Secondary Structure Preferences of Mn<sup><b>2+</b></sup> Binding Sites in Bacterial Proteins

Khrustaleva, Tatyana Aleksandrovna

doi:10.1155/2014/501841

Cited by 9 publications

(7 citation statements)

References 24 publications

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“…A closer look at the C′ side chain region displaying mainly Glu Cδ and Asp Cγ resonances reveals that most corresponding signals are significantly attenuated. As Asp and Glu are good binders of Mn 2+ , this is likely to be due to the surplus Mn 2+ interacting with the negatively charged side chains of these residues (see also Figure S15a). In line with this result, the Glu Cγ/Cδ cross signal is attenuated by about 80 % (Figure S15b).…”

Section: Figurementioning

confidence: 99%

Solid‐state NMR and EPR Spectroscopy of Mn²⁺‐Substituted ATP‐Fueled Protein Engines

et al. 2017

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Paramagnetic metal ions deliver structural information both in EPR and solid-state NMR experiments, offering a profitable synergetic approach to study bio-macromolecules. We demonstrate the spectral consequences of Mg / Mn substitution and the resulting information contents for two different ATP:Mg -fueled protein engines, a DnaB helicase from Helicobacter pylori active in the bacterial replisome, and the ABC transporter BmrA, a bacterial efflux pump. We show that, while EPR spectra report on metal binding and provide information on the geometry of the metal centers in the proteins, paramagnetic relaxation enhancements identified in the NMR spectra can be used to localize residues at the binding site. Protein engines are ubiquitous and the methods described herein should be applicable in a broad context.

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Section: Figurementioning

confidence: 99%

Solid‐state NMR and EPR Spectroscopy of Mn²⁺‐Substituted ATP‐Fueled Protein Engines

et al. 2017

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“…So one may speculate that interactions with ligand cause the destruction of 3/10 helices. Some other similar cases have been described for apo- and holo-forms of proteins coordinating Mn 2+ ions [ 21 ]. Of course, ion binding is just one of the multiple causes of 3/10 helices disappearing.…”

Section: Resultsmentioning

confidence: 78%

“…Functional groups able to bind ligands (including ions) should be already connected by hydrogen bonds (“side chain-side chain” or “side chain-main chain” ones) or involved in polar interactions with other amino acids more frequently if they are included in 3/10 helices than if they are situated in pure random coil [ 28 ]. On one hand, amino acids from 3/10 helices should bind ligands less effectively than those from coil (as they actually do [ 21 ]). On the other hand, 3/10 helices may sometimes disappear after the binding of ion or other ligand due to the destruction of functional group interactions stabilizing those 3/10 helices.…”

Section: Discussionmentioning

confidence: 99%

The Influence of Flanking Secondary Structures on Amino Acid Content and Typical Lengths of 3/10 Helices

Khrustalev

Barkovsky

Khrustaleva

2014

International Journal of Proteomics

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We used 3D structures of a highly redundant set of bacterial proteins encoded by genes of high, average, and low GC-content. Four types of connecting bridges—regions situated between any of two major elements of secondary structure (alpha helices and beta strands)—containing a pure random coil were compared with connecting bridges containing 3/10 helices. We included discovered trends in the original “VVTAK Connecting Bridges” algorithm, which is able to predict more probable conformation for a given connecting bridge. The highest number of significant differences in amino acid usage was found between 3/10 helices containing bridges connecting two beta strands (they have increased Phe, Tyr, Met, Ile, Leu, Val, and His usages but decreased usages of Asp, Asn, Gly, and Pro) and those without 3/10 helices. The typical (most common) length of 3/10 helices situated between two beta strands and between beta strand and alpha helix is equal to 5 amino acid residues. The preferred length of 3/10 helices situated between alpha helix and beta strand is equal to 3 residues. For 3/10 helices situated between two alpha helices, both lengths (3 and 5 amino acid residues) are typical.

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“…We suggest that in ALP the Mn 2+ interactions involve a new type of ligation between E190, N213, Q215, D217, E288, and K290 and the Mn 2+ ions; similar residue types interact with Mn 2+ ions in others proteins [38]. While aspartate is often found stabilizing binuclear metal centers, residues such as glutamate and asparagine can also play this role [35].…”

Section: Manganese Binding Site In Alpmentioning

confidence: 90%

Insights into the Mn2+ Binding Site in the Agmatinase-Like Protein (ALP): A Critical Enzyme for the Regulation of Agmatine Levels in Mammals

Reyes

Martínez‐Oyanedel

Navarrete

et al. 2020

IJMS

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Agmatine is a neurotransmitter with anticonvulsant, anti-neurotoxic and antidepressant-like effects, in addition it has hypoglycemic actions. Agmatine is converted to putrescine and urea by agmatinase (AGM) and by an agmatinase-like protein (ALP), a new type of enzyme which is present in human and rodent brain tissues. Recombinant rat brain ALP is the only mammalian protein that exhibits significant agmatinase activity in vitro and generates putrescine under in vivo conditions. ALP, despite differing in amino acid sequence from all members of the ureohydrolase family, is strictly dependent on Mn2+ for catalytic activity. However, the Mn2+ ligands have not yet been identified due to the lack of structural information coupled with the low sequence identity that ALPs display with known ureohydrolases. In this work, we generated a structural model of the Mn2+ binding site of the ALP and we propose new putative Mn2+ ligands. Then, we cloned and expressed a sequence of 210 amino acids, here called the “central-ALP”, which include the putative ligands of Mn2+. The results suggest that the central-ALP is catalytically active, as agmatinase, with an unaltered Km for agmatine and a decreased kcat. Similar to wild-type ALP, central-ALP is activated by Mn2+ with a similar affinity. Besides, a simple mutant D217A, a double mutant E288A/K290A, and a triple mutant N213A/Q215A/D217A of these putative Mn2+ ligands result on the loss of ALP agmatinase activity. Our results indicate that the central-ALP contains the active site for agmatine hydrolysis, as well as that the residues identified are relevant for the ALP catalysis.

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Secondary Structure Preferences of Mn²⁺ Binding Sites in Bacterial Proteins

Cited by 9 publications

References 24 publications

Solid‐state NMR and EPR Spectroscopy of Mn²⁺‐Substituted ATP‐Fueled Protein Engines

Solid‐state NMR and EPR Spectroscopy of Mn²⁺‐Substituted ATP‐Fueled Protein Engines

The Influence of Flanking Secondary Structures on Amino Acid Content and Typical Lengths of 3/10 Helices

Insights into the Mn2+ Binding Site in the Agmatinase-Like Protein (ALP): A Critical Enzyme for the Regulation of Agmatine Levels in Mammals

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Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

Cited by 9 publications

References 24 publications

Solid‐state NMR and EPR Spectroscopy of Mn2+‐Substituted ATP‐Fueled Protein Engines

Solid‐state NMR and EPR Spectroscopy of Mn2+‐Substituted ATP‐Fueled Protein Engines

The Influence of Flanking Secondary Structures on Amino Acid Content and Typical Lengths of 3/10 Helices

Insights into the Mn2+ Binding Site in the Agmatinase-Like Protein (ALP): A Critical Enzyme for the Regulation of Agmatine Levels in Mammals

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Secondary Structure Preferences of Mn²⁺ Binding Sites in Bacterial Proteins

Solid‐state NMR and EPR Spectroscopy of Mn²⁺‐Substituted ATP‐Fueled Protein Engines

Solid‐state NMR and EPR Spectroscopy of Mn²⁺‐Substituted ATP‐Fueled Protein Engines