Fixation of atmospheric carbon dioxide by a series of hydroxo complexes of divalent metal ions and the implication for the catalytic role of metal ion in carbonic anhydrase. Synthesis, characterization, and molecular structure of [LM(OH)]n (n = 1 or 2) and LM(.mu.-CO3)ML (M(II) = Mn, Fe, Co, Ni, Cu, Zn; L = HB(3,5-iso-Pr2pz)3)

ABSTRACT The last gene in the genome of the bacteriophage HK97 encodes gp74, an HNH endonuclease. HNH motifs contain two conserved His residues and an invariant Asn residue, and they adopt a ββα structure. gp74 is essential for phage head morphogenesis, likely because gp74 enhances the specific endonuclease activity of the HK97 terminase complex. Notably, the ability of gp74 to enhance the terminase-mediated cleavage of the phage cos site requires an intact HNH motif in gp74. Mutation of H82, the conserved metal-binding His residue in the HNH motif, to Ala abrogates gp74-mediated stimulation of terminase activity. Here, we present nuclear magnetic resonance (NMR) studies demonstrating that gp74 contains an α-helical insertion in the Ω-loop, which connects the two β-strands of the ββα fold, and a disordered C-terminal tail. NMR data indicate that the Ω-loop insert makes contacts to the ββα fold and influences the ability of gp74 to bind divalent metal ions. Further, the Ω-loop insert and C-terminal tail contribute to gp74-mediated DNA digestion and to gp74 activity in phage morphogenesis. The data presented here enrich our molecular-level understanding of how HNH endonucleases enhance terminase-mediated digestion of the cos site and contribute to the phage replication cycle. IMPORTANCE This study demonstrates that residues outside the canonical ββα fold, namely, the Ω-loop α-helical insert and a disordered C-terminal tail, regulate the activity of the HNH endonuclease gp74. The increased divalent metal ion binding when the Ω-loop insert is removed compared to reduced cos site digestion and phage formation indicates that the Ω-loop insert plays multiple regulatory roles. The data presented here provide insights into the molecular basis of the involvement of HNH proteins in phage DNA packing.

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Elucidating the role of metal ions in carbonic anhydrase catalysis

Nature Communications ◽

10.1038/s41467-020-18425-5 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 1

Author(s):

Jin Kyun Kim ◽

Cheol Lee ◽

Seon Woo Lim ◽

Aniruddha Adhikari ◽

Jacob T. Andring ◽

...

Keyword(s):

Carbonic Anhydrase ◽

Metal Ions ◽

Metal Ion ◽

Catalytic Mechanism ◽

Chemical Properties ◽

Water Network ◽

Native Metal ◽

Trigonal Bipyramidal ◽

Electrostatic Effect

Abstract Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the catalytic roles of metal ions in a model metalloenzyme system, human carbonic anhydrase II (CA II). Through a comparative study on the intermediate states of the zinc-bound native CA II and non-native metal-substituted CA IIs, we demonstrate that the characteristic metal ion coordination geometries (tetrahedral for Zn2+, tetrahedral to octahedral conversion for Co2+, octahedral for Ni2+, and trigonal bipyramidal for Cu2+) directly modulate the catalytic efficacy. In addition, we reveal that the metal ions have a long-range (~10 Å) electrostatic effect on restructuring water network in the active site. Our study provides evidence that the metal ions in metalloenzymes have a crucial impact on the catalytic mechanism beyond their primary chemical properties.

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Identification of Molecular Fluorophore as a Component of Carbon Dots able to Induce Gelation in a Fluorescent Multivalent-Metal-Ion-Free Alginate Hydrogel

Scientific Reports ◽

10.1038/s41598-019-51512-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Peter Kasak ◽

Martin Danko ◽

Sifani Zavahir ◽

Miroslav Mrlik ◽

Yuan Xiong ◽

...

Keyword(s):

Optical Properties ◽

Carbon Dots ◽

Metal Ion ◽

Divalent Metal ◽

Simple Approach ◽

Sodium Ions ◽

Divalent Metal Ions ◽

Alginate Hydrogel ◽

Carboxylic Acid Groups ◽

Multivalent Metal

Abstract We introduce a simple approach to fabricate fluorescent multivalent metal ion-free alginate hydrogels, which can be produced using carbon dots accessible from natural sources (citric acid and L-cysteine). Molecular fluorophore 5-oxo-2,3-dihydro-5H-[1,3]-thiazolo[3,2-a] pyridine-3,7-dicarboxylic acid (TPDCA), which is formed during the synthesis of carbon dots, is identified as a key segment for the crosslinking of hydrogels. The crosslinking happens through dynamic complexation of carboxylic acid groups of TPDCA and alginate cages along with sodium ions. The TPDCA derived hydrogels are investigated regarding to their thermal, rheological and optical properties, and found to exhibit characteristic fluorescence of this aggregated molecular fluorophore. Moreover, gradient hydrogels with tunable mechanical and optical properties and controlled release are obtained upon immersion of the hydrogel reactors in solutions of divalent metal ions (Ca2+, Cu2+, and Ni2+) with a higher affinity to alginate.

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