Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, ape1: implications for the catalytic mechanism 1 1Edited by I. A. Wilson

2001 ◽  
Vol 307 (4) ◽  
pp. 1023-1034 ◽  
Author(s):  
Peter T Beernink ◽  
Brent W Segelke ◽  
Masood Z Hadi ◽  
Jan P Erzberger ◽  
David M Wilson ◽  
...  
Keyword(s):  
Metal Ions ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Crystal Form ◽  
Divalent Metal ◽  
Divalent Metal Ions

scholarly journals Structure of the endonuclease IV homologue fromThermotoga maritimain the presence of active-site divalent metal ions

2010 ◽  
Vol 66 (9) ◽  
pp. 1003-1012 ◽  
Author(s):  
Stephen J. Tomanicek ◽  
Ronny C. Hughes ◽  
Joseph D. Ng ◽  
Leighton Coates
Keyword(s):  
Metal Ions ◽  
Active Site ◽  
Excision Repair ◽  
Divalent Metal ◽  
Hydroxyl Group ◽  
Divalent Metal Ions ◽  
Ap Endonuclease ◽  
Phosphodiester Bond ◽  
Dna Base ◽  
Ap Site

The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5′-phosphodiester bond at an AP site to generate a free 3′-hydroxyl group and a 5′-terminal sugar phosphate using their AP nuclease activity. Specifically,Thermotoga maritimaendonuclease IV is a member of the second conserved AP endonuclease family that includesEscherichia coliendonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of theT. maritimaendonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of theT. maritimaendonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily.

scholarly journals Structural and Binding Analysis of Pyrimidinol Carboxylic Acid andN-Hydroxy Quinazolinedione HIV-1 RNase H Inhibitors

2011 ◽  
Vol 55 (6) ◽  
pp. 2905-2915 ◽  
Author(s):  
Eric B. Lansdon ◽  
Qi Liu ◽  
Stephanie A. Leavitt ◽  
Mini Balakrishnan ◽  
Jason K. Perry ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Metal Ions ◽  
Active Site ◽  
Water Environment ◽  
Divalent Metal ◽  
Rnase H ◽  
Accurate Assessment ◽  
Divalent Metal Ions ◽  
Substrate State ◽  
Hiv 1

ABSTRACTHIV-1 RNase H breaks down the intermediate RNA-DNA hybrids during reverse transcription, requiring two divalent metal ions for activity. Pyrimidinol carboxylic acid andN-hydroxy quinazolinedione inhibitors were designed to coordinate the two metal ions in the active site of RNase H. High-resolution (1.4 Å to 2.1 Å) crystal structures were determined with the isolated RNase H domain and reverse transcriptase (RT), which permit accurate assessment of the metal and water environment at the active site. The geometry of the metal coordination suggests that the inhibitors mimic a substrate state prior to phosphodiester catalysis. Surface plasmon resonance studies confirm metal-dependent binding to RNase H and demonstrate that the inhibitors do not bind at the polymerase active site of RT. Additional evaluation of the RNase H site reveals an open protein surface with few additional interactions to optimize active-site inhibitors.

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 Coordination of Divalent Metal Ions in the Active Site of Poly(A)-specific Ribonuclease

2004 ◽  
Vol 279 (47) ◽  
pp. 48702-48706 ◽  
Author(s):  
Yan-Guo Ren ◽  
Leif A. Kirsebom ◽  
Anders Virtanen
Keyword(s):  
Metal Ions ◽  
Active Site ◽  
Divalent Metal ◽  
Divalent Metal Ions

Hydrated metal ion as a general acid in the catalytic mechanism of the 8-17 DNAzyme

2021 ◽  
Author(s):  
Marjorie Cepeda Plaza ◽  
Francisca Rojas-Hernández ◽  
Romina Paillao-Bustos ◽  
Catalina Cortés-Guajardo
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Catalytic Mechanism ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
General Acid ◽  
Catalytic Dna

The RNA-cleaving 8-17 DNAzyme, which is a metalloenzyme that depends on divalent metal ions for function, is the most studied catalytic DNA in terms of its mechanism. By the end...

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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