ライフサイエンスコーパス: catalytic residue

1 otype in HeLa cells, implicating Glu431 as a catalytic residue.

2 of O-fucose in a specific orientation to the catalytic residue.

3 it into the active site until it reaches the catalytic residue.

4 between Cys192, on this helix, and Cys138, a catalytic residue.

5 enesis has confirmed the role of Lys144 as a catalytic residue.

6 during the nucleophilic attack by the Ser278 catalytic residue.

7 is residue to serve as the general acid/base catalytic residue.

8 411 residues contain 70 of the annotated 111 catalytic residues.

9 es, neural networks were trained to identify catalytic residues.

10 e core fold of this enzymatic domain and its catalytic residues.

11 intrinsically disordered proteins (IDPs) and catalytic residues.

12 oved relative pK(a) predictions for proximal catalytic residues.

13 d mutagenesis was carried out to confirm the catalytic residues.

14 oid-like pseudoproteases that lack essential catalytic residues.

15 2, indicating the relative importance of the catalytic residues.

16 intramembrane serine proteases that lack key catalytic residues.

17 as well as altering the positions of certain catalytic residues.

18 due to misalignment of the substrate and/or catalytic residues.

19 rate specifically though the loss or gain of catalytic residues.

20 This function is independent of the putative catalytic residues.

21 ure of VopS and its evolutionarily conserved catalytic residues.

22 sertions at second-shell sites that abut key catalytic residues.

23 to Sts-1(PGM), including conservation of all catalytic residues.

24 ly as a dimer with each subunit contributing catalytic residues.

25 and acts as a switch to correctly orient key catalytic residues.

26 the role and relative importance of putative catalytic residues.

27 ional flexibility, which could encompass the catalytic residues.

28 es only three polar side chains as potential catalytic residues.

29 hat hindered binding or accessibility to the catalytic residues.

30 s provide improved ranked positions of known catalytic residues.

31 mplicate histidine 45 and arginine 70 as key catalytic residues.

32 e Lys to Arg mutation significantly distorts catalytic residues.

33 ributed effects that propagate long-range to catalytic residues.

34 probe the functional roles of such putative catalytic residues.

35 degree of sequence identity around the four catalytic residues.

36 ydrolysis of the polysaccharide close to the catalytic residues.

37 ational analysis, we confirmed the essential catalytic residues.

38 r chemotype, which did not interact with the catalytic residues.

39 nal studies in their efforts to characterize catalytic residues.

40 elations, as well as the solvent exposure of catalytic residues.

41 on the basis of distance restraints between catalytic residues.

42 AMP share conserved secondary structures and catalytic residues.

43 cterial DHNAs, except when using alternative catalytic residues.

44 aining (pro) sequences, yet retain essential catalytic residues.

45 equence analysis allowed us to identify four catalytic residues, a proton relay cascade, and a substr

46 s shows that by decoupling the action of the catalytic residues acting on each strand we can inhibit

47 properties and evolutionary conservation of catalytic residue activity.

48 eral C(t)-FDH mutants in which two essential catalytic residues adjacent to the nicotinamide ring of

49 mutants indicates that His-228 is a critical catalytic residue along with the metal cofactor.

50 ining issues is ranked positions of putative catalytic residues among all ranked residues.

51 enesis experiments suggest that YjgF lacks a catalytic residue and that it facilitates ammonia releas

52 [with the underlined histidine acting as the catalytic residue and the underlined serine as the nucle

53 (i) a water molecule frequently bridges the catalytic residues and (ii) the bridging water molecule

54 trinsically active kinase conformation, with catalytic residues and a catalytic mechanism remarkably

55 Catalytic residues and APRs were also found to be in str

56 (beta1, beta2, and beta5) bear the protease catalytic residues and are synthesized with N-terminal p

57 Catalytic residues and cleavage sites for each of the SH

58 and TgtA2 reveal that TgtA2 lacks key arcTGT catalytic residues and contains an additional module.

59 shows a dimer with conserved topology of the catalytic residues and fold as non-mammalian PDFs.

60 show that Thr 42, Glu 50, and His 76 are key catalytic residues and identify several factors that inf

61 arge-scale breathing motion that exposes key catalytic residues and lowers the hydrophobicity of the

62 logues, forming putative hydrogen bonds with catalytic residues and mimicking the charge distribution

63 8 are proposed to position appropriately the catalytic residues and participate in substrate binding.

64 evaluated INTREPID on two tasks: predicting catalytic residues and predicting specificity determinan

65 ted mutagenesis of RadH was used to identify catalytic residues and provide insight into the mechanis

66 In addition to conserving the same catalytic residues and structural fold, both homologues

67 chain binding, (2) the atypical active site catalytic residues and surrounding oxyanion hole that co

68 In order to improve ranking of catalytic residues and their prediction accuracy, we hav

69 lation reaction the same active site and one catalytic residue, and utilizes molecular oxygen as sour

70 ies revealed that Asp(202) and Glu(361) were catalytic residues, and Trp(270), Tyr(461), and Asn(462)

71 e-site residues are conserved in TgALD1, key catalytic residues are absent in TgDPA.

72 studies, which revealed that the motions of catalytic residues are constrained by the second C-extei

73 In this approach putative catalytic residues are first substituted to noncarboxyli

74 edge base, we have seen that the top 10 most catalytic residues are histidine, aspartate, glutamate,

75 The catalytic residues are located approximately 10 A into t

76 The relative positioning of the putative catalytic residues are most consistent with a retaining

77 ormations in loops 2 and 3, but the critical catalytic residues are positioned for catalysis.

78 Two catalytic residues are proposed, mutations of which resu

79 hereas saphire mutants lacking key conserved catalytic residues are viable but thermosensitive, sugge

80 an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interactio

81 sites in protein-protein interfaces, unlike catalytic residues, are only weakly conserved and induce

82 ite in the major groove and thereby recruits catalytic residue Arg(130) to the active site.

83 uced structural alignment or misalignment of catalytic residues as a third dimension on the free-ener

84 aking into account the local conformation of catalytic residues as well as protein dynamics during th

85 have unique three-dimensional structures and catalytic residues as well as specific tissue localizati

86 ural studies confirmed the importance of key catalytic residues as well as the importance of residues

87 horylated reaction cycle intermediate at the catalytic residue Asp-488, whereas, among all plant nutr

88 ilized by selected mutations of two critical catalytic residues, Asp105 and His88.

89 sis of this structure-function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as w

90 that CSmetaPred_poc is able to rank putative catalytic residues at lower (better) ranked positions, w

91 Substitution of key non-catalytic residues at the Dnmt3a-Dnmt3L interface or the

92 vided into donor and acceptor sites with the catalytic residues at their junction; a number of loops

93 for the first time detailed knowledge about catalytic residues, available through the Catalytic Site

94 kernel-based algorithm for the prediction of catalytic residues based on protein sequence, structure

95 Smaller amplicons, lacking hyaluronidase catalytic residues because of 768 bp or 855 bp central d

96 Surprisingly, although not among the catalytic residues, both mutations affected heme co-fact

97 n mutant versions of hOGG1 having changes in catalytic residues but not on variants having altered 7,

98 s S(N)2 reaction, His-374 and Asn-397 act as catalytic residues by enhancing the nucleophilicity of t

99 We also substituted hallmark catalytic residues by site-directed mutagenesis and anal

100 effect", whereby mutations in peripheral non-catalytic residues can cause subtle allosteric changes i

101 Knowledge of catalytic residues can play an essential role in elucida

102 Mutation of the p29 catalytic residues caused an accumulation of unprocessed

103 whilst the differences between EC classes in catalytic residue composition are not immediately obviou

104 The calculated pK(a) values of catalytic residues confirm their proposed roles from str

105 erminal domain, and it identified additional catalytic residues conserved throughout eukaryotic RNase

106 onclude that factors other than first-sphere catalytic residue contacts contribute to binding of inhi

107 otonation state for the substrate and nearby catalytic residues could be uniquely distinguished by th

108 it forms a thioimide covalent linkage to the catalytic residue Cys-55.

109 nt, thus preventing an in-line attack by the catalytic residue Cys-99 of Srx.

110 the active-site loop and the position of the catalytic residue Cys75 are unchanged with respect to th

111 However, replacement of conserved putative catalytic residues (D(321), R(324), and Q(330)) had no e

112 The importance of the predicted catalytic residues D89, H90, N106 and H115 in N.varphiGa

113 active site and interacts directly with the catalytic residues despite its bulky planar nature.

114 linker, located more than 11 A away from the catalytic residues, determines the fidelity of these Y-f

115 This unique feature of HS 2-OST catalytic residues directed us to characterize the Droso

116 ggesting that the spatial arrangement of the catalytic residues does not change during the dephosphor

117 wever, both NF90 and NF45 have lost critical catalytic residues during evolution and are therefore no

118 often be generated by mutating the canonical catalytic residue (e.g. Ras Q61L) to impair GTP hydrolys

119 Changes in the positioning of conserved catalytic residues (e.g. Lys-73, Ser-130, and Tyr-105) a

120 Substitution of the putative catalytic residue E211 with a nonacidic amino acid gluta

121 We propose that Glu226 still acts as the catalytic residue even for an L-sugar substrate.

122 Two groups of catalytic residues exhibit differential line broadening,

123 C10 peptide binding blocks access to OASS catalytic residues, explaining how complex formation dow

124 nts lacking either its RNA-binding domain or catalytic residue fail to promote synapse formation, sug

125 Ras superfamily of GTPases, lacks a defined catalytic residue for carrying out guanosine triphosphat

126 conserved histidine (H225) functions as the catalytic residue for this enzymatic activity, and mutat

127 f the RecQ ATPase active site that positions catalytic residues for ATP hydrolysis.

128 we demonstrate a requirement of the putative catalytic residues for EGL-26 function in vivo.

129 and requires conserved caspase-like putative catalytic residues for its function.

130 Although MiD51 lacks catalytic residues for transferase activity, it specific

131 teins, but it does not contain the motifs of catalytic residues found in these structural homologues.

132 formation for high-performance prediction of catalytic residues from 3D structures.

133 is stabilized by polar interactions with the catalytic residue Glu(226) rather than by a covalent lin

134 ith CD38 or its inactive mutant in which the catalytic residue Glu-226 is mutated.

135 used to explore the interaction of the CD38 catalytic residue Glu-226 with the "northern" ribose.

136 expected, the results provided evidence that catalytic residue Glu-44 of SpoIVFB is near the cleavage

137 sidues on this loop with residue 370 and the catalytic residues Glu-235 and Glu-340.

138 intermediate formed a close linkage with the catalytic residue (Glu-179), whereas the adenine ring at

139 onent, in which the PIWI domain provides the catalytic residues governing guide-strand mediated site-

140 As a result, the computational prediction of catalytic residues has the potential to identify novel c

141 us, despite possessing all of the putatively catalytic residues, has no detectable RNA cleavage activ

142 ite-directed single mutants of BphD in which catalytic residues His-265 and Ser-112 were replaced wit

143 HNH catalytic domain contains the conserved catalytic residues His-Asn-His and a zinc-binding site [

144 del also illuminated the three putative RebM catalytic residues (His140/141 and Asp166) subsequently

145 Alanine mutations of catalytic residues His147 and His149 abolish DNAppG de-c

146 prompted us to elucidate the role of the new catalytic residue (His33) in the active site of spDHFR.

147 ticipation in a salt bridge network with two catalytic residues identified previously: Arg38, which b

148 % at a corresponding recall (the fraction of catalytic residues identified) of 57% on a standard benc

149 phenylalanine, indicating that the acid-base catalytic residue, identified in other AKRs, has a conse

150 l-DNA phosphodiesterase (TDP), and conserved catalytic residues imply a similar mechanism.

151 l measurement of a pKa near neutrality for a catalytic residue in a ribozyme and show that ribozymes,

152 e features, such as Ser replacing Thr as the catalytic residue in certain BPH subfamilies, suggest a

153 tionally, we identified Glu-176, a conserved catalytic residue in GH16 endo-beta-1,3-glucanases, as e

154 the polypeptide chain and mutation of a key catalytic residue in one of the duplicated segments.

155 role of this invariant glutamate as the key catalytic residue in SleB and CwlJ.

156 tical mechanism for this reaction involves a catalytic residue in the H-box active-site region.

157 e to multiple disease models, we mutated the catalytic residue in the JHM strain of MHV (JHMV), which

158 arly with increasing distance to the nearest catalytic residue in the protein structure.

159 e activity in vitro, and point mutation of a catalytic residue in this domain disrupted the deadenyla

160 heterozygous mutation, affecting a critical catalytic residue in TREX1, that results in typical Aica

161 port pervasive conservation gradients toward catalytic residues in a dataset of 524 distinct enzymes:

162 Understanding which are the catalytic residues in an enzyme and what function they p

163 The role of the predicted catalytic residues in autoproteolytic processing of p29

164 We find that conserved catalytic residues in both cytidine deaminase domains ar

165 rg-73, and Glu-114, previously identified as catalytic residues in Cg10062, have also been implicated

166 rotein, such as sites in the protein core or catalytic residues in enzymes, are evolutionarily more c

167 comparable with those observed for identical catalytic residues in homologues.

168 Similar to the catalytic residues in motif D, G1100 in motif A, T1157 i

169 Model-free analysis shows that the catalytic residues in RNase H are preorganized on ps-ns

170 In particular, the geometry of the catalytic residues in the active site of UCH-L1 is disto

171 Based on the positioning of catalytic residues in the enzyme active site, the lack o

172 arison of the shifts in the positions of the catalytic residues in the inhibitor complex presented he

173 ases lack conservation of one or more of the catalytic residues in the kinase core and as a consequen

174 This activity required specific catalytic residues in the PGBD5 transposase domain as we

175 uggested by the structure to act as critical catalytic residues in the transglycosylation.

176 Cleavage is mediated by catalytic residues in the two conserved Higher Eukaryote

177 ion, eliminating one of the highly conserved catalytic residues in this class of endonucleases, drama

178 Catalytic residues in TmGalA were inferred through struc

179 GTP hydrolysis, the TBC domain supplies two catalytic residues in trans, an arginine finger analogou

180 Point mutations at predicted catalytic residues in UGT2B7 abrogated activity, strongl

181 ed with a set of hydrophilic and potentially catalytic residues, including essential aspartic acids.

182 y the presence of equivalently placed acidic catalytic residues, including one at the end of the firs

183 how that functional sites, and in particular catalytic residues, induce long-range evolutionary const

184 bstrate-induced conformational changes bring catalytic residues into alignment, alter the local envir

185 hitotriose, to identify Asp75 as the primary catalytic residue involved in this cleavage, and to solv

186 and Tyr-410, were proposed as candidates for catalytic residues involved in deprotonation of the meth

187 ted, so that it includes the function of the catalytic residues involved in the reaction and the chem

188 ated so that it includes the function of the catalytic residues involved in the reaction and the mech

189 ates, whereas an E72Q mutant in the presumed catalytic residue is much less active.

190 The identification of catalytic residues is a key step in understanding the fu

191 However, experimental identification of catalytic residues is a tedious and time-consuming task,

192 How these regulatory sites communicate with catalytic residues is not well understood.

193 Moreover, the relative orientation of these catalytic residues is similar to that observed in the an

194 Importantly, median predicted rank of catalytic residues is the lowest (best) for CSmetaPred_p

195 to tolerate a mutation of its most conserved catalytic residue (its histidine general base), and the

196 , as well as blocks target DNA access to key catalytic residues lining the RuvC pocket.

197 We impute a role for +1T in recruiting the catalytic residue Lys-167 to the active site.

198 residues in catalysis including the primary catalytic residue Lys-171.

199 ma-phosphate which indicate dynamic roles of catalytic residues Lys15 and Arg117.

200 ntification and characterization of possible catalytic residues, Lys184, which is responsible for for

201 The inhibitor interacts with the catalytic residues Lys599 and Glu612 and displaces the k

202 ing to the active site, which houses the key catalytic residue, lysine 122.

203 ive point mutation was introduced at the key catalytic residue, mutant DNMT1 failed to rescue any of

204 Through mutagenesis and activity assays, catalytic residues N335 and D449 have been identified.

205 and contains one degenerate site with a non-catalytic residue next to the Walker B motif.

206 Although this domain contains neither catalytic residues nor substrate sites, its removal impa

207 K, a naturally occurring variation at the NA catalytic residue of A(H7N9) viruses, conferred reduced

208 ting that this lysine represents a conserved catalytic residue of Dicers.

209 The catalytic residue of NylC was identified as the N-termin

210 ro(427), Gly(428), and Gly(429) activate the catalytic residue of the enzyme, Thr(352), and stabilize

211 topology, which was carried out to locate a catalytic residue of the protein, showed that modificati

212 FGly is the key catalytic residue of the sulfatase family, comprising 17

213 Cys-195 mutant of thrombin revealed that the catalytic residue of thrombin is modulated by Na(+), but

214 lyses in ago mutant plants revealed that the catalytic residues of AGO1, AGO2, and AGO7 are required

215 of the interplay between the regulatory and catalytic residues of c-Met, and by comparison between t

216 lix of FliM(M) (alpha1) does not contain the catalytic residues of CheC and CheX but does include pos

217 Point mutations in the catalytic residues of each analyzed recombinant OsCAF1 p

218 By making inactivating mutations to the catalytic residues of human Hyal2, we found that hyaluro

219 Molecular modeling demonstrated that the catalytic residues of mNsp15 are superimposable with its

220 show that mutation of each of the five RNase catalytic residues of PICV NP diminishes the IFN suppres

221 be a novel sensitive method to identify both catalytic residues of retaining beta-glucosidases by the

222 The catalytic residues of the CheX.CheY3 complex are virtual

223 oordinated by the nucleic acid substrate and catalytic residues of the enzyme.

224 ects were relieved by either mutation of the catalytic residues of the SAMHD1 phosphohydrolase domain

225 ified Arg(64), Lys(269), and Tyr(309) as key catalytic residues of VioA.

226 at the motion influences the geometry of key catalytic residues on opposite faces of the NNIBP.

227 sents an approximately 14-fold enrichment of catalytic residues on the entire input set (correspondin

228 Mutation of putative catalytic residues only resulted in loss of activity of

229 stability, lowering the pKa of proton donor catalytic residue, optimized spatial distribution of the

230 ntial chemical properties of the first-shell catalytic residues, particularly their spatial arrangeme

231 Protein binding site residues, especially catalytic residues, play a central role in protein funct

232 oss the RNase dimer interface that place key catalytic residues poised for reaction.

233 periments show that Discern's improvement in catalytic residue prediction is derived from the combina

234 n shown to boost the recall and precision of catalytic residue prediction over other sequence-based m

235 In catalytic residue prediction, INTREPID provides signific

236 residue-level scores derived from well-known catalytic residue predictors can improve prediction accu

237 residue scores derived from four well-known catalytic residue predictors.

238 gB bound to the ribosome revealing potential catalytic residues proximal to the mRNA substrate.

239 lly-competent conformation and pre-organizes catalytic residue Q61; mutations disturb the R789/Q61 or

240 inant viruses with mutant NA-encoding genes (catalytic residues R152K and R292K, framework residues E

241 f the scissile phosphate and coordination of catalytic residues relative to each other so that DNA cl

242 Because Arg(104) is a key catalytic residue responsible for stabilization of the g

243 isC has provided the first insights into the catalytic residues responsible for the cyclization step

244 Inactivation of PLP1 catalytic residues resulted in a mutant virus that did n

245 ite, and is abrogated by inactivation of the catalytic residue Ser-195.

246 ion of the protein--which includes the known catalytic residue, Ser(195).

247 state kinetic analyses revealed two critical catalytic residues, Ser-35 and Asp-125.

248 s dependent on the presence of the predicted catalytic residue Ser141 and was inhibited by the lipase

249 ad residues, is directed away from the other catalytic residues Ser194 and Glu310.

250 tein side chain (approximately 13 A from the catalytic residue Ser273).

251 was compromised upon mutation of any of the catalytic residues (Ser366, His147 and Asp533).

252 Alanine-scanning mutagenesis of predicted catalytic residues showed the predicted loss of in vitro

253 Substitution of catalytic residues shows that the mART function is respo

254 ite a domain architecture and positioning of catalytic residues similar to those of other family 39 g

255 se activity and suggests Y181 as a potential catalytic residue similarly to His-hydrophobe-His relaxa

256 Mutation of conserved catalytic residues substantially reduced activity consis

257 A highly purified wild-type CPAF but not a catalytic residue-substituted mutant CPAF was sufficient

258 We identified a rare catalytic residue substitution in the last two, and perf

259 f 7.7 is measured for the amine group of the catalytic residue T1, confirming that it can act as a pr

260 so revealed tightly bound chlorides near the catalytic residue that may contribute to catalytic activ

261 hieve a precision (the fraction of predicted catalytic residues that are catalytic) of 18.5% at a cor

262 on of the active site and positioning of the catalytic residues that are consistent with an inverting

263 arily distinct enzymes characterize key APE1 catalytic residues that are potentially functionally sim

264 Structure-guided mutagenesis revealed four catalytic residues that enabled the re-programming of Sd

265 similar positioning of donor, acceptor, and catalytic residues that provide a common structural fram

266 cted mutagenesis of PxaTPS8 revealed several catalytic residues that, together with quantum chemical

267 the SeV L protein invariant lysine 1782 as a catalytic residue, the recombinant virus with a single K

268 tivity is ensured by the absence of critical catalytic residues, the filling of the substrate groove,

269 Though not a catalytic residue, this Trp is a hinge residue in a cons

270 a putative S1 pocket and conserved candidate catalytic residues Thr1, Asp17 and Lys32(33).

271 water) and uncover a previously unrecognized catalytic residue (Thr197).

272 rvation that AGO3 has retained the necessary catalytic residues throughout its evolution.

273 as designed to affect the reactivity of that catalytic residue to allow for capture of the preacylati

274 oups on the cofactor, substrates, and nearby catalytic residues to be established.

275 ciative fashion, Tth UDGb relies on multiple catalytic residues to facilitate its excision of hypoxan

276 topoisomerase III where DNA binding realigns catalytic residues to form a functional active site.

277 ubstrate-binding energy to actively misalign catalytic residues to reduce the rate of misincorporatio

278 bstrate-binding residues (as well as one key catalytic residue) to expand the substrate range provide

279 In addition to the proposed catalytic residues, transmitter phosphatase activity als

280 steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr(58) and Glu(120).

281 finasteride accepts hydrogen bonds from the catalytic residues Tyr-58 and Glu-120 in the active site

282 istance between the substrate and both a key catalytic residue (Tyr157) and the enzyme-bound NAD+ cof

283 ism of entropy compensation for ordering the catalytic residues upon ligand binding by disordering sp

284 conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; ho

285 t of catalytic residues which act upon other catalytic residues, using a set of 60 enzyme structures.

286 utating both intermolecular dimerization and catalytic residues was CPAF activation completely blocke

287 Its catalytic residues were identified as Glu(184) and Glu(2

288 ed their substrate preference, whereas their catalytic residues were identified using site-directed m

289 se of other arteriviruses, and the predicted catalytic residues were shown to be proximal by homology

290 We have also assembled a separate dataset of catalytic residues which act upon other catalytic residu

291 provide limits on "expected geometries" for catalytic residues, which will help to identify these re

292 tatistics describing the typical geometry of catalytic residues with regard to the substrate and one

293 regulatory mechanism, in which engagement of catalytic residues with the substrate is coupled to corr

294 We identified a putative catalytic residue within a highly conserved region of Rb

295 ation (D269A) that alters a highly conserved catalytic residue within the T7 loop completely eliminat

296 cs of reaction chemistry and the geometry of catalytic residues within active sites.

297 monstrates the relationship of substrate and catalytic residues within the active site, confirming ea

298 Whereas the identity and position of catalytic residues within the PD(D/E)XK superfamily are

299 the same dataset CSmetaPred_poc predicts all catalytic residues within top 20 ranks for 73% of enzym

300 st that, in addition to the highly conserved catalytic residues, YopJ family effectors also require c