PDP3 / YLR455W Overview


Standard Name
PDP3 1
Systematic Name
YLR455W
SGD ID
SGD:S000004447
Feature Type
ORF , Verified
Description
Component of the NuA3b histone acetyltransferase complex; binds to Pol II and stimulates elongation; regulates interaction between NuA3b and H3K36me3 at transcribed regions of genes; contains PWWP domain; protein abundance increases in response to DNA replication stress; relocalizes to the cytosol in response to hypoxia; extensive sequence similarity (~25% identity; ~39% similarity) to the N-terminal region of human NDF 1 2 3 4 5 6 7
Name Description
PWWP Domain-containing Protein 1
Comparative Info
Sequence Details

Sequence

The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C. Download DNA or protein sequence, view genomic context and coordinates. Click "Sequence Details" to view all sequence information for this locus, including that for other strains.


Summary
PDP3 is located on the right arm of chromosome XII near the telomere between YLRCdelta27 Ty1 LTR and uncharacterized gene YLR456W; coding sequence is 915 nucleotides long with 7 SNPs, two of which cause amino acid polymorphisms
Protein Details

Protein

Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein.


Summary
Pdp3p is 304 amino acids long, shorter-lived, and low-to-moderate in abundance; contains a PWWP domain; sumoylated on K152 and K167, phosphorylated on 3 residues; protein abundance increases in response to DNA replication stress; relocalizes to the cytosol in response to hypoxia
Length (a.a.)
304
Mol. Weight (Da)
35521.0
Isoelectric Point
9.94
Median Abundance (molecules/cell)
3177 +/- 410
Half-life (hr)
7.4

Alleles

Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results. Click "YeastMine" to view all alleles in YeastMine.


View all PDP3 alleles in SGD search | YeastMine

Gene Ontology Details

Gene Ontology

GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes.


Summary
Chromatin-binding subunit of the NuA3 histone acetyltransferase complex that catalyzes the acetylation of histone H3; involved in positive regulation of transcription by RNA Pol II; localizes to both the nucleus and cytosol

View computational annotations

Molecular Function

Manually Curated

Biological Process

Manually Curated

Cellular Component

Manually Curated
Phenotype Details

Phenotype

Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). Whenever possible, allele information and additional details are provided. Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes.


Summary
Non-essential gene; null displays small defect in vacuolar fragmentation, slow growth, decreased starvation resistance, altered oxidative stress resistance, increased lifespan, decreased heat sensitivity, slow fermentative metabolism
Interaction Details

Interaction

Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g., Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization.


Summary
Pdp3p interacts physically with proteins involved in chromatin organization; PDP3 interacts genetically with genes involved in transcription

147 total interactions for 101 unique genes

Physical Interactions

  • Affinity Capture-MS: 94
  • Affinity Capture-RNA: 9
  • Affinity Capture-Western: 3
  • Biochemical Activity: 2
  • Protein-peptide: 1
  • Reconstituted Complex: 1
  • Two-hybrid: 1

Genetic Interactions

  • Negative Genetic: 26
  • Phenotypic Enhancement: 3
  • Phenotypic Suppression: 2
  • Positive Genetic: 2
  • Synthetic Rescue: 3
Regulation Details

Regulation

The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. This evidence includes data generated through high-throughput techniques. Click "Regulation Details" to view all regulation annotations, shared GO enrichment among regulation Targets, and a regulator/target diagram for the locus.


Summary
PDP3 promoter is bound by Fkh1p, and by Bur6p in response to heat; PDP3 transcription is regulated by Ixr1p, and by Sfp1p in response to stress
Regulators
4
Targets
0
Expression Details

Expression

Expression data are derived from records contained in the Gene Expression Omnibus (GEO), and are first log2 transformed and normalized. Referenced datasets may contain one or more condition(s), and as a result there may be a greater number of conditions than datasets represented in a single clickable histogram bar. The histogram division at 0.0 separates the down-regulated (green) conditions and datasets from those that are up-regulated (red). Click "Expression Details" to view all expression annotations and details for this locus, including a visualization of genes that share a similar expression pattern.


Literature Details

Literature

All manually curated literature for the specified gene, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review). Click "Literature Details" to view all literature information for this locus, including shared literature between genes.


Primary
11
Additional
8
Reviews
3

Resources