An updated classification and mechanistic insights into ligand binding of the substrate‐binding proteins

Chandravanshi, Monika; Tripathi, Sisir Kant; Kanaujia, Shankar Prasad

doi:10.1002/1873-3468.14174

Cited by 18 publications

(18 citation statements)

References 59 publications

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“…Three‐dimensional structure prediction revealed that the structure of the protein SerBP (Figure 4b) was highly similar to that of the LAO (Figure 4c) and HisJ (Figure 4d), with RMSD being 0.630 and 0.784 Å, respectively. Both of the LAO and HisJ SBPs belonged to class F of ABC transporter [26]. This kind of SBP consists of two domains connected by two hinge regions of about 8–10 amino acids residues, with the ligand‐binding site buried in the gap between the two domains, and the ligand of this class F SBPs is usually amino acids [26].…”

Section: Resultsmentioning

confidence: 99%

“…Both of the LAO and HisJ SBPs belonged to class F of ABC transporter [26]. This kind of SBP consists of two domains connected by two hinge regions of about 8–10 amino acids residues, with the ligand‐binding site buried in the gap between the two domains, and the ligand of this class F SBPs is usually amino acids [26]. Therefore, we speculated that the protein encoded by the mutant gene might be an orphan SBP of the ABC transporter to transport a certain amino acid.…”

Section: Resultsmentioning

confidence: 99%

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A new l‐serine binding orphan SerBP affects indole synthesis in Pantoea ananatis

Zhang

Zheng

et al. 2023

J Basic Microbiol

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Indole is traditionally known as a metabolite of l‐tryptophan and now as an important signaling molecule in bacteria, however, the understanding of its upstream synthesis regulation is very limited. Pantoea ananatis YJ76, a predominant diazotrophic endophyte isolated from rice (Oryza sativa), can produce indole to regulate various physiological and biochemical behaviors. We constructed a mutant library of YJ76 using the mTn5 transposon insertion mutation method, from which an indole‐deficient mutant was screened out. Via high‐efficiency thermal asymmetric interlaced PCR (hiTAIL‐PCR), the transposon was determined to be inserted in a gene (RefSeq: WP014605468.1) of unknown function that is highly conserved at the intraspecific level. Bioinformatics analysis implied that the protein (Protein ID: WP089517194.1) encoded by the mutant gene is most likely to be a new orphan substrate‐binding protein (SBP) for amino acid ABC transporters. Amino acid supplement cultivation experiments and surface plasmon resonance revealed that the protein could bind to l‐serine (KD = 6.149 × 10−5 M). Therefore, the SBP was named as SerBP. This is the first case that a SBP responds to l‐serine ABC transports. As a precursor of indole synthesis, the transmembrane transported l‐serine was directly correlated with indole signal production and the mutation of serBP gene weakened the resistance of YJ76 to antibiotics, alkali, heavy metals, and starvation. This study provided a new paradigm for exploring the upstream regulatory pathway for indole synthesis of bacteria.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

A new l‐serine binding orphan SerBP affects indole synthesis in Pantoea ananatis

Zhang

Zheng

et al. 2023

J Basic Microbiol

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“…One group of proteins that have been used for this purpose are periplasmic binding proteins (PBPs). They are involved in the cellular transport of a wide variety of small molecules such as carbohydrates, amino acids, vitamins and ions (Chandravanshi et al, 2021;Felder et al, 1999). The structurally symmetric bilobal architecture of their fold has long been thought to originate from a duplication and fusion event of an individual lobe (Fukami-Kobayashi et al, 1999;Louie, 1993).…”

Section: Introductionmentioning

confidence: 99%

Structures of permuted halves of a modern ribose-binding protein

Michel

Shanmugaratnam

Romero‐Romero

et al. 2023

Acta Cryst Sect D Struct Biol

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Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular transport of various ligands. They have been used as model systems to study mechanisms in protein evolution, such as duplication, recombination and domain swapping. It has been suggested that PBPs evolved from precursors half their size. Here, the crystal structures of two permuted halves of a modern ribose-binding protein (RBP) from Thermotoga maritima are reported. The overexpressed proteins are well folded and show a monomer–dimer equilibrium in solution. Their crystal structures show partially noncanonical PBP-like fold type I conformations with structural deviations from modern RBPs. One of the half variants forms a dimer via segment swapping, suggesting a high degree of malleability. The structural findings on these permuted halves support the evolutionary hypothesis that PBPs arose via a duplication event of a flavodoxin-like protein and further support a domain-swapping step that might have occurred during the evolution of the PBP-like fold, a process that is necessary to generate the characteristic motion of PBPs essential to perform their functions.

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“…ABC transporters typically consist of a substrate binding protein (SBP), one or two hydrophobic membrane-spanning permeases, and one or two nucleotide-binding ATPases that supply the energy for active transport of the metal ion. SBPs are lipoproteins that localize to the membrane via the secretory (Sec) pathway in Gram-positive bacteria and are further organized into eight clusters, named A–H, based on protein structure and the binding dynamics that are outlined in Table 1 [ 8 , 9 , 10 ]. Typically, metal binds at the cleft between two conserved domains that are connected by an α-helical linker, which closes in most SBPs to bury the metal ion.…”

Section: Introductionmentioning

confidence: 99%

Metal Homeostasis in Pathogenic Streptococci

2022

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Streptococcus spp. are an important genus of Gram-positive bacteria, many of which are opportunistic pathogens that are capable of causing invasive disease in a wide range of populations. Metals, especially transition metal ions, are an essential nutrient for all organisms. Therefore, to survive across dynamic host environments, Streptococci have evolved complex systems to withstand metal stress and maintain metal homeostasis, especially during colonization and infection. There are many different types of transport systems that are used by bacteria to import or export metals that can be highly specific or promiscuous. Focusing on the most well studied transition metals of zinc, manganese, iron, nickel, and copper, this review aims to summarize the current knowledge of metal homeostasis in pathogenic Streptococci, and their role in virulence.

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An updated classification and mechanistic insights into ligand binding of the substrate‐binding proteins

Cited by 18 publications

References 59 publications

A new l‐serine binding orphan SerBP affects indole synthesis in Pantoea ananatis

A new l‐serine binding orphan SerBP affects indole synthesis in Pantoea ananatis

Structures of permuted halves of a modern ribose-binding protein

Metal Homeostasis in Pathogenic Streptococci

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