FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2145992215> ?p ?o ?g. }

• W2145992215 endingPage "33" @default.
• W2145992215 startingPage "22" @default.
• W2145992215 abstract "The structure of a pectin-bound complex of rhamnogalacturonase was modeled to identify the amino acid residues involved in catalysis and substrate binding. The hairy region of pectin, represented by six repeating stretches of (1-->4)-D-galacturonate-(1-->2)-L-rhamnose dimer, was flexibly docked into the putative binding site of rhamnogalacturonase from Aspergillus aculeatus whose X-ray structure is known. A search of the complex configurational space was performed using AutoDock for the dimeric and tetrameric sugar units in which the -1 galacturonate residue has various ring conformations. Then the plausible AutoDock solutions were manually extended to the dodecameric pectin models. Subsequently, the resulting complex models were subjected to solvated molecular dynamics using AMBER. In the best model, the substrate has an extended pseudo-threefold helix with the -1 ring in a 4H3 half-chair that approaches the transition state conformation. The catalytic machinery is clearly defined: Asp197 is a general acid and the activated water bound between Asp177 and Glu198 is a nucleophile. The active site is similar, with a small yet significant difference, to that of polygalacturonase that degrades the pectic smooth region of linear homopolymer of D-(1-->4)-linked galacturonic acid. Rhamnogalacturonase has ten binding subsites ranging from -3 to +7, while polygalacturonase has eight subsites from -5 to +3. The model suggests that the eight amino acids including three arginine and three lysine residues, all of which are invariantly conserved in the rhamnogalacturonase family of proteins, are important in substrate binding. The present study may aid in designing mutational studies to characterize rhamnogalacturonase." @default.
• W2145992215 created "2016-06-24" @default.
• W2145992215 creator A5004926657 @default.
• W2145992215 creator A5009045260 @default.
• W2145992215 creator A5009725517 @default.
• W2145992215 creator A5049761480 @default.
• W2145992215 date "2004-02-20" @default.
• W2145992215 modified "2023-10-17" @default.
• W2145992215 title "Computer modeling of the rhamnogalacturonase-“hairy” pectin complex" @default.
• W2145992215 cites W1488171676 @default.
• W2145992215 cites W1595145094 @default.
• W2145992215 cites W1908822140 @default.
• W2145992215 cites W1935712031 @default.
• W2145992215 cites W1964536616 @default.
• W2145992215 cites W1974579245 @default.
• W2145992215 cites W1981917391 @default.
• W2145992215 cites W1987250042 @default.
• W2145992215 cites W1995874012 @default.
• W2145992215 cites W1996524561 @default.
• W2145992215 cites W2002302483 @default.
• W2145992215 cites W2003186781 @default.
• W2145992215 cites W2016822801 @default.
• W2145992215 cites W2016854453 @default.
• W2145992215 cites W2016934650 @default.
• W2145992215 cites W2022395923 @default.
• W2145992215 cites W2028231353 @default.
• W2145992215 cites W2035266068 @default.
• W2145992215 cites W2036603805 @default.
• W2145992215 cites W2040921242 @default.
• W2145992215 cites W2057535425 @default.
• W2145992215 cites W2060183170 @default.
• W2145992215 cites W2061758567 @default.
• W2145992215 cites W2061900269 @default.
• W2145992215 cites W2065504666 @default.
• W2145992215 cites W2065893364 @default.
• W2145992215 cites W2066401197 @default.
• W2145992215 cites W2067026233 @default.
• W2145992215 cites W2070304794 @default.
• W2145992215 cites W2074219304 @default.
• W2145992215 cites W2075536361 @default.
• W2145992215 cites W2076615456 @default.
• W2145992215 cites W2087673249 @default.
• W2145992215 cites W2098211196 @default.
• W2145992215 cites W2106121486 @default.
• W2145992215 cites W2114341071 @default.
• W2145992215 cites W2127183344 @default.
• W2145992215 cites W2147732011 @default.
• W2145992215 cites W2158534713 @default.
• W2145992215 cites W2159080918 @default.
• W2145992215 cites W2159688944 @default.
• W2145992215 cites W2766407610 @default.
• W2145992215 cites W4245461700 @default.
• W2145992215 doi "https://doi.org/10.1002/prot.10434" @default.
• W2145992215 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/14997537" @default.
• W2145992215 hasPublicationYear "2004" @default.
• W2145992215 type Work @default.
• W2145992215 sameAs 2145992215 @default.
• W2145992215 citedByCount "12" @default.
• W2145992215 countsByYear W21459922152013 @default.
• W2145992215 countsByYear W21459922152014 @default.
• W2145992215 countsByYear W21459922152015 @default.
• W2145992215 countsByYear W21459922152016 @default.
• W2145992215 countsByYear W21459922152017 @default.
• W2145992215 countsByYear W21459922152018 @default.
• W2145992215 countsByYear W21459922152021 @default.
• W2145992215 crossrefType "journal-article" @default.
• W2145992215 hasAuthorship W2145992215A5004926657 @default.
• W2145992215 hasAuthorship W2145992215A5009045260 @default.
• W2145992215 hasAuthorship W2145992215A5009725517 @default.
• W2145992215 hasAuthorship W2145992215A5049761480 @default.
• W2145992215 hasConcept C104317684 @default.
• W2145992215 hasConcept C107824862 @default.
• W2145992215 hasConcept C161790260 @default.
• W2145992215 hasConcept C185592680 @default.
• W2145992215 hasConcept C2775905019 @default.
• W2145992215 hasConcept C2780152424 @default.
• W2145992215 hasConcept C41183919 @default.
• W2145992215 hasConcept C47701112 @default.
• W2145992215 hasConcept C55493867 @default.
• W2145992215 hasConcept C71240020 @default.
• W2145992215 hasConceptScore W2145992215C104317684 @default.
• W2145992215 hasConceptScore W2145992215C107824862 @default.
• W2145992215 hasConceptScore W2145992215C161790260 @default.
• W2145992215 hasConceptScore W2145992215C185592680 @default.
• W2145992215 hasConceptScore W2145992215C2775905019 @default.
• W2145992215 hasConceptScore W2145992215C2780152424 @default.
• W2145992215 hasConceptScore W2145992215C41183919 @default.
• W2145992215 hasConceptScore W2145992215C47701112 @default.
• W2145992215 hasConceptScore W2145992215C55493867 @default.
• W2145992215 hasConceptScore W2145992215C71240020 @default.
• W2145992215 hasFunder F4320322348 @default.
• W2145992215 hasIssue "1" @default.
• W2145992215 hasLocation W21459922151 @default.
• W2145992215 hasLocation W21459922152 @default.
• W2145992215 hasOpenAccess W2145992215 @default.
• W2145992215 hasPrimaryLocation W21459922151 @default.
• W2145992215 hasRelatedWork W1523821527 @default.
• W2145992215 hasRelatedWork W1914280947 @default.

• next