDH mutant Primer sequence R186M 5’-CCTGGAGAAATCGATCATGAGCTTCGCTCAGTCGTG-3’ 5’-CACGACTGAGCGAAGCTCATGATCGATTTCTCCAGG-3’ 5’-AAAAGGTCGACATCTGGATGGCGACGAAAGACACGATC-3’ ... lacked interdomain Structure and thermal stability of T maritima ˚ ionic networks at a cut-off of 4.0 A and the size of the networks were not as dramatically increased at 4.2 and ˚ 6.0 A cut-offs...

Ngày tải lên: 23/03/2014, 10:21