ライフサイエンスコーパス: catalytic residue

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

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

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

4 active site by sitting directly between two catalytic residues.

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

6 on the basis of distance restraints between catalytic residues.

7 AMP share conserved secondary structures and catalytic residues.

8 cterial DHNAs, except when using alternative catalytic residues.

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

10 411 residues contain 70 of the annotated 111 catalytic residues.

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

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

13 intrinsically disordered proteins (IDPs) and catalytic residues.

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

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

16 rate RTA's active site and interact with key catalytic residues.

17 oid-like pseudoproteases that lack essential catalytic residues.

18 2, indicating the relative importance of the catalytic residues.

19 intramembrane serine proteases that lack key catalytic residues.

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

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

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

23 This function is independent of the putative catalytic residues.

24 ure of VopS and its evolutionarily conserved catalytic residues.

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

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

27 Pol epsilon-D290A,E292A variant lacking the catalytic residues.

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

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

30 the role and relative importance of putative catalytic residues.

31 ional flexibility, which could encompass the catalytic residues.

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

33 hat hindered binding or accessibility to the catalytic residues.

34 ated the conservation of previous identified catalytic residues.

35 ational modifications, allosteric sites, and catalytic residues.

36 nown structures and experimentally annotated catalytic residues.

37 conservation of Ser482 to the same degree as catalytic residues.

38 nal studies in their efforts to characterize catalytic residues.

39 e active site for proper alignment with MutY catalytic residues.

40 the membrane that encloses highly conserved catalytic residues.

41 s provide improved ranked positions of known catalytic residues.

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

43 probe the functional roles of such putative catalytic residues.

44 ydrolysis of the polysaccharide close to the catalytic residues.

45 es from modified substrates) using identical catalytic residues.

46 ational analysis, we confirmed the essential catalytic residues.

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

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

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

50 properties and evolutionary conservation of catalytic residue activity.

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

52 analysis around three key properties of the catalytic residues: amino acid type, catalytic function,

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

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

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

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

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

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

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

60 Catalytic residues and cleavage sites for each of the SH

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

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

63 tudies have led to the identification of key catalytic residues and have provided insight into the ra

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

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

66 raction alters the relationships between the catalytic residues and may allow for a pH-dependent regu

67 nerated several DNMT3A variants with mutated catalytic residues and measured their activities in 5mC

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

69 8 are proposed to position appropriately the catalytic residues and participate in substrate binding.

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

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

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

73 ups in influencing the protonation states of catalytic residues and subsequently the progression of t

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

75 hat they are often found at interfaces, near catalytic residues and tend to harbor functionally impor

76 or bound complex reveals the geometry of the catalytic residues and the conformation of the inhibitor

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

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

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

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

81 ExoN catalytic residues are arranged in three motifs: I (DE),

82 The structures disclosed that although catalytic residues are conserved with the mammalian enzy

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

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

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

86 We observe that catalytic residues are increasingly rigidified, the acti

87 The catalytic residues are located approximately 10 A into t

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

89 Two catalytic residues are proposed, mutations of which resu

90 Catalytic residues are typically highly conserved, but t

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

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

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

94 sformations are catalyzed by the same set of catalytic residues, Arg88 and Glu35-Wat-Glu211 cluster,

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

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

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

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

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

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

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

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

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

104 nally, we show the mutation tolerance of the catalytic residues based on their roles.

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

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

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

108 ided by the RgNanOx structure, we identified catalytic residues by site-directed mutagenesis.

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

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

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

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

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

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

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

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

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

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

119 el via the conformational changes of its two catalytic residues Cys282 and Glu248.

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

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

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

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

124 firming the hypothesis that proximity to the catalytic residue determines the site of electrophilic a

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

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

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

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

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

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

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

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

133 Two groups of catalytic residues exhibit differential line broadening,

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

135 We identified Cys(74) as the catalytic residue for both ubiquitination and deamidatio

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

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

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

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

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

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

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

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

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

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

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

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

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

149 Interestingly, in OTUB2, the catalytic residues His(224) and Asn(226) formed a stable

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

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

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

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

154 served N-terminal end of RbgA containing the catalytic residue Histidine 9.

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

156 % at a corresponding recall (the fraction of catalytic residues identified) of 57% on a standard benc

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

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

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

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

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

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

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

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

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

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

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

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

169 The catalytic residues in all three active sites are arrange

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

185 However, the protonation states of the catalytic residues in this complex have never been fully

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

215 Here, we review the data on the catalytic residues of 648 enzymes, as annotated in the M

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

217 The catalytic residues of an enzyme comprise the amino acids

218 (referred as ligand 1) that binds to the key catalytic residues of BACE1 and predicts to inhibit abno

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

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

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

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

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

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

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

226 TNFAIP3 allele encoded substitutions at non-catalytic residues of the ubiquitin protease OTU domain

227 By mutating catalytic residues of two such enzymes, we engineered mu

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

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

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

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

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

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

234 ApbE activity indicate that the pK(a) of the catalytic residue (pK (ES1)) increases by 2 pH units in

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

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

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

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

239 In catalytic residue prediction, INTREPID provides signific

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

257 Mutation of conserved catalytic residues substantially reduced activity consis

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

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

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

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

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

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

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

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

266 ember of the SidE family-at E860, one of the catalytic residues that is required for the mono-ADP-rib

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

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

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

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

271 The characterization of the catalytic residues, their functions, and conservation, a

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

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

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

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

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

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

278 e proper alignment of the substrate with key catalytic residues to facilitate acylation.

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

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

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

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

283 The catalytic residue, Tyr(250) , is under the hydrogen bond

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

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

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

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

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

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

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

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

292 ear the nucleotide potentially acting as the catalytic residue with minimal rearrangements.

293 cing D27G,N,F chromosomal mutations in a key catalytic residue with subsequent adaptation by an autom

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

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

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

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

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 enzyme

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