ProSup: a refined tool for protein structure alignment

Lackner, Peter; Koppensteiner, Walter A.; Sippl, Manfred J.; Domingues, Francisco S.

doi:10.1093/protein/13.11.745

Cited by 106 publications

(86 citation statements)

References 27 publications

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“…3. Superimposition of SIs and oligo-1,6-glucosidase onto the amylosucrase-sucrose complex based on the atoms of the five conserved active-site residues (11,14,25,26). Based on this model of the binding-site structure, the residues that are involved directly in the hydrolysis of the glycosidic bond, i.e., His 145 , Asp 241 , Glu 295 , His 368 , and Asp 369 , were observed to be highly conserved in ␣-glucosidase family 13.…”

Section: Resultsmentioning

confidence: 99%

Isomaltose Production by Modification of the Fructose-Binding Site on the Basis of the Predicted Structure of Sucrose Isomerase from “ Protaminobacter rubrum ”

Lee¹,

Kim²,

Kim³

et al. 2008

Appl Environ Microbiol

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"Protaminobacter rubrum" sucrose isomerase (SI) catalyzes the isomerization of sucrose to isomaltulose and trehalulose. SI catalyzes the hydrolysis of the glycosidic bond with retention of the anomeric configuration via a mechanism that involves a covalent glycosyl enzyme intermediate. It possesses a 325 RLDRD 329 motif, which is highly conserved and plays an important role in fructose binding. The predicted three-dimensional activesite structure of SI was superimposed on and compared with those of other ␣-glucosidases in family 13. We identified two Arg residues that may play important roles in SI-substrate binding with weak ionic strength. Mutations at Arg 325 and Arg 328 in the fructose-binding site reduced isomaltulose production and slightly increased trehalulose production. In addition, the perturbed interactions between the mutated residues and fructose at the fructose-binding site seemed to have altered the binding affinity of the site, where glucose could now bind and be utilized as a second substrate for isomaltose production. From eight mutant enzymes designed based on structural analysis, the R 325 Q mutant enzyme exhibiting high relative activity for isomaltose production was selected. We recorded 40.0% relative activity at 15% (wt/vol) additive glucose with no temperature shift; the maximum isomaltose concentration and production yield were 57.9 g liter ؊1 and 0.55 g of isomaltose/g of sucrose, respectively. Furthermore, isomaltose production increased with temperature but decreased at a temperature of >35°C. Maximum isomaltose production (75.7 g liter ؊1 ) was recorded at 35°C, and its yield for the consumed sucrose was 0.61 g g ؊1 with the addition of 15% (wt/vol) glucose. The relative activity for isomaltose production increased progressively with temperature and reached 45.9% under the same conditions.Isomaltose (6-O-␣-D-glucopyranosyl-D-glucose) is a disaccharide that comprises an ␣-1,6-glycosidic bond between two glucose molecules. Its caloric value is less than 50% that of sucrose, and its viscosity is lower than that of maltose (8). Further, its properties are similar to those of other well-known low-cariogenic sugar alcohols or sucrose isomers, since much less acid and glucan are formed by Streptococcus mutans than sucrose. Isomaltose is a member of the isomalto-oligosaccharide group, whose members contain at least one ␣-1,6-glycosidic linkage, such as pannose, isomaltotriose, isomaltotetraose, nigerose, and isopanose. Isomalto-oligosaccharides are known to improve the general well-being of humans and animals when ingested orally on a daily basis. Isomaltose has potential applications, not only in the food industry, such as in confections, processed fruits and vegetables, and canned and bottled food, but also as an ingredient in animal feed, cosmetics, and medicines. It is generated as a by-product during chemical and enzymatic reactions that use liquefied starch or a glucose-containing solution as a reactant. However, it has not yet been possible to obtain a disaccharide-enriched product ...

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Section: Resultsmentioning

confidence: 99%

Isomaltose Production by Modification of the Fructose-Binding Site on the Basis of the Predicted Structure of Sucrose Isomerase from “ Protaminobacter rubrum ”

Lee¹,

Kim²,

Kim³

et al. 2008

Appl Environ Microbiol

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“…e, Backbone r.m.s. deviations between the Prp19p U-box and three RING fingers using ProSup 34 . Panels (b-d) were generated using MolMol 35 .…”

Section: Coordinatesmentioning

confidence: 99%

Structural insights into the U-box, a domain associated with multi-ubiquitination

Ohi

Kooi

Rosenberg

et al. 2003

Nat Struct Mol Biol

262

232

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The structure of the U-box in the essential Saccharomyces cerevisiae pre-mRNA splicing factor Prp19p has been determined by NMR. The conserved zinc-binding sites supporting the crossbrace arrangement in RING-finger domains are replaced by hydrogen-bonding networks in the Ubox. These hydrogen-bonding networks are necessary for the structural stabilization and activity of the U-box. A conservative Val→Ile point mutation in the Prp19p U-box domain leads to premRNA splicing defects in vivo. NMR analysis of this mutant shows that the substitution disrupts structural integrity of the U-box domain. Furthermore, comparison of the Prp19p U-box domain with known RING-E2 complex structures demonstrates that both U-box and RING-fingers contain a conserved interaction surface. Mutagenesis of residues at this interface, while not perturbing the structure of the U-box, abrogates Prp19p function in vivo. These comparative structural and functional analyses imply that the U-box and its associated ubiquitin ligase activity are critical for Prp19p function in vivo.Ubiquitin (Ub) targeting of proteins for degradation by the proteosome involves polyubiquination of substrate proteins via an enzyme cascade consisting of activating (E1), conjugating (E2) and ligating (E3) enzymes. E3 ubiquitin ligases vary widely in size, composition and enzymology, reflecting their regulatory role in substrate recognition 1 . HECT and RING finger domain-containing proteins constitute two classes of E3 ligases. HECT domains bind Ub through a thioester bond and transfer Ub directly to substrate. RING finger E3s facilitate the transfer of Ub from the E2 to the substrate, rather than binding Ub directly.Correspondence should be addressed to K.L.G. kathy.gould@mcmail.vanderbilt.edu or W.J.C. walter.chazin@vanderbilt.edu. 3 These authors contributed equally to this work. Competing interests statementThe authors declare that they have no competing financial interests. HHS Public Access Author Manuscript Author ManuscriptAuthor Manuscript Author ManuscriptA third class of E3 ubiquitin ligases has been recently identified 2,3 . This class of proteins contains a U-box motif, first identified in Saccharomyces cerevisiae Ufd2p. Ufd2p promotes the elongation of poly-ubiquitin chains in a U-box-dependent manner (recently termed an 'E4' activity) 4 . An alignment of U-boxes and RING motifs indicated that U-boxes lack the strictly conserved histidine and cysteine Zn 2+ -chelating residues found in RING fingers, but they share a similar pattern of hydrophobic and polar amino acids (Fig. 1a), raising the possibility that they have similar folds 5 .S. cerevisiae Prp19p is an essential pre-mRNA splicing factor that contains an N-terminal Ubox 6,7 . Interestingly, a mutation within the Prp19p U-box that results in the substitution of an isoleucine for a conserved valine (prp19-1) leads to pre-mRNA splicing defects and the disruption of several key protein-protein interactions within the spliceosome 8,9 . The profound physiological consequences that result from th...

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“…A set of 10 pairs of proteins with lower structural similarity was recognized as difficult structures for comparison, and was evaluated by VAST (Madej et al, 1995;Gibrat et al, 1996), DALI (Holm & Sander, 1993;Holm & Park, 2000), CE (Shindyalov & Bourne, 1998), Prosup (Lackner et al, 2000) and LGA (Zemla, 2003) methods respectively. The structural similarity was evaluated by two optimistic parameters, i.e.…”

Section: Pfsa Vs Other Methodsmentioning

confidence: 99%

“…3D-BLAST method (Mavridis & Ritchie, 2010) is developed to align the protein structures using 3D spherical polar Fourier for protein shape. There are many of well known methods, including DAL (Kryshtafovych et al, 2005;Hvidsten et al, 2003), MAMMOTH (Ortiz et al, 2002), ProSup (Lackner et al, 2000), VAST (Madej et al, 1995;Gibrat et al, 1996), SSAP (Taylor & Orengo, 1989), STRUCTAL (Subbiah et al, 1993), LSQMAN (Kleywegt & Jones, 1994), SSM (Krissinel & Henrick, 2004), FlexProt (Shatsky et al, 2002), FATCAT (Yuzhen & Adam, (2003) and TM-align/score (Zhang Y & Skolnick J. 2005).…”

Section: Introductionmentioning

confidence: 99%