Detection of Reaction Intermediates in Mg2+-Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography

被引：17

作者：

Samara, Nadine L. ^{[1
,2
]}

Gao, Yang ^{[1
]}

Wu, Jinjun ^{[1
]}

Yang, Wei ^{[1
]}

机构：

[1] NIDDK, Mol Biol Lab, NIH, Bethesda, MD 20892 USA

[2] NIDCR, Sect Biol Chem, NIH, Bethesda, MD USA

来源：

DNA REPAIR ENZYMES: STRUCTURE, BIOPHYSICS, AND MECHANISM | 2017年 / 592卷

关键词：

ESCHERICHIA-COLI; RIBONUCLEASE H; ENDONUCLEASE V; DEOXYINOSINE; 3-ENDONUCLEASE; SUBSTRATE-SPECIFICITY; CRYSTAL-STRUCTURE; POLYMERASE-BETA; LAUE STRUCTURES; RNA/DNA HYBRID; METAL-IONS;

D O I：

10.1016/bs.mie.2017.03.022

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Structures of enzyme-substrate/product complexes have been studied for over four decades but have been limited to either before or after a chemical reaction. Recently using in crystallo catalysis combined with X-ray diffraction, we have discovered that many enzymatic reactions in nucleic acid metabolism require additional metal ion cofactors that are not present in the substrate or product state. By controlling metal ions essential for catalysis, the in crystallo approach has revealed unprecedented details of reaction intermediates. Here we present protocols used for successful studies of Mg2+-dependent DNA polymerases and ribonucleases that are applicable to analyses of a variety of metal ion-dependent reactions.

引用

页码：283 / 327

页数：45

共 10 条

[1] Following replicative DNA synthesis by time-resolved X-ray crystallography
Chim, Nicholas
Meza, Roman A.
Trinh, Anh M.
Yang, Kefan
Chaput, John C.
NATURE COMMUNICATIONS, 2021, 12 (01)
[2] Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources
Schmidt, Marius
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2019, 20 (06)
[3] Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser
Kupitz, Christopher
Basu, Shibom
Grotjohann, Ingo
Fromme, Raimund
Zatsepin, Nadia A.
Rendek, Kimberly N.
Hunter, Mark S.
Shoeman, Robert L.
White, Thomas A.
Wang, Dingjie
James, Daniel
Yang, Jay-How
Cobb, Danielle E.
Reeder, Brenda
Sierra, Raymond G.
Liu, Haiguang
Barty, Anton
Aquila, Andrew L.
Deponte, Daniel
Kirian, Richard A.
Bari, Sadia
Bergkamp, Jesse J.
Beyerlein, Kenneth R.
Bogan, Michael J.
Caleman, Carl
Chao, Tzu-Chiao
Conrad, Chelsie E.
Davis, Katherine M.
Fleckenstein, Holger
Galli, Lorenzo
Hau-Riege, Stefan P.
Kassemeyer, Stephan
Laksmono, Hartawan
Liang, Mengning
Lomb, Lukas
Marchesini, Stefano
Martin, Andrew V.
Messerschmidt, Marc
Milathianaki, Despina
Nass, Karol
Ros, Alexandra
Roy-Chowdhury, Shatabdi
Schmidt, Kevin
Seibert, Marvin
Steinbrener, Jan
Stellato, Francesco
Yan, Lifen
Yoon, Chunhong
Moore, Thomas A.
Moore, Ana L.
NATURE, 2014, 513 (7517) : 261 - +
[4] Pump-Probe Time-Resolved Serial Femtosecond Crystallography at X-Ray Free Electron Lasers
Pandey, Suraj
Poudyal, Ishwor
Malla, Tek Narsingh
CRYSTALS, 2020, 10 (07): : 1 - 16
[5] Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches
Westenhoff, Sebastian
Nazarenko, Elena
Malmerberg, Erik
Davidsson, Jan
Katona, Gergely
Neutze, Richard
ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, 2010, 66 : 207 - 219
[6] Cs-exchange in birnessite: Reaction mechanisms inferred from time-resolved X-ray diffraction and transmission electron microscopy
Lopano, Christina L.
Heaney, Peter J.
Post, Jeffrey E.
AMERICAN MINERALOGIST, 2009, 94 (5-6) : 816 - 826
[7] X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters
Nicolet, Yvain
Rohac, Roman
Martin, Lydie
Fontecilla-Camps, Juan C.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (18) : 7188 - 7192
[8] Bond Shortening (1.4 Å) in the Singlet and Triplet Excited States of [Ir2(dimen)4]2+ in Solution Determined by Time-Resolved X-ray Scattering
Haldrup, Kristoffer
Harlang, Tobias
Christensen, Morten
Dohn, Asmus
van Driel, Tim Brandt
Kjaer, Kasper Skov
Harrit, Niels
Vibenholt, Johan
Guerin, Laurent
Wulff, Michael
Nielsen, Martin Meedom
INORGANIC CHEMISTRY, 2011, 50 (19) : 9329 - 9336
[9] Time-resolved in-situ X-ray diffraction and crystal structure analysis of porous coordination polymer CPL-1 in CO2 adsorption
Ashitani, Hirotaka
Kawaguchi, Shogo
Furukawa, Hiromichi
Ishibashi, Hiroki
Otake, Kenichi
Kitagawa, Susumu
Kubota, Yoshiki
JOURNAL OF SOLID STATE CHEMISTRY, 2023, 319
[10] Structure and Thermal Stability of (H2O)4 Tetrahedron and (H2O)6 Hexagon Adsorbed on NaY Zeolite Studied by Synchrotron-Based Time-Resolved X-ray Diffraction
Hu, Maocong
Hanson, Jonathan C.
Wang, Xianqin
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 2018, 57 (14) : 4988 - 4995

← 1 →