YMR1/YJR110W Summary Help

Standard Name YMR1 1
Systematic Name YJR110W
Feature Type ORF, Verified
Description Phosphatidylinositol 3-phosphate (PI3P) phosphatase; involved in various protein sorting pathways, including CVT targeting and endosome to vacuole transport; has similarity to the conserved myotubularin dual specificity phosphatase family (1, 2 and see Summary Paragraph)
Name Description Yeast Myotubularin Related 1
Chromosomal Location
ChrX:633615 to 635681 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All YMR1 GO evidence and references
  View Computational GO annotations for YMR1
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
High-throughput
Regulators 8 genes
Resources
Pathways
Classical genetics
null
overexpression
Large-scale survey
null
Resources
52 total interaction(s) for 48 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 14
  • Affinity Capture-RNA: 2
  • Two-hybrid: 1

Genetic Interactions
  • Dosage Growth Defect: 1
  • Dosage Rescue: 16
  • Negative Genetic: 6
  • Positive Genetic: 7
  • Synthetic Lethality: 3
  • Synthetic Rescue: 2

Resources
Expression Summary
histogram
Resources
Length (a.a.) 688
Molecular Weight (Da) 80,151
Isoelectric Point (pI) 7.58
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrX:633615 to 635681 | ORF Map | GBrowse
SGD ORF map
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Relative
Coordinates
Chromosomal
Coordinates
Most Recent Updates
Coordinates Sequence
CDS 1..2067 633615..635681 2011-02-03 1996-07-31
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
Resources
External Links All Associated Seq | E.C. | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000003871
SUMMARY PARAGRAPH for YMR1

YMR1 encodes a PtdIns3P (phosphotidylinositol 3-phosphate) specific phosphatase that is involved in various endosomal and vacuolar protein sorting pathways (reviewed in ). Ymr1p partially overlaps in function with other lipid phosphatases, in particular Inp53p (2). Due to this partial redundancy, ymr1 null mutants are viable and do not display any obvious phenotype beyond elevated levels of PtdIns3P (1). ymr1 inp53 double null mutants, however, have fragmented vacuoles and show defects in cytoplasm to vacuole transport (Cvt pathway), endosome to vacuole transport, sorting via multivesicular bodies, and localization of retromer complex members. ymr1 inp52 inp53 triple null mutants are inviable (2).

Ymr1p is homologous to phosphatases in the myotubularin family. The founding member of this group is the human gene MTM1, mutations in which cause the severe congenitive muscle disorder X-linked recessive myotubular myopathy (1, 3 and references therein).

About Phosphatidylinositol Phosphate Biosynthesis

The phosphorylated products of phosphatidylinositol (PtdIns, PI), collectively referred to as phosphoinositides or phosphatidylinositol phosphates (PtdInsPs, PIPs), are membrane-bound lipids that function as structural components of membranes, as well as regulators of many cellular processes in eukaryotes, including vesicle-mediated membrane trafficking, cell wall integrity, and actin cytoskeleton organization (reviewed in 4 and 5). PtdInsPs are also precursors of the water-soluble inositol phosphates (IPs), an important class of intracellular signaling molecules (reviewed in 6, 7 and 8).

The inositol ring of the membrane phospholipids and the water-soluble IPs are readily phosphorylated and dephosphorylated at a number of positions making them well suited as key regulators. PtdIns can be phosphorylated at one or a combination of positions (3', 4', or 5') on the inositol headgroup, generating a set of unique stereoisomers that have specific biological functions (reviewed in 4). These stereoisomers have been shown to be restricted to certain membranes (reviewed in 4). Phosphatidylinositol 4-phosphate (PtdIns4P) is the major PtdInsP species of the Golgi apparatus, where it plays a role in the vesicular trafficking of secretory proteins from the Golgi to the plasma membrane (reviewed in 4). Phosphatidylinositol 4,5-bisphosphate (PtdIns[4,5]P2) is the major species found at the plasma membrane and is involved in the regulation of actin cytoskeleton organization, as well as cell wall integrity, and heat shock response pathways (reviewed in 4). Phosphatidylinositol 3-phosphate (PtdIns3P) is found predominantly at endosomal membranes and in multivesicular bodies (MVB), where it plays a role in endosomal and vacuolar membrane trafficking. Phosphatidylinositol 3,5-bisphosphate (PtdIns[3,5]P2) is found on vacuolar membranes where it plays an important role in the MVB sorting pathway (reviewed in 4).

Phosphorylation and dephosphorylation of the inositol headgroups of PtdInsPs at specific membrane locations signals the recruitment of certain proteins essential for vesicular transport (5, and reviewed in 4). PtdInsPs recruit proteins that contain PtdInsP-specific binding domains, such as the well-studied pleckstrin homology (PH) domain that recognizes the phosphorylation pattern of specific PtdInsP inositol headgroups (reviewed in 4).

A number of kinases and phosphatases are involved in the generation and interconversions of PtdInsPs, the majority of which have been well conserved during evolution (reviewed in 4). The PtdInsP kinases, in contrast to the lipid phosphatases, have a higher degree of specificity. While each kinase appears to phosphorylate only one substrate, many of the lipid phosphatases can dephosphorylate a number of substrates.

Last updated: 2008-05-08 Contact SGD

References cited on this page View Complete Literature Guide for YMR1
1) Taylor GS, et al.  (2000) Myotubularin, a protein tyrosine phosphatase mutated in myotubular myopathy, dephosphorylates the lipid second messenger, phosphatidylinositol 3-phosphate. Proc Natl Acad Sci U S A 97(16):8910-5
2) Parrish WR, et al.  (2004) Essential role for the myotubularin-related phosphatase Ymr1p and the synaptojanin-like phosphatases Sjl2p and Sjl3p in regulation of phosphatidylinositol 3-phosphate in yeast. Mol Biol Cell 15(8):3567-79
3) Laporte J, et al.  (1998) Characterization of the myotubularin dual specificity phosphatase gene family from yeast to human. Hum Mol Genet 7(11):1703-12
4) Strahl T and Thorner J  (2007) Synthesis and function of membrane phosphoinositides in budding yeast, Saccharomyces cerevisiae. Biochim Biophys Acta 1771(3):353-404
5) De Camilli P, et al.  (1996) Phosphoinositides as regulators in membrane traffic. Science 271(5255):1533-9
6) York JD  (2006) Regulation of nuclear processes by inositol polyphosphates. Biochim Biophys Acta 1761(5-6):552-9
7) Bennett M, et al.  (2006) Inositol pyrophosphates: metabolism and signaling. Cell Mol Life Sci 63(5):552-64
8) Bhandari R, et al.  (2007) Inositol pyrophosphate pyrotechnics. Cell Metab 5(5):321-3