Analysis of nucleotide diphosphate sugar dehydrogenases reveals family and group‐specific relationships

Freas, Nicholas; Newton, Peter W.; Perozich, John

doi:10.1002/2211-5463.12022

Cited by 5 publications

(10 citation statements)

References 54 publications

(107 reference statements)

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“…thermophilus LACS. A high proportion of the conserved residues were glycines, a phenomenon seen in several other enzyme families [38, 65–68]. These conserved residues are responsible for structural and functional aspects common to all superfamily members, such as magnesium and ATP binding, and hydrophobic packing.…”

Section: Discussionmentioning

confidence: 99%

In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations

et al. 2018

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Luciferases, aryl- and fatty-acyl CoA synthetases, and non-ribosomal peptide synthetase proteins belong to the class I adenylate-forming enzyme superfamily. The reaction catalyzed by the adenylate-forming enzymes is categorized by a two-step process of adenylation and thioesterification. Although all of these proteins perform a similar two-step process, each family may perform the process to yield completely different results. For example, luciferase proteins perform adenylation and oxidation to produce the green fluorescent light found in fireflies, while fatty-acyl CoA synthetases perform adenylation and thioesterification with coenzyme A to assist in metabolic processes involving fatty acids. This study aligned a total of 374 sequences belonging to the adenylate-forming superfamily. Analysis of the sequences revealed five fully conserved residues throughout all sequences, as well as 78 more residues conserved in at least 60% of sequences aligned. Conserved positions are involved in magnesium and AMP binding and maintaining enzyme structure. Also, ten conserved sequence motifs that included most of the conserved residues were identified. A phylogenetic tree was used to assign sequences into nine different groups. Finally, group entropy analysis identified novel conservations unique to each enzyme group. Common group-specific positions identified in multiple groups include positions critical to coordinating AMP and the CoA-bound product, a position that governs active site shape, and positions that help to maintain enzyme structure through hydrogen bonds and hydrophobic interactions. These positions could serve as excellent targets for future research.

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Section: Discussionmentioning

confidence: 99%

In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations

et al. 2018

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“…The procedure used here was similar to that previously published [34]. The project began by downloading the amino acid sequences and tertiary structures of human HO1 (PDB IDs: 1NI6 & 1N45), human HO2 (PDB ID: 2RGZ), TenA from P. furiosus (PDB ID: 1RTW), Treg from Streptococcus pneumoniae (PDB ID: 1UDD), TenA from B. subtilis (PDB ID: 2QCX), HO-like domain from Shewanella denitrificans (PDB ID: 3DDE), THI20 from Sac.…”

Section: Methodsmentioning

confidence: 99%

“…This residue is found in the turn between a-1 and a-2 [30]. Conserved glycines are often found in turns in enzyme structures or at positions where a side chain would lead to steric conflicts in many enzyme families [31][32][33][34]. Phe47{173} is 71% conserved overall and is found in RNR1As, most thiaminases, and HOs except plant species.…”

Section: Structure and Residue Conservationsmentioning

confidence: 99%

“…5) was generated from the entire amino acid sequence alignment. This neighbor-joining method was chosen because it has been shown to yield excellent evolutionary relationships in some families [34,39]. Maximum-likelihood and parsimony methods require excessive computations for large data sets.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

“…Also, GEnt does not consider positions with gaps [40]. The GEnt program has been used to identify group-specific conservations in Class 3 aldehyde dehydrogenases [40] and NDPsugar dehydrogenases [34]. Eight residues were found to have the highest Group Entropy scores in the HO group (Table 2, complete GEnt results can be found in Table S1).…”

Section: Group Entropy Analysis Of Hosmentioning

confidence: 99%

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In silico analysis of heme oxygenase structural homologues identifies group‐specific conservations

2017

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Heme oxygenases (HO) catalyze the breakdown of heme, aiding the recycling of its components. Several other enzymes have homologous tertiary structures to HOs, while sharing little sequence homology. These homologues include thiaminases, the hydroxylase component of methane monooxygenases, and the R2 component of Class I ribonucleotide reductases (RNR). This study compared these structural homologues of HO, using a large number of protein sequences for each homologue. Alignment of a total of 472 sequences showed little sequence conservation, with no residues having conservation in more than 80% of aligned sequences and only five residues conserved in at least 60% of the sequences. Fourteen additional positions, most of which were critical for hydrophobic packing, displayed amino acid similarity of 60% or higher. Ten conserved sequence motifs were identified in HOs and RNRs. Phylogenetic analysis verified the existence of the four distinct groups of HO homologues, which were then analyzed by group entropy analysis to identify residues critical to the unique function of each enzyme. Other methods for determining functional residues were also performed. Several common index positions identified represent critical evolutionary changes that resulted in the unique function of each enzyme, suggesting potential targets for site‐directed mutagenesis. These positions included residues that coordinate ligands, form the active sites, and maintain enzyme structure. Enzymes Heme oxygenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/14/18.html), methane monooxygenase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/13/25.html), ribonucleotide reductase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/17/4/1.html), thiaminase II (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/5/99/2.html).

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From an extremophilic community to an electroautotrophic production strain: identifying a novel Knallgas bacterium as cathodic biofilm biocatalyst

et al. 2020

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Coupling microbial electrosynthesis to renewable energy sources can provide a promising future technology for carbon dioxide conversion. However, this technology suffers from a limited number of suitable biocatalysts, resulting in a narrow product range. Here, we present the characterization of the first thermoacidophilic electroautotrophic community using chronoamperometric, metagenomic, and 13C-labeling analyses. The cathodic biofilm showed current consumption of up to −80 µA cm−2 over a period of 90 days (−350 mV vs. SHE). Metagenomic analyses identified members of the genera Moorella, Desulfofundulus, Thermodesulfitimonas, Sulfolobus, and Acidianus as potential primary producers of the biofilm, potentially thriving via an interspecies sulfur cycle. Hydrogenases seem to be key for cathodic electron uptake. An isolation campaign led to a pure culture of a Knallgas bacterium from this community. Growth of this organism on cathodes led to increasing reductive currents over time. Transcriptomic analyses revealed a distinct gene expression profile of cells grown at a cathode. Moreover, pressurizable flow cells combined with optical coherence tomography allowed an in situ observation of cathodic biofilm growth. Autotrophic growth was confirmed via isotope analysis. As a natural polyhydroxybutyrate (PHB) producer, this novel species, Kyrpidia spormannii, coupled the production of PHB to CO2 fixation on cathode surfaces.

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Analysis of nucleotide diphosphate sugar dehydrogenases reveals family and group‐specific relationships

Cited by 5 publications

References 54 publications

In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations

In silico analysis of class I adenylate-forming enzymes reveals family and group-specific conservations

In silico analysis of heme oxygenase structural homologues identifies group‐specific conservations

From an extremophilic community to an electroautotrophic production strain: identifying a novel Knallgas bacterium as cathodic biofilm biocatalyst

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