Crystal Structures of an NH2-Terminal Fragment of T4 DNA Polymerase and Its Complexes with Single-Stranded DNA and with Divalent Metal Ions†

Biochemistry ◽  
1996 ◽  
Vol 35 (25) ◽  
pp. 8110-8119 ◽  
Author(s):  
J. Wang ◽  
P. Yu ◽  
T. C. Lin ◽  
W. H. Konigsberg ◽  
T. A. Steitz
Keyword(s):  
Metal Ions ◽  
Crystal Structures ◽  
Dna Polymerase ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Single Stranded Dna ◽  
Terminal Fragment

scholarly journals Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69

2021 ◽  
Vol 8 ◽  
Author(s):  
Jongseo Park ◽  
Hyung-Seop Youn ◽  
Jun Yop An ◽  
Youngjin Lee ◽  
Soo Hyun Eom ◽  
...  
Keyword(s):  
Metal Ions ◽  
Dna Polymerase ◽  
Metal Ion ◽  
Ternary Complex ◽  
Critical Role ◽  
Divalent Metal ◽  
Binary Complex ◽  
Divalent Metal Ions ◽  
Divalent Metal Ion ◽  
Initial Binding

DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed.

Crystal structures with infinite chains based on antimony tartrate dimers

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Xiqu Wang ◽  
Allan J. Jacobson
Keyword(s):  
Aqueous Solutions ◽  
Metal Ions ◽  
Single Crystal ◽  
Crystal Structures ◽  
Crystal Form ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Complex Metal ◽  
Metal Nitrates ◽  
Tartar Emetic

Abstract Seven complex metal antimony tartrates have been synthesized in single crystal form by slowly evaporating aqueous solutions of potassium antimony tartrate (tartar emetic) and divalent metal nitrates or perchlorates. Crystal structures of these compounds all contain infinite chains formed by linking antimony tartrate dimers with divalent metal ions. While infinite chains of antimony tartrate dimers bridged by single Zn2+ ions or by double Mg2+ ions were reported previously, new types of chains with alternating single and double bridging cations are observed in this work.

scholarly journals Binding of Mn-deoxyribonucleoside triphosphates to the active site of the DNA polymerase of bacteriophage T7

2011 ◽  
Vol 26 (2) ◽  
pp. 159-162 ◽  
Author(s):  
Barak Akabayov ◽  
Charles C. Richardson
Keyword(s):  
Metal Ions ◽  
Dna Polymerase ◽  
Active Site ◽  
Divalent Metal ◽  
Enzymatic Activities ◽  
Bacteriophage T7 ◽  
Divalent Metal Ions ◽  
X Ray ◽  
Full Activity

Divalent metal ions are crucial as cofactors for a variety of intracellular enzymatic activities. Mg2+, as an example, mediates binding of deoxyribonucleoside 5′-triphosphates followed by their hydrolysis in the active site of DNA polymerase. It is difficult to study the binding of Mg2+ to an active site because Mg2+ is spectroscopically silent and Mg2+ binds with low affinity to the active site of an enzyme. Therefore, we substituted Mg2+ with Mn2+:Mn2+ that is not only visible spectroscopically but also provides full activity of the DNA polymerase of bacteriophage T7. In order to demonstrate that the majority of Mn2+ is bound to the enzyme, we have applied site-directed titration analysis of T7 DNA polymerase using X-ray near edge spectroscopy. Here we show how X-ray near edge spectroscopy can be used to distinguish between signal originating from Mn2+ that is free in solution and Mn2+ bound to the active site of T7 DNA polymerase. This method can be applied to other enzymes that use divalent metal ions as a cofactor.

scholarly journals Metal ions and phosphate binding in the H-N-H motif: Crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions

2009 ◽  
Vol 11 (12) ◽  
pp. 2947-2957 ◽  
Author(s):  
Meng-Jiun Sui ◽  
Li-Chu Tsai ◽  
Kuo-Chiang Hsia ◽  
Lyudmila G. Doudeva ◽  
Wen-Yen Ku ◽  
...  
Keyword(s):  
Metal Ions ◽  
Crystal Structures ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Phosphate Binding ◽  
Phosphate Ion ◽  
Nuclease Domain

scholarly journals Crystal Structures of Bacillus Alkaline Phytase in Complex with Divalent Metal ions and Inositol Hexasulfate

2011 ◽  
Vol 409 (2) ◽  
pp. 214-224 ◽  
Author(s):  
Yi-Fang Zeng ◽  
Tzu-Ping Ko ◽  
Hui-Lin Lai ◽  
Ya-Shan Cheng ◽  
Tzu-Hui Wu ◽  
...  
Keyword(s):  
Metal Ions ◽  
Crystal Structures ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Alkaline Phytase

Interaction of divalent metal ions with the NADP+-malic enzyme from maize leaves

1991 ◽  
Vol 81 (4) ◽  
pp. 462-466 ◽  
Author(s):  
Maria Fabiana Drincovich ◽  
Alberto A. Iglesias ◽  
Carlos S. Andreo
Keyword(s):  
Metal Ions ◽  
Malic Enzyme ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Maize Leaves
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