YNK1/YKL067W Summary Help

Standard Name YNK1 1
Systematic Name YKL067W
Alias NDK1 2
Feature Type ORF, Verified
Description Nucleoside diphosphate kinase; catalyzes the transfer of gamma phosphates from nucleoside triphosphates, usually ATP, to nucleoside diphosphates by a mechanism that involves formation of an autophosphorylated enzyme intermediate; protein abundance increases in response to DNA replication stress (1, 3, 4 and see Summary Paragraph)
Name Description Yeast Nucleoside diphosphate Kinase 1
Chromosomal Location
ChrXI:314812 to 315273 | ORF Map | GBrowse
Gbrowse
Gene Ontology Annotations All YNK1 GO evidence and references
  View Computational GO annotations for YNK1
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
High-throughput
Pathways
Classical genetics
null
Large-scale survey
null
Resources
48 total interaction(s) for 41 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 19
  • Affinity Capture-RNA: 2
  • Biochemical Activity: 1
  • Co-crystal Structure: 1
  • PCA: 2
  • Reconstituted Complex: 1
  • Two-hybrid: 4

Genetic Interactions
  • Negative Genetic: 14
  • Positive Genetic: 3
  • Synthetic Rescue: 1

Resources
Expression Summary
histogram
Resources
Length (a.a.) 153
Molecular Weight (Da) 17,167
Isoelectric Point (pI) 9.13
Localization
Phosphorylation PhosphoGRID | PhosphoPep Database
Structure
Homologs
sequence information
ChrXI:314812 to 315273 | 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..462 314812..315273 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 SGDIDS000001550
SUMMARY PARAGRAPH for YNK1

Ynk1p is a nucleoside diphosphate kinase (NDPK; EC 2.7.4.6) with broad substrate specificity that is involved in both DNA and RNA metabolism, and catalyzes the phosphorylation of nucleoside diphosphates into the corresponding triphosphates. Further, it is important for maintaining the intracellular levels of all nucleotide triphosphates, except ATP (3, 1, 5, 6). Ynk1p displays different relative activities for the various nucleoside diphosphates (NDPs) as phosphate acceptors, and different relative activities for various triphosphate (NTP) donors (5). Ynk1p also binds Cdc8p, and this complex may facilitate nucleotide channeling in the cell (6).

Ynk1p is a predominantly cytoplasmic homo-oligomeric protein that can rapidly phosphorylate itself in vitro, and its abundance does not appear to be cell-cycle regulated (3, 6). Approximately 40-50% of Ynk1p activity appears to be associated with the cell membrane, approximately 3% of Ynk1p activity is found in mitochondrial fractions, and less than 1% of total activity can be detected in the nuclear fraction (6). The mitochondrial fraction of Ynk1p specifically localizes to the intermembrane space (IMS), and this localization may occur through the targeting of Ynk1p intermediates to the mitochondrial IMS by Tom40p (the core component of the protein-conducting channel of the outer mitochondrial membrane), and subsequent trapping there by folding and oligomerization (3). This scenario is suggested by in vitro studies demonstrating that Tom40p recognizes only denatured, not native, Ynk1p, and this recognition of denatured Ynk1p by Tom40p is inhibited by autophosphorylation (3). The mitochondrial fraction of Ynk1p may be required to supply GTP for various mitochondrial processes (3).

ynk1 null mutants are viable and display normal sporulation, mating, morphology, and growth rates (1).

Nucleoside diphosphate kinases are ubiquitous, highly-conserved enzymes, and have been suggested to serve as signaling molecules in a variety of species due to their involvement in development, cell differentiation, proliferation, cell motility, tumor metastasis, and apoptosis (3). Ynk1p displays similarity to E. coli NDPK, Myxococcus xanthus NDPK, Dictyostelium discoideum NDPK, Schizosaccharomyces pombe Ndk1p, Drosophila melanogaster awd, pigeon NDPK, rat NDPK alpha and beta, mouse Nm23, and human NME4, NME2, NME3, and NME1, which is associated with inhibition of the tumor metastatic process (3, 7, 8, 1, 2, 5).

Last updated: 2005-10-25 Contact SGD

References cited on this page View Complete Literature Guide for YNK1
1) Fukuchi T, et al.  (1993) Isolation, overexpression and disruption of a Saccharomyces cerevisiae YNK gene encoding nucleoside diphosphate kinase. Gene 129(1):141-6
2) Izumiya H and Yamamoto M  (1995) Cloning and functional analysis of the ndk1 gene encoding nucleoside-diphosphate kinase in Schizosaccharomyces pombe. J Biol Chem 270(46):27859-64
3) Amutha B and Pain D  (2003) Nucleoside diphosphate kinase of Saccharomyces cerevisiae, Ynk1p: localization to the mitochondrial intermembrane space. Biochem J 370(Pt 3):805-15
4) Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76
5) Jong AY and Ma JJ  (1991) Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. Arch Biochem Biophys 291(2):241-6
6) Zhang SQ, et al.  (1995) Temporal and spatial distributions of yeast nucleoside diphosphate kinase activities and its association with the Cdc8p. Cell Mol Biol Res 41(5):333-46
7) Engel M, et al.  (1994) Phosphorylation of nm23/nucleoside diphosphate kinase by casein kinase 2 in vitro. Biochem Biophys Res Commun 199(2):1041-8
8) Foury F  (1997) Human genetic diseases: a cross-talk between man and yeast. Gene 195(1):1-10