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Structure of Bacterial Proteins

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Molecular Structure".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 7075

Special Issue Editor

Special Issue Information

Dear Colleagues,

Bacteria and Archaea, collectively called Prokaryotes, are the most abundant and diverse living organisms of our planet. The most studied species among them are those that are pathogenic for humans, animals or plants, but many others exist and the majority of them have probably not yet been classified. A prokaryotic cell is structurally and functionally much simpler than an eukaryotic one and, in this sense, bacterial or archaeal proteins, easier to obtain in relatively large amount and sometimes to manipulate, have been very often used as models for studying biochemical or biological processes. The knowledge of the 3D structure of bacterial proteins is fundamental, since they can be relevant for human health or may find important biotechnological applications in industrial processes. A searching in the Protein Data Bank, the data base that gathers the coordinates of all the 3D structures published, gives a total of 41392 Bacterial and 3634 Archaeal structures, corresponding to about 25% of the total number of the structures present in the data base. They seem huge numbers, nevertheless it must be considered that they do not identify unique molecules, but the number of different files, part of them corresponding to the same macromolecule in complex with different ligands, or mutants of the same protein, and from them it is hard to estimate the real level of our comprehension of the prokaryotic world at the structural level. This is particularly relevant in view of one of the biggest threats to global health, the antibiotic resistance: in fact, the disegn of new drugs is strongly accelerated if the 3D structure of the target protein is available. The objective of this topical issue in Molecules is to gather papers about the structural aspects of prokaryotic proteins, with the aim of summarizing the state of the art of the field. Ideally, we would like to receive reviews focused about specific classes of bacterial or archaeal proteins, or about the structural studies of a specific prokaryotic organism, or papers that analyze these structures. Also papers describing new structures or new aspects of the structure of prokaryotic proteins are welcome.

Prof. Dr. Giuseppe Zanotti
Guest Editor

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Keywords

  • Prokaryotes
  • Bacteria
  • Archaea
  • 3D structure
  • X-ray diffraction
  • CryoEM
  • NMR

Published Papers (4 papers)

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Research

13 pages, 2172 KiB  
Article
Copper Binding and Oligomerization Studies of the Metal Resistance Determinant CrdA from Helicobacter pylori
Molecules 2022, 27(11), 3387; https://doi.org/10.3390/molecules27113387 - 24 May 2022
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Abstract
Within this research, the CrdA protein from Helicobacter pylori (HpCrdA), a putative copper-binding protein important for the survival of bacterium, was biophysically characterized in a solution, and its binding affinity toward copper was experimentally determined. Incubation of HpCrdA with Cu(II) [...] Read more.
Within this research, the CrdA protein from Helicobacter pylori (HpCrdA), a putative copper-binding protein important for the survival of bacterium, was biophysically characterized in a solution, and its binding affinity toward copper was experimentally determined. Incubation of HpCrdA with Cu(II) ions favors the formation of the monomeric species in the solution. The modeled HpCrdA structure shows a conserved methionine-rich region, a potential binding site for Cu(I), as in the structures of similar copper-binding proteins, CopC and PcoC, from Pseudomonas syringae and from Escherichia coli, respectively. Within the conserved amino acid motif, HpCrdA contains two additional methionines and two glutamic acid residues (MMXEMPGMXXMXEM) in comparison to CopC and PcoC but lacks the canonical Cu(II) binding site (two His) since the sequence has no His residues. The methionine-rich site is in a flexible loop and can adopt different geometries for the two copper oxidation states. It could bind copper in both oxidation states (I and II), but with different binding affinities, micromolar was found for Cu(II), and less than nanomolar is proposed for Cu(I). Considering that CrdA is a periplasmic protein involved in chaperoning copper export and delivery in the H. pylori cell and that the affinity of the interaction corresponds to a middle or strong metal–protein interaction depending on the copper oxidation state, we conclude that the interaction also occurs in vivo and is physiologically relevant for H. pylori. Full article
(This article belongs to the Special Issue Structure of Bacterial Proteins)
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12 pages, 2454 KiB  
Communication
Unique Properties of Heme Binding of the Porphyromonas gingivalis HmuY Hemophore-like Protein Result from the Evolutionary Adaptation of the Protein Structure
Molecules 2022, 27(5), 1703; https://doi.org/10.3390/molecules27051703 - 05 Mar 2022
Cited by 4 | Viewed by 1737
Abstract
To acquire heme, Porphyromonas gingivalis uses a hemophore-like protein (HmuY). HmuY sequesters heme from host hemoproteins or heme-binding proteins produced by cohabiting bacteria, and delivers it to the TonB-dependent outer-membrane receptor (HmuR). Although three-dimensional protein structures of members of the novel HmuY family [...] Read more.
To acquire heme, Porphyromonas gingivalis uses a hemophore-like protein (HmuY). HmuY sequesters heme from host hemoproteins or heme-binding proteins produced by cohabiting bacteria, and delivers it to the TonB-dependent outer-membrane receptor (HmuR). Although three-dimensional protein structures of members of the novel HmuY family are overall similar, significant differences exist in their heme-binding pockets. Histidines (H134 and H166) coordinating the heme iron in P. gingivalis HmuY are unique and poorly conserved in the majority of its homologs, which utilize methionines. To examine whether changes observed in the evolution of these proteins in the Bacteroidetes phylum might result in improved heme binding ability of HmuY over its homologs, we substituted histidine residues with methionine residues. Compared to the native HmuY, site-directed mutagenesis variants bound Fe(III)heme with lower ability in a similar manner to Bacteroides vulgatus Bvu and Tannerella forsythia Tfo. However, a mixed histidine-methionine couple in the HmuY was sufficient to bind Fe(II)heme, similarly to T. forsythia Tfo, Prevotella intermedia PinO and PinA. Double substitution resulted in abolished heme binding. The structure of HmuY heme-binding pocket may have been subjected to evolution, allowing for P. gingivalis to gain an advantage in heme acquisition regardless of environmental redox conditions. Full article
(This article belongs to the Special Issue Structure of Bacterial Proteins)
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17 pages, 5132 KiB  
Article
Structural Analysis of Saccharomyces cerevisiae Dihydroorotase Reveals Molecular Insights into the Tetramerization Mechanism
Molecules 2021, 26(23), 7249; https://doi.org/10.3390/molecules26237249 - 29 Nov 2021
Cited by 7 | Viewed by 1386
Abstract
Dihydroorotase (DHOase), a dimetalloenzyme containing a carbamylated lysine within the active site, is a member of the cyclic amidohydrolase family, which also includes allantoinase (ALLase), dihydropyrimidinase (DHPase), hydantoinase, and imidase. Unlike most known cyclic amidohydrolases, which are tetrameric, DHOase exists as a monomer [...] Read more.
Dihydroorotase (DHOase), a dimetalloenzyme containing a carbamylated lysine within the active site, is a member of the cyclic amidohydrolase family, which also includes allantoinase (ALLase), dihydropyrimidinase (DHPase), hydantoinase, and imidase. Unlike most known cyclic amidohydrolases, which are tetrameric, DHOase exists as a monomer or dimer. Here, we report and analyze two crystal structures of the eukaryotic Saccharomyces cerevisiae DHOase (ScDHOase) complexed with malate. The structures of different DHOases were also compared. An asymmetric unit of these crystals contained four crystallographically independent ScDHOase monomers. ScDHOase shares structural similarity with Escherichia coli DHOase (EcDHOase). Unlike EcDHOase, ScDHOase can form tetramers, both in the crystalline state and in solution. In addition, the subunit-interacting residues of ScDHOase for dimerization and tetramerization are significantly different from those of other DHOases. The tetramerization pattern of ScDHOase is also different from those of DHPase and ALLase. Based on sequence analysis and structural evidence, we identify two unique helices (α6 and α10) and a loop (loop 7) for tetramerization, and discuss why the residues for tetramerization in ScDHOase are not necessarily conserved among DHOases. Full article
(This article belongs to the Special Issue Structure of Bacterial Proteins)
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14 pages, 52804 KiB  
Article
Structural Investigations on the SH3b Domains of Clostridium perfringens Autolysin through NMR Spectroscopy and Structure Simulation Enlighten the Cell Wall Binding Function
Molecules 2021, 26(18), 5716; https://doi.org/10.3390/molecules26185716 - 21 Sep 2021
Cited by 3 | Viewed by 1718
Abstract
Clostridium perfringens autolysin (CpAcp) is a peptidoglycan hydrolase associated with cell separation, division, and growth. It consists of a signal peptide, ten SH3b domains, and a catalytic domain. The structure and function mechanisms of the ten SH3bs related to cell wall peptidoglycan binding [...] Read more.
Clostridium perfringens autolysin (CpAcp) is a peptidoglycan hydrolase associated with cell separation, division, and growth. It consists of a signal peptide, ten SH3b domains, and a catalytic domain. The structure and function mechanisms of the ten SH3bs related to cell wall peptidoglycan binding remain unclear. Here, the structures of CpAcp SH3bs were studied through NMR spectroscopy and structural simulation. The NMR structure of SH3b6 was determined at first, which adopts a typical β-barrel fold and has three potential ligand-binding pockets. The largest pocket containing eight conserved residues was suggested to bind with peptide ligand in a novel model. The structures of the other nine SH3bs were subsequently predicted to have a fold similar to SH3b6. Their ligand pockets are largely similar to those of SH3b6, although with varied size and morphology, except that SH3b1/2 display a third pocket markedly different from those in other SH3bs. Thus, it was supposed that SH3b3-10 possess similar ligand-binding ability, while SH3b1/2 have a different specificity and additional binding site for ligand. As an entirety, ten SH3bs confer a capacity for alternatively binding to various peptidoglycan sites in the cell wall. This study presents an initial insight into the structure and potential function of CpAcp SH3bs. Full article
(This article belongs to the Special Issue Structure of Bacterial Proteins)
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