Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments

Bacterial microcompartments are large supramolecular structures comprising an outer proteinaceous shell that encapsulates various enzymes in order to optimize metabolic processes. The outer shells of bacterial microcompartments are made of several thousand protein subunits, generally forming hexameric building blocks based on the canonical bacterial microcompartment (BMC) domain. Among the diverse metabolic types of bacterial microcompartments, the structures of those that use glycyl radical enzymes to metabolize choline have not been adequately characterized. Here, six structures of hexameric shell proteins from type I and type II choline-utilization microcompartments are reported. Sequence and structure analysis reveals electrostatic surface properties that are shared between the four types of shell proteins described here.

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MCPdb: The bacterial microcompartment database

PLoS ONE ◽

10.1371/journal.pone.0248269 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0248269

Author(s):

Jessica M. Ochoa ◽

Kaylie Bair ◽

Thomas Holton ◽

Thomas A. Bobik ◽

Todd O. Yeates

Keyword(s):

Tertiary Structure ◽

Protein Structures ◽

Structural Features ◽

Protein Subunits ◽

The Public ◽

Bacterial Microcompartments ◽

Bacterial Microcompartment ◽

Metabolic Functions ◽

Shell Proteins ◽

Metabolic Reactions

Bacterial microcompartments are organelle-like structures composed entirely of proteins. They have evolved to carry out several distinct and specialized metabolic functions in a wide variety of bacteria. Their outer shell is constructed from thousands of tessellating protein subunits, encapsulating enzymes that carry out the internal metabolic reactions. The shell proteins are varied, with single, tandem and permuted versions of the PF00936 protein family domain comprising the primary structural component of their polyhedral architecture, which is reminiscent of a viral capsid. While considerable amounts of structural and biophysical data have been generated in the last 15 years, the existing functionalities of current resources have limited our ability to rapidly understand the functional and structural properties of microcompartments (MCPs) and their diversity. In order to make the remarkable structural features of bacterial microcompartments accessible to a broad community of scientists and non-specialists, we developed MCPdb: The Bacterial Microcompartment Database (https://mcpdb.mbi.ucla.edu/). MCPdb is a comprehensive resource that categorizes and organizes known microcompartment protein structures and their larger assemblies. To emphasize the critical roles symmetric assembly and architecture play in microcompartment function, each structure in the MCPdb is validated and annotated with respect to: (1) its predicted natural assembly state (2) tertiary structure and topology and (3) the metabolic compartment type from which it derives. The current database includes 163 structures and is available to the public with the anticipation that it will serve as a growing resource for scientists interested in understanding protein-based metabolic organelles in bacteria.

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Evaluation of an enzyme immunoassay kit for estrogen receptor measurement--report II.

Clinical Chemistry ◽

10.1093/clinchem/34.10.2053 ◽

1988 ◽

Vol 34 (10) ◽

pp. 2053-2057 ◽

Cited By ~ 2

Author(s):

S Raam ◽

D M Vrabel

Keyword(s):

Enzyme Immunoassay ◽

Binding Sites ◽

Solid Phase ◽

Functional Characterization ◽

Quantitative Agreement ◽

Type I ◽

Type Ii ◽

Immunoreactive Protein ◽

Estrogen Binding

Abstract We present evidence to show that monoclonal antibodies to estrogen receptors (ER) in solid phase recognize the secondary estrogen binding sites with moderate to low affinity for estradiol (E2). An excellent quantitative agreement was found in five cytosols between the ER values obtained by the enzyme immunoassay (ER-EIA) and the amount of secondary estrogen binding sites measured by the assay involving dextran-coated charcoal (Clin Chem 1986;32:1496). The immunoreactive protein recognized by the antibody-coated beads, when allowed to react with ER(+) cytosols, is shown to bind [3H]estradiol only when the ligand concentration exceeds 8 nmol/L. Further biochemical and functional characterization of the immunoreactive protein is required to establish similarities/dissimilarities between this protein, high-affinity Type I ER sites, and the secondary sites such as Type II sites.

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Geochemical characterization of hydrocarbon source rocks of the Triassic-Jurassic time interval in the Mandawa basin, southern Tanzania: Implications for petroleum generation potential

South African Journal of Geology ◽

10.25131/sajg.123.0037 ◽

2020 ◽

Vol 123 (4) ◽

pp. 587-596

Author(s):

A. Emanuel ◽

C.H. Kasanzu ◽

M. Kagya

Keyword(s):

Source Rocks ◽

Geochemical Data ◽

Time Interval ◽

Type I ◽

Hydrocarbon Generation ◽

Type Ii ◽

Geochemical Characterization ◽

Type Iii ◽

Petroleum Generation

Abstract Triassic to mid-Jurassic core samples of the Mandawa basin, southern Tanzania (western coast of the Indian Ocean), were geochemically analyzed in order to constrain source rock potentials and petroleum generation prospects of different stratigraphic formations within the coastal basin complex. The samples were collected from the Mihambia, Mbuo and Nondwa Formations in the basin. Geochemical characterization of source rocks intersected in exploration wells drilled between 503 to 4042 m below surface yielded highly variable organic matter contents (TOC) rated between fair and very good potential source rocks (0.5 to 8.7 wt%; mean ca. 2.3 wt%). Based on bulk geochemical data obtained in this study, the Mandawa source rocks are mainly Type I, Type II, Type III, mixed Types II/III and Type IV kerogens, with a predominance of Type II, Type III and mixed Type II/III. Based on pyrolysis data (Tmax 417 to 473oC; PI = 0.02 to 0.47; highly variable HI = 13 to 1 000 mg/gTOC; OI = 16 to 225 mg/g; and VR values of between 0.24 to 0.95% Ro) we suggest that the Triassic Mbuo Formation and possibly the mid-Jurassic Mihambia Formation have a higher potential for hydrocarbon generation than the Nondwa Formation as they are relatively thermally mature.

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Characterization of type I and type II diacylglycerol acyltransferases from the emerging model alga Chlorella zofingiensis reveals their functional complementarity and engineering potential

Biotechnology for Biofuels ◽

10.1186/s13068-019-1366-2 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 17

Author(s):

Xuemei Mao ◽

Tao Wu ◽

Yaping Kou ◽

Ying Shi ◽

Yu Zhang ◽

...

Keyword(s):

Type I ◽

Type Ii ◽

Chlorella Zofingiensis ◽

Functional Complementarity

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Redox Characterization of Electrode-Immobilized Bacterial Microcompartment Shell Proteins Engineered To Bind Metal Centers

ACS Applied Bio Materials ◽

10.1021/acsabm.9b01023 ◽

2019 ◽

Vol 3 (1) ◽

pp. 685-692 ◽

Cited By ~ 3

Author(s):

Jefferson S. Plegaria ◽

Matthew D. Yates ◽

Sarah M. Glaven ◽

Cheryl A. Kerfeld

Keyword(s):

Metal Centers ◽

Bacterial Microcompartment ◽

Shell Proteins

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Cover Picture: Synthesis and Structural Characterization of Highly Fluorinated Sulfimides and Sulfoximides as Functional Building Blocks for Materials Science (Eur. J. Org. Chem. 5/2005)

European Journal of Organic Chemistry ◽

10.1002/ejoc.200590010 ◽

2005 ◽

Vol 2005 (5) ◽

pp. 773-773

Author(s):

Peer Kirsch ◽

Marc Lenges ◽

Daniel Kühne ◽

Karl-Peter Wanczek

Keyword(s):

Structural Characterization ◽

Materials Science ◽

Building Blocks

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Characterization of two types of azedinha in the region of Sete Lagoas, Brazil

Horticultura Brasileira ◽

10.1590/s0102-05362013000200025 ◽

2013 ◽

Vol 31 (2) ◽

pp. 328-331 ◽

Cited By ~ 3

Author(s):

Ernani C da Silva ◽

Lanamar de A Carlos ◽

Ana Paula Araújo ◽

Leila de CL Ferraz ◽

Marinalva W Pedrosa ◽

...

Keyword(s):

Transverse Diameter ◽

Type I ◽

Type Ii ◽

Vegetable Crop ◽

Rumex Acetosa ◽

Crop Species ◽

Minas Gerais State ◽

Length Width ◽

Longitudinal Diameter

Azedinha (Rumex acetosa) is a vegetable crop species consumed in natura in salads and pertains to the group of non-conventional vegetables. These rustic plants are often considered weeds plants. There exist two types of native azedinha in the Sete Lagoas region, Minas Gerais state, Brazil, that are usually grown in family gardens and here denominated Type I and Type II. In this study we characterized the morphologic, physic-chemical and chromatic characteristic of these two types of azedinha. The study was carried out in randomized complete blocks with four replications in dependences of the EPAMIG (Non-Conventional Vegetable Bank) in Prudente de Morais, Brazil. Plants were trained to the point of harvest, 90 days after the planting of seedlings, when they were harvested for analysis. We evaluated the characteristics on the leaves: weight, length, width, number of veins, width/length ratio, transverse and longitudinal diameter of the base of the petiole and longitudinal and transverse diameter ratio of the base of the petiole. We also evaluated the contents of macro and micronutrients and chemical characteristics of the plant. There are significant differences between the assessed characteristics between azedinha types I and II. We concluded that the plants probably belong to two different varieties.

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