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Parabacteroides merdae

ABSTRACT: Normal gut bacterium

PROVIDER: PRJNA35017 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
		Other
	SRR275665.fastq.gz	Fastqsanger.gz
	SRR285207_1.fastq.gz	Fastqsanger.gz
	SRR285207_2.fastq.gz	Fastqsanger.gz
	SRR285208.fastq.gz	Fastqsanger.gz

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Parabacteroides distasonis

Project description:Normal gastrointestinal bacterium

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Active site flexibility revealed in crystal structures of Parabacteroides merdae β-glucuronidase from the human gut microbiome.

Project description:β-Glucuronidase (GUS) enzymes in the gastrointestinal tract are involved in maintaining mammalian-microbial symbiosis and can play key roles in drug efficacy and toxicity. Parabacteroides merdae GUS was identified as an abundant mini-Loop 2 (mL2) type GUS enzyme in the Human Microbiome Project gut metagenomic database. Here, we report the crystal structure of P. merdae GUS and highlight the differences between this enzyme and extant structures of gut microbial GUS proteins. We find that P. merdae GUS exhibits a distinct tetrameric quaternary structure and that the mL2 motif traces a unique path within the active site, which also includes two arginines distinctive to this GUS. We observe two states of the P. merdae GUS active site; a loop repositions itself by more than 50 Å to place a functionally-relevant residue into the enzyme's catalytic site. Finally, we find that P. merdae GUS is able to bind to homo and heteropolymers of the polysaccharide alginic acid. Together, these data broaden our understanding of the structural and functional diversity in the GUS family of enzymes present in the human gut microbiome and point to specialization as an important feature of microbial GUS orthologs.

| S-EPMC6237702 | biostudies-literature

Parabacteroides merdae CL03T12C32

Project description:Reference genome for the Human Microbiome Project

| PRJNA64891 | ENA

Parabacteroides merdae UC1_BHI_R

Project description:Human Microbiome Project (HMP) reference genome

| PRJNA212669 | ENA

Parabacteroides merdae CL09T00C40

Project description:Reference genome for the Human Microbiome Project

| PRJNA64893 | ENA

Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome.

Project description:Clan CD cysteine peptidases, a structurally related group of peptidases that include mammalian caspases, exhibit a wide range of important functions, along with a variety of specificities and activation mechanisms. However, for the clostripain family (denoted C11), little is currently known. Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution. PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain. It shares core structural elements with clan CD cysteine peptidases but otherwise structurally differs from the other families in the clan. These studies also revealed a well ordered break in the polypeptide chain at Lys(147), resulting in a large conformational rearrangement close to the active site. Biochemical and kinetic analysis revealed Lys(147) to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation. PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca(2+) for activity. Collectively, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.

| S-EPMC4850288 | biostudies-literature

Parabacteroides merdae strain:GSH2021

Project description:Parabacteroides merdae strain:GSH2021 Genome sequencing and assembly

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Parabacteroides merdae TSDC10.1-1.1

Project description:Strain Parabacteroides merdae TSDC10.1-1.1 (species Parabacteroides merdae) was isolated from the fecal microbiota of a USA female at time point zero (bacterial isolates were sequenced from this donor on day 0 and 42). The species name was assigned by genome clustering.

| PRJEB3569 | ENA

Parabacteroides merdae TSDC19.1-1.1

Project description:Strain Parabacteroides merdae TSDC19.1-1.1 (species Parabacteroides merdae) was isolated from the fecal microbiota of a USA female at time point zero (bacterial isolates were sequenced from this donor on day 0 and 47). The species name was assigned by genome clustering.

| PRJEB3808 | ENA

Parabacteroides merdae CAG:48

Project description:Parabacteroides merdae CAG:48 overview

| PRJNA207258 | ENA