Contribution of the Active Site Histidine Residues of Ribonuclease A to Nucleic Acid Binding†

Biochemistry ◽  
2001 ◽  
Vol 40 (16) ◽  
pp. 4949-4956 ◽  
Author(s):  
Chiwook Park ◽  
L. Wayne Schultz ◽  
Ronald T. Raines
Keyword(s):  
Nucleic Acid ◽  
Active Site ◽  
Ribonuclease A ◽  
Nucleic Acid Binding ◽  
Histidine Residues ◽  
Active Site Histidine

scholarly journals The dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae contains two active-site histidine residues

2008 ◽  
Vol 14 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Danuta M. Gillner ◽  
David L. Bienvenue ◽  
Boguslaw P. Nocek ◽  
Andrzej Joachimiak ◽  
Vincentos Zachary ◽  
...  
Keyword(s):  
Haemophilus Influenzae ◽  
Active Site ◽  
Diaminopimelic Acid ◽  
Histidine Residues ◽  
Active Site Histidine

scholarly journals SAMHD1 is a single-stranded nucleic acid binding protein with no active site-associated nuclease activity

2015 ◽  
Vol 43 (13) ◽  
pp. 6486-6499 ◽  
Author(s):  
Kyle J. Seamon ◽  
Zhiqiang Sun ◽  
Luda S. Shlyakhtenko ◽  
Yuri L. Lyubchenko ◽  
James T. Stivers
Keyword(s):  
Nucleic Acid ◽  
Active Site ◽  
Binding Protein ◽  
Nuclease Activity ◽  
Nucleic Acid Binding ◽  
Nucleic Acid Binding Protein ◽  
Acid Binding Protein

scholarly journals Identification of Active-Site Histidine Residues of a Self-Incompatibility Ribonuclease from a Wild Tomato

1997 ◽  
Vol 115 (4) ◽  
pp. 1421-1429 ◽  
Author(s):  
S. Parry ◽  
E. Newbigin ◽  
G. Currie ◽  
A. Bacic ◽  
D. Oxley
Keyword(s):  
Active Site ◽  
Self Incompatibility ◽  
Histidine Residues ◽  
Wild Tomato ◽  
Active Site Histidine

scholarly journals Malate dehydrogenase of the cytosol. Ionizations of the enzyme-reduced-coenzyme complex and a comparison with lactate dehydrogenase

1978 ◽  
Vol 173 (2) ◽  
pp. 597-605 ◽  
Author(s):  
A Lodola ◽  
D M Parker ◽  
R Jeck ◽  
J J Holbrook
Keyword(s):  
Lactate Dehydrogenase ◽  
Malate Dehydrogenase ◽  
Active Site ◽  
Histidine Residue ◽  
Histidine Residues ◽  
Coenzyme Binding ◽  
Active Site Histidine

1. The pH-dependencies of the binding of NADH and reduced nicotinamide–benzimidazole dinucleotide to pig heart cytoplasmic malate dehydrogenase and lactate dehydrogenase are reported. 2. Two ionizing groups were observed in the binding of both reduced coenzymes to lactate dehydrogenase. One group, with pKa in the range 6.3–6.7, is the active-site histidine residue and its deprotonation weakens binding of reduced coenzyme 3-fold. Binding of both coenzymes is decreased to zero when a second group, of pKa 8.9, deprotonates. This group is not cysteine-165.3. Only one ionization is required to characterize the binding of the two reduced coenzymes to malate dehydrogenase. The group involved appears to be the active-site histidine residue, since its ethoxycarbonylation inhibits the enzyme and abolishes binding of reduced coenzyme. Binding of either reduced coenzyme increases the pKa of the group from 6.4 to 7.4, and deprotonation of the group is accompanied by a 10-fold weakening of coenzyme binding. 4. Two reactive histidine residues were detected per malate dehydrogenase dimer. 5. A mechanism which emphasizes the homology between the two enzymes is presented.

Inhibitor Binding Modulates Protonation States in the Active Site of SARS-CoV-2 Main Protease

2021 ◽  
Author(s):  
Daniel W. Kneller ◽  
Gwyndalyn Phillips ◽  
Kevin L. Weiss ◽  
Qiu Zhang ◽  
Leighton Coates ◽  
...  
Keyword(s):  
Active Site ◽  
Rational Drug Design ◽  
Inhibitor Binding ◽  
Histidine Residues ◽  
Main Protease ◽  
Rational Drug ◽  
Ligand Free ◽  
Essential Enzyme ◽  
Neutron Protein Crystallography ◽  
Active Site Histidine

ABSTRACTThe main protease (3CL Mpro) from SARS-CoV-2, the virus that causes COVID-19, is an essential enzyme for viral replication with no human counterpart, making it an attractive drug target. Although drugs have been developed to inhibit the proteases from HIV, hepatitis C and other viruses, no such therapeutic is available to inhibit the main protease of SARS-CoV-2. To directly observe the protonation states in SARS-CoV-2 Mpro and to elucidate their importance in inhibitor binding, we determined the structure of the enzyme in complex with the α-ketoamide inhibitor telaprevir using neutron protein crystallography at near-physiological temperature. We compared protonation states in the inhibitor complex with those determined for a ligand-free neutron structure of Mpro. This comparison revealed that three active-site histidine residues (His41, His163 and His164) adapt to ligand binding, altering their protonation states to accommodate binding of telaprevir. We suggest that binding of other α-ketoamide inhibitors can lead to the same protonation state changes of the active site histidine residues. Thus, by studying the role of active site protonation changes induced by inhibitors we provide crucial insights to help guide rational drug design, allowing precise tailoring of inhibitors to manipulate the electrostatic environment of SARS-CoV-2 Mpro.

Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

1992 ◽  
Vol 50 (1) ◽  
pp. 762-763
Author(s):  
Stephen D. Jett
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Carbon Coated ◽  
Nucleoprotein Complexes ◽  
Mobility Shift Assay ◽  
Protein Nucleic Acid ◽  
Gel Mobility Shift ◽  
Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

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