Reaction pathway of ADP-ribose pyrophosphatase, revealed by time-resolved X-ray crystallography

2008 ◽  
Vol 64 (a1) ◽  
pp. C271-C272
Author(s):  
N. Kamiya ◽  
K. Kai ◽  
N. Nakagawa ◽  
S. Kuramitsu ◽  
I. Miyahara
Keyword(s):  
Reaction Pathway ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Following replicative DNA synthesis by time-resolved X-ray crystallography

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nicholas Chim ◽  
Roman A. Meza ◽  
Anh M. Trinh ◽  
Kefan Yang ◽  
John C. Chaput
Keyword(s):  
Dna Synthesis ◽  
Structural Changes ◽  
Reaction Pathway ◽  
Dna Polymerases ◽  
Enzymatic Catalysis ◽  
Time Resolved ◽  
X Ray ◽  
Tyrosine Residues ◽  
X Ray Crystallography ◽  
Unidirectional Movement

AbstractThe mechanism of DNA synthesis has been inferred from static structures, but the absence of temporal information raises longstanding questions about the order of events in one of life’s most central processes. Here we follow the reaction pathway of a replicative DNA polymerase using time-resolved X-ray crystallography to elucidate the order and transition between intermediates. In contrast to the canonical model, the structural changes observed in the time-lapsed images reveal a catalytic cycle in which translocation precedes catalysis. The translocation step appears to follow a push-pull mechanism where the O-O1 loop of the finger subdomain acts as a pawl to facilitate unidirectional movement along the template with conserved tyrosine residues 714 and 719 functioning as tandem gatekeepers of DNA synthesis. The structures capture the precise order of critical events that may be a general feature of enzymatic catalysis among replicative DNA polymerases.

A flow cell suitable for time-resolved X-ray crystallography by the Laue method

1997 ◽  
Vol 30 (5) ◽  
pp. 555-556 ◽  
Author(s):  
G. Kurisu ◽  
A. Sugimoto ◽  
Y. Kai ◽  
S. Harada
Keyword(s):  
Flow Cell ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
Laue Method

scholarly journals Reactions of Titanocene- and Zirconocene-Bis(trimethylsilyl)acetylene Complexes with Selected Heterocyclic and Aromatic NH and OH Acid Compounds

2007 ◽  
Vol 72 (4) ◽  
pp. 475-491 ◽  
Author(s):  
Perdita Arndt ◽  
Vladimir V. Burlakov ◽  
Ulrike Jäger-Fiedler ◽  
Marcus Klahn ◽  
Anke Spannenberg ◽  
...  
Keyword(s):  
Bond Activation ◽  
Reaction Pathway ◽  
Reaction Products ◽  
X Ray ◽  
X Ray Crystallography

The titanocene complexes Cp'2Ti(η2-Me3SiC2SiMe3) (Cp' = Cp (1), Cp* (2)) react with pyrrole under the formation of the titanium(III) mono-N-pyrrolides Cp'2Ti(NC4H4) (Cp' = Cp (6), Cp* (7)); whereas the corresponding zirconocene system Cp2Zr(η2-Me3SiC2SiMe3)(thf) (3) forms in a different reaction pathway first the Cp2Zr(NC4H4)[C(SiMe3)=CH(SiMe3)] (8) and then the zirconium(IV) bis-N-pyrrolide Cp2Zr(NC4H4)2 (11). With Cp*2Zr(η2-Me3SiC2SiMe3) (4) and pyrrole, the zirconium(IV) mono-N-pyrrolide with an agostic alkenyl group Cp*2Zr(NC4H4)[C(SiMe3)=CH(SiMe3)] (9) was obtained. In the reaction of the ethylenebistetrahydroindenyl (ebthi) complex rac-(ebthi)Zr(η2-Me3SiC2SiMe3) (5) with 2,3,5,6-tetrafluoroaniline under N-H bond activation, a complex with an agostic alkenyl group rac-(ebthi)Zr(NH-C6HF4)[C(SiMe3)=CH(SiMe3)] (10) was formed. Compound 10 reacts with additional 2,3,5,6-tetrafluoroaniline to give the bisanilide rac-(ebthi)Zr(NH-C6HF4)2 (12) which was obtained directly from 5 with two equivalents of 2,3,5,6-tetrafluoroaniline. In reactions of complex 5 with unsubstituted aniline to rac-(ebthi)Zr(NH-C6H5)2 (13) and with pentafluorophenol to bisphenolate rac-(ebthi)Zr(O-C6F5)2 (14), no intermediates could be isolated. The new reaction products 6, 9, 10, 12, 13 and 14 were investigated by X-ray crystallography.

scholarly journals Approach of Serial Crystallography

Crystals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 854
Author(s):  
Ki Hyun Nam
Keyword(s):  
Radiation Damage ◽  
Room Temperature ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Past ◽  
Wide Range ◽  
Experimental Limitation ◽  
Serial Crystallography ◽  
Collection Strategies

Radiation damage and cryogenic sample environment are an experimental limitation observed in the traditional X-ray crystallography technique. However, the serial crystallography (SX) technique not only helps to determine structures at room temperature with minimal radiation damage, but it is also a useful tool for profound understanding of macromolecules. Moreover, it is a new tool for time-resolved studies. Over the past 10 years, various sample delivery techniques and data collection strategies have been developed in the SX field. It also has a wide range of applications in instruments ranging from the X-ray free electron laser (XFEL) facility to synchrotrons. The importance of the various approaches in terms of the experimental techniques and a brief review of the research carried out in the field of SX has been highlighted in this editorial.

Time-resolved molecular dynamics of bacteriophage HK97 capsid maturation interpreted by electron cryo-microscopy and X-ray crystallography

2006 ◽  
Vol 153 (3) ◽  
pp. 300-306 ◽  
Author(s):  
William R. Wikoff ◽  
James F. Conway ◽  
Jinghua Tang ◽  
Kelly K. Lee ◽  
Lu Gan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
Capsid Maturation

Mapping the conformational itinerary of β-glycosidases by X-ray crystallography

2003 ◽  
Vol 31 (3) ◽  
pp. 523-527 ◽  
Author(s):  
G.J. Davies ◽  
V.M.-A. Ducros ◽  
A. Varrot ◽  
D.L. Zechel
Keyword(s):  
Transition State ◽  
Reaction Pathway ◽  
Tight Binding ◽  
Three Dimensional ◽  
Intermediate Structure ◽  
Active Centre ◽  
X Ray ◽  
Solution Structures ◽  
X Ray Crystallography ◽  
Covalent Intermediate

The conformational agenda harnessed by different glycosidases along the reaction pathway has been mapped by X-ray crystallography. The transition state(s) formed during the enzymic hydrolysis of glycosides features strong oxocarbenium-ion-like character involving delocalization across the C-1–O-5 bond. This demands planarity of C-5, O-5, C-1 and C-2 at or near the transition state. It is widely, but incorrectly, assumed that the transition state must be 4H3 (half-chair). The transition-state geometry is equally well supported, for pyranosides, by both the 4H3 and 3H4 half-chair and 2,5B and B2,5 boat conformations. A number of retaining β-glycosidases acting on gluco-configured substrates have been trapped in Michaelis and covalent intermediate complexes in 1S3 (skew-boat) and 4C1 (chair) conformations, respectively, pointing to a 4H3-conformed transition state. Such a 4H3 conformation is consistent with the tight binding of 4E- (envelope) and 4H3-conformed transition-state mimics to these enzymes and with the solution structures of compounds bearing an sp2 hybridized anomeric centre. Recent work reveals a 1S5 Michaelis complex for β-mannanases which, together with the 0S2 covalent intermediate, strongly implicates a B2,5 transition state for β-mannanases, again consistent with the solution structures of manno-configured compounds bearing an sp2 anomeric centre. Other enzymes may use different strategies. Xylanases in family GH-11 reveal a covalent intermediate structure in a 2,5B conformation which would also suggest a similarly shaped transition state, while 2S0-conformed substrate mimics spanning the active centre of inverting cellulases from family GH-6 may also be indicative of a 2,5B transition-state conformation. Work in other laboratories on both retaining and inverting α-mannosidases also suggests non-4H3 transition states for these medically important enzymes. Three-dimensional structures of enzyme complexes should now be able to drive the design of transition-state mimics that are specific for given enzymes, as opposed to being generic or merely fortuitous.

Combining X-ray crystallography and single-crystal spectroscopy to probe enzyme mechanisms

2009 ◽  
Vol 37 (2) ◽  
pp. 378-381 ◽  
Author(s):  
Arwen R. Pearson ◽  
Robin L. Owen
Keyword(s):  
Data Collection ◽  
Single Crystal ◽  
Diffraction Data ◽  
Reaction Pathway ◽  
X Ray ◽  
X Ray Crystallography ◽  
Enzyme Systems ◽  
Catalytic Intermediates ◽  
Trapping Methods ◽  
Induced Changes

The combination of X-ray crystallography and rapid cryo-trapping methods has enabled the visualization of catalytic intermediates in a variety of enzyme systems. However, the resolution of the X-ray experiment is not always sufficient to precisely place the structure on the reaction pathway. In addition, many trapped intermediates are X-ray-sensitive and can decay during diffraction data collection, resulting in a final structure that may not be representative of the initial trapped species. Complementary methods, such as single-crystal spectroscopy, provide a means to precisely identify the cryo-trapped species as well as detect any X-ray-induced changes during diffraction data collection.

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