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2 Lys86 and Lys201 interact with the left arm scissile adenine base differently than in structures tha
3 catalytic core domain of MutY show that the scissile adenine is extruded from the DNA helix to be bo
4 between these molecules in the region of the scissile amide bond of MSmB and provides structural evid
5 y a structural rearrangement that places the scissile amide into an oxyanion hole and forces the nucl
7 onal asymmetry of abasic interference on the scissile and nonscissile strands highlights the importan
8 analog indole at individual positions of the scissile and nonscissile strands on the rate of single-t
9 basic lesions at individual positions of the scissile and nonscissile strands on the rate of single-t
10 specificity depends on the stability of the scissile base-sugar bond by determining the maximal acti
11 ptide was developed based on the fibronectin scissile bond (269)RAA downward arrowVal(272), and this
12 a double latch structure that sequesters the scissile bond (between Arg(234) and Lys(235)) and minimi
13 d to an unfolded state, in which the cryptic scissile bond (Y1605-M1606) is exposed and can then be p
14 tes for the ubiquitins on either side of the scissile bond allow hOtu1 to discriminate among differen
15 pproximately 9-10 residues C-terminal of the scissile bond and acts as an inducer of conformational f
17 propeptide cleavage, thereby identifying the scissile bond and characterizing the basic amino acids r
18 ding of the VWF A2 domain, which exposes the scissile bond and exosite for interaction with complemen
19 ysis requires mechanical force to expose the scissile bond and is regulated by a calcium-binding site
20 nt of cleavage-optimal residues flanking the scissile bond and modulate the mechanism for procofactor
23 of enzyme-mediated scission at the opposite scissile bond and was sufficient to stimulate the format
26 ophilic attack on the carbonyl carbon of the scissile bond are present; it is also the first peptidog
27 ible that quinolone interactions at a single scissile bond are sufficient to distort both strands of
29 te composition to the C-terminal side of the scissile bond as well as interactions of larger substrat
32 membrane alpha-helices, which results in the scissile bond being positioned adjacent to a glutamate-a
33 is remarkable that the peptide spanning the scissile bond binds to but bypasses cleavage by the enzy
34 nserved A9 and A10 bases reside close to the scissile bond but make distinct contributions to catalys
35 ement of two residues that contribute to the scissile bond by Ala did not eliminate cleavage, but rat
36 pin ribozyme-vanadate complex, indicated the scissile bond can adopt a variety of conformations resul
37 or CG bp at the pb position adjacent to the scissile bond can suppress cleavage without inhibiting b
38 ility were most likely caused by alternative scissile bond choices by tissue-specific gamma-secretase
39 B and TeNT: residues adjacent to the site of scissile bond cleavage (cleavage region) and residues lo
40 ', P3, and P5 sites of SNAP25 contributed to scissile bond cleavage by LC/A, whereas the P1' and P2 s
44 the active site of the enzyme and across the scissile bond contribute to defining the rate of process
45 indicate that the presence of a nick at one scissile bond dramatically increases the rate of cleavag
46 riants were prepared with mutations swapping scissile bond flanking sequences in the heavy chain indi
49 ine) folded properly, but exhibited nonideal scissile bond geometries (tau ranging from 118 degrees t
52 or conformational change to expose the first scissile bond in prothrombin, which is the likely event
53 nding site and resultant displacement of the scissile bond in the active site results in the observed
54 force is transduced from the polymer to the scissile bond in the mechanophore (i.e., mechanochemical
56 presence of the quinolone CP-115,953 at one scissile bond increased the extent of enzyme-mediated sc
57 rtially coordinated and that cleavage at one scissile bond increases the degree of cleavage at the ot
60 form of CPD was determined and revealed the scissile bond Leu(3428)-Ala(3429) captured in the cataly
61 horothioate substitution is installed at the scissile bond normally cleaved by the HHRz, Pt(II) cross
66 rmational changes in C4 are induced, and its scissile bond region becomes ordered and inserted into t
67 n GLP-1 and GIP, a single thioamide near the scissile bond renders these peptides up to 750-fold more
70 tended peptide sequences before or after the scissile bond showed endopeptidase to be superior to dip
71 of the metalloprotease domain of ADAMTS13 in scissile bond specificity, we identified 3 variable regi
73 yl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for
76 orts the binding loop in the vicinity of the scissile bond was found to be important both for enzyme
77 that replaced the 3'-bridging oxygen of the scissile bond with a sulfur atom (i.e. 3'-bridging phosp
80 VWF) unfolding which exposes the Y1605-M1606 scissile bond within the VWF A2 domain for cleavage by A
82 (at the +2 or +3 position 3' relative to the scissile bond), 3,N(4)-ethenodeoxycytidine, 3,N(4)-ethen
84 f short amino acid sequences surrounding the scissile bond, -Pro(12)-Asn(13)-, indicated that P2 Gly
86 NA and DNA IBS1 targets, presentation of the scissile bond, and stabilization of the structure by met
87 s a hydroxyethylamine moiety in place of the scissile bond, binds in two equivalent antiparallel orie
89 intact fibronectin at the Ala(271)/Val(272) scissile bond, generating an approximately 30-kd fragmen
90 ds the leucine 10 residues C-terminal to the scissile bond, is critical for collagenolysis and repres
91 neurotoxin (TeNT) cleave VAMP-2 at the same scissile bond, their mechanism(s) of VAMP-2 recognition
92 bunit favors acidic residues proximal to the scissile bond, while the alpha subunit prefers small or
112 in conjunction with the phosphate 3' to the scissile bond; the same Lys is also hydrogen bonded with
113 ve site suggested that Asp195 may facilitate scissile-bond activation and that His247 is oriented to
115 uential presentation and cleavage of the two scissile bonds in prothrombin activation is accomplished
117 t CA and UA dinucleotides, preferentially at scissile bonds located more than five nucleotides away f
118 , the human enzyme appears to ligate the two scissile bonds of a cleavage site in a nonconcerted fash
121 urface for optimum proteolytic attack on the scissile bonds of membrane-bound protein substrates such
123 core sequence of amino acids surrounding the scissile bonds responsible for governing the relative pr
124 for etoposide, which must be present at both scissile bonds to stabilize a double-stranded DNA break.
126 , interacts with the sequences distal to the scissile bonds whereas the CTD beta1-beta2 loop binds to
128 of polymers bearing three putatively "weak" scissile bonds: the carbon-nitrogen bond of an azobisdia
130 ne mass unit is added to the carbon end of a scissile C-H bond and when one mass unit is added to the
131 hydroxylation that correlated well with the scissile C-H bond energy, indicating a homolytic hydroge
132 hat substrate binding forces the substrate's scissile carboxylate group into the neighborhood of seve
133 DCase) furnishes a counterion that helps the scissile carboxylate group of the substrate leave water
135 inner-sphere metal interactions made by the scissile DNA phosphate and conserved Asp90 carboxylate a
136 ne metal ion shifts away from binding at the scissile DNA phosphate to a position near the 3'-adjacen
137 the small subunit and the nicked ends of the scissile DNA strand, mimicking the previously unseen tra
139 S the specificity for a 3'-O location of the scissile ester bond could be forced to the 2'-position b
144 particular interest is the activation of non-scissile mechanophores in which latent reactivity can be
149 eases cleave the serpin reactive center loop scissile P1-P1' bond, resulting in serpin-protease suici
150 The (1)J(NC') coupling constant for the (-1) scissile peptide bond at the N-extein-intein junction wa
151 ity to both the active site Cys(184) and the scissile peptide bond between threonine and glycine.
152 loy a splicing pathway in which the upstream scissile peptide bond is consecutively rearranged into t
156 ature, a highly strained conformation at the scissile peptide bond, had been identified and was hypot
163 revious work showed that substitution of the scissile phosphate (P) by methylphosphonate (MeP) permit
164 ious work we showed that substitution of the scissile phosphate (P) by the charge neutral methylphosp
165 VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction
167 Five of the metals bind within 12 A of the scissile phosphate and coordinate the majority of the ox
168 y be required for correct positioning of the scissile phosphate and coordination of catalytic residue
169 interaction with the 3'-bridging atom of the scissile phosphate and facilitates DNA scission by the b
170 ltured in isolation, and it shows an ordered scissile phosphate and nucleotide 5' to the cleavage sit
171 ed at 3.1-A resolution exhibits a disordered scissile phosphate and nucleotide 5' to the cleavage sit
173 del suggests that the pro-R(P) oxygen of the scissile phosphate and the 2'-hydroxyl nucleophile are i
174 Trp330 also assists in the activation of the scissile phosphate and the departure of the 5'-hydroxyl
176 e optimal spacing between the 5' end and the scissile phosphate appears to be eight nucleotides for R
178 r, a single phosphorothioate in place of the scissile phosphate blocks cleavage; the phosphorothioate
180 a fully assembled active site including the scissile phosphate bound by a divalent metal ion cofacto
181 ied at the end of the active site, while the scissile phosphate bridges two active site Mg(2+) ions.
182 nt is mediated by nucleophilic attack on the scissile phosphate by a conserved tyrosine residue, form
184 by replacement of the 5'-oxygen atom at the scissile phosphate by sulfur (5'-PS), which is a much be
185 eway, and double-base unpairing flanking the scissile phosphate control precise flap incision by the
186 ft in position together with movement of the scissile phosphate deeper into the active site cleft.
189 nt manganese rescue was not observed for the scissile phosphate diester linkage implying that electro
190 double nucleotide unpairing that places the scissile phosphate diester on active site divalent metal
191 unpairing the 5'-end of duplex to permit the scissile phosphate diester to contact catalytic divalent
192 interactions that successively position the scissile phosphate for bottom-strand cleavage at the DNA
193 hree-base interaction may be to position the scissile phosphate for cleavage, rather than to directly
197 nt metal ion and the 3'-bridging atom of the scissile phosphate greatly enhances enzyme-mediated DNA
198 eaturing a common, novel conformation of the scissile phosphate group as compared to all previous Eco
201 S1 nucleotide) or 3' (S1' nucleotide) of the scissile phosphate had large effects on substrate utiliz
202 t 1.95 A, reveals an Mg(2+) ion bound to the scissile phosphate in a position corresponding to Mg(B)
204 om in place of the 3'-bridging oxygen of the scissile phosphate in the presence of Mg2+, Mn2+, or Ca2
207 tereospecific phosphorothioate effect at the scissile phosphate is consistent with a significant stab
209 rate helix docking event that constrains the scissile phosphate linkage and positions G8 and A38 for
210 tonated C75 to the nonbridging oxygen of the scissile phosphate occurs to stabilize the phosphorane i
213 I domain, which can be extended to place the scissile phosphate of the target strand adjacent to the
214 Ruler to form a protein-DNA complex with the scissile phosphate positioned at the active site for opt
215 catalysis, the nucleophile is aligned with a scissile phosphate positioned proximal to the A-9 phosph
218 cond metal ion and a nonbridging atom of the scissile phosphate that stimulates DNA cleavage mediated
219 ics; neutralizing the negative charge on the scissile phosphate through methylphosphonate (MeP) subst
220 by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modificat
221 roup (the non-bridging 3'-oxygen atom of the scissile phosphate) during the hydrolysis reaction.
222 PPT positions -2, -4 and +1 (relative to the scissile phosphate) substantially reduces (+)-strand pri
223 tive site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for
224 taining the complete intron, both exons, the scissile phosphate, and all of the functional groups imp
225 s state, the nucleophile is in line with the scissile phosphate, and the N1 position of G33 and N3 po
226 coordinated by a conserved aspartate and the scissile phosphate, as observed in the restriction endon
227 a U-1 forms the most robust kink around the scissile phosphate, exposing it to the catalytic C75 in
228 2') to G40 is concomitant with attack of the scissile phosphate, followed by the remainder of the cle
229 ting SRL, containing a 3'-sulfur atom at the scissile phosphate, reacts at a fully diffusion-limited
230 R(p) oxygen of the phosphate group 3' of the scissile phosphate, suggesting possible roles for these
232 the modeled G53 2'-OH group that attacks the scissile phosphate, thus suggesting a direct role in gen
233 The citrate fills the binding site for the scissile phosphate, wherein it is coordinated by Arg237,
234 cleophile requiring a closer approach to the scissile phosphate, which in turn increases the barrier.
235 interaction with the 3'-bridging atom of the scissile phosphate, while the other (M(2)(2+)) is believ
236 ng oligodeoxynucleotides substituted, at the scissile phosphate, with isomeric phosphorothioates and
258 ated to the non-bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence
260 more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with that of
262 aining a phosphoramidate substitution at the scissile phosphates were resistant to cleavage by the en
264 We find that resolution is optimal when the scissile phosphodiester (Tp/N) is located two nucleotide
265 The residues in ONC that are proximal to the scissile phosphodiester bond (His10, Lys31, and His97) a
268 ed at the catalytic center, bringing the two scissile phosphodiester bonds into close proximity.
271 6-deoxyadenosine (dA) positions flanking the scissile phosphodiester slow the rate of DNA religation
272 II recognizes its substrates and selects the scissile phosphodiester(s) by recognizing specific RNA s
275 icked-site substrate at the positions of the scissile phosphodiesters result in abolition or inhibiti
276 water molecule to the phosphorus atom of the scissile phosphoester bond, with the attacking water bei
277 s via an in-line-attack by CYT 17 O2' on the scissile phosphorous (ADE 1.1 P), and is therefore consi
278 with an abortive 3'-terminal dC close to the scissile position in the enzyme active site, providing i
279 design, the adenosine ribonucleotide at the scissile position of the 8-17 DNAzyme was replaced by 2'
281 troducing tetrahydrofuran lesions around the scissile PPT/unique 3'-sequence junction indicate that t
283 the AT(1)R-associated short form suggested a scissile site located within the Arg(363)-Arg(393) regio
284 delivery to the active site of the selected scissile sites further implicates the existence of a pre
285 ed to determine the timing of three selected scissile sites in lambdaN approaching the proteolytic si
286 ts the "almost complete" delivery of all the scissile sites in lambdaN to the proteolytic site in an
288 eptide bond cleavage and the delivery of the scissile sites near the amino- versus carboxyl-terminal
290 ns become energetically more damaging as the scissile strand is shortened from 32 to 24 and 18 nucleo
291 rand in the context of duplexes in which the scissile strand length was progressively shortened.
292 -Oxo substitutions at the -1 position in the scissile strand slowed single-turnover cleavage by a fac
293 s effects of eliminating the +2T base on the scissile strand were rectified by introducing the nonpol
294 aced the -1N, +1T, +2T, and +4C bases of the scissile strand, but abasic lesions at +5C and +3C had l
295 basic sites within the CCCTT sequence of the scissile strand, but an abasic lesion at the 5'-OH nucle
298 eus cleaves LPXTG-containing proteins at the scissile T-G peptide bond and ligates protein-LPXT to th
300 leavage by analyzing the conformation of the scissile X-Pro peptide bond, and by comparing the rate c
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