Pdp1 pyruvate dehydrogenase phosphatase catalytic subunit 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pdp1provided by RGD
Official Full Name: pyruvate dehydrogenase phosphatase catalytic subunit 1provided by RGD
Primary source: RGD:620393
See related: Ensembl:ENSRNOG00000016180 AllianceGenome:RGD:620393
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Ppm2c
Summary: Enables calcium ion binding activity; magnesium ion binding activity; and protein serine/threonine phosphatase activity. Predicted to be involved in peptidyl-threonine dephosphorylation and positive regulation of pyruvate dehydrogenase activity. Located in mitochondrion. Human ortholog(s) of this gene implicated in obesity and pyruvate decarboxylase deficiency. Orthologous to human PDP1 (pyruvate dehydrogenase phosphatase catalytic subunit 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Muscle (RPKM 371.6), Heart (RPKM 325.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q13

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (30245699..30252494, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (25446843..25455107, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (25577593..25584325, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

MiR-18a-3p improves cartilage matrix remodeling and inhibits inflammation in osteoarthritis by suppressing PDP1.
Title: MiR-18a-3p improves cartilage matrix remodeling and inhibits inflammation in osteoarthritis by suppressing PDP1.
divergent alterations of PDP1 mRNA expression were found in different brain regions following traumatic brain injury.
Title: Pyruvate dehydrogenase phosphatase1 mRNA expression is divergently and dynamically regulated between rat cerebral cortex, hippocampus and thalamus after traumatic brain injury: a potential biomarker of TBI-induced hyper- and hypo-glycaemia and neuronal vulnerability.
Results suggest that decreased PDP activity in oxidative skeletal muscles may play a role in the impairment of carbohydrate metabolism in obese rats, which is reversible with endurance training.
Title: Skeletal muscle type comparison of pyruvate dehydrogenase phosphatase activity and isoform expression: effects of obesity and endurance training.
Results report the crystal structure of the rat pyruvate dehydrogenase phosphatase 1 catalytic subunit at 1.8 A resolution.
Title: Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications.
role of PP2C and AMPK in the derangements of cardiac lipid metabolism in obesity
Title: Role of PP2C in cardiac lipid accumulation in obese rodents and its prevention by troglitazone.
Asp445 might be involved in the control of interactions between PDP1c and the protein substrate pyruvate dehydrogenase
Title: Probing a putative active site of the catalytic subunit of pyruvate dehydrogenase phosphatase 1 (PDP1c) by site-directed mutagenesis.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity	IEA Inferred from Electronic Annotation more info
enables [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity	ISO Inferred from Sequence Orthology more info
enables [pyruvate dehydrogenase (lipoamide)] phosphatase regulator activity	IEA Inferred from Electronic Annotation more info
enables calcium ion binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine phosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein serine/threonine phosphatase activity	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in protein dephosphorylation	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial; pyruvate dehydrogenase [acetyl-transferring]-phosphatase 1, mitochondrial

Names: PDP 1; PDPC 1; protein phosphatase 2C, magnesium dependent, catalytic subunit; pyruvate dehydrogenase phosphatase isoenzyme 1; pyruvate dehyrogenase phosphatase catalytic subunit 1

NP_001258037.1

EC 3.1.3.43

NP_062245.2

EC 3.1.3.43

XP_006237969.2

EC 3.1.3.43

XP_006237970.1

EC 3.1.3.43

XP_006237971.1

EC 3.1.3.43

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001271108.2 → NP_001258037.1 [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial isoform 1

See identical proteins and their annotated locations for NP_001258037.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A0G2JWE0, A0A0G2QC17, A6II75

Related

ENSRNOP00000062054.3, ENSRNOT00000067823.4

Conserved Domains (1) summary

cd00143
Location:134 → 550

PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...
NM_019372.4 → NP_062245.2 [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial isoform 2

See identical proteins and their annotated locations for NP_062245.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream AUG, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

FN800686, JAXUCZ010000005

UniProtKB/Swiss-Prot

A1L1J4, F1LP63, O88483

UniProtKB/TrEMBL

A0A0G2JWE0, A0A0G2JY56

Related

ENSRNOP00000070525.2, ENSRNOT00000090376.2

Conserved Domains (1) summary

cd00143
Location:109 → 525

PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

30245699..30252494 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006237909.5 → XP_006237971.1 pyruvate dehydrogenase [acetyl-transferring]-phosphatase 1, mitochondrial isoform X3

See identical proteins and their annotated locations for XP_006237971.1

UniProtKB/TrEMBL

A0A0G2JWE0, A0A0G2QC17, A6II75

Conserved Domains (1) summary

cd00143
Location:134 → 550

PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...
XM_006237908.4 → XP_006237970.1 pyruvate dehydrogenase [acetyl-transferring]-phosphatase 1, mitochondrial isoform X2

UniProtKB/TrEMBL

A0A0G2JWE0

Conserved Domains (1) summary

cd00143
Location:149 → 565

PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...
XM_006237907.5 → XP_006237969.2 pyruvate dehydrogenase [acetyl-transferring]-phosphatase 1, mitochondrial isoform X1

UniProtKB/TrEMBL

A0A0G2JWE0, A6II74

Related

ENSRNOP00000069844.2

Conserved Domains (1) summary

cd00143
Location:145 → 561

PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...