MATALPHA2/YCR039C Summary Help

Standard Name MATALPHA2 1
Systematic Name YCR039C
Alias ALPHA2
Feature Type ORF, Verified
Description Homeobox-domain protein; with Mcm1p, represses a-specific genes in haploids; acts with A1p to repress transcription of haploid-specific genes in diploids; one of two genes encoded by the MATalpha mating type cassette (2, 3 and see Summary Paragraph)
Name Description MATing type protein ALPHA
Chromosomal Location
ChrIII:200178 to 199546 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
Gene Ontology Annotations All MATALPHA2 GO evidence and references
  View Computational GO annotations for MATALPHA2
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Regulators 2 genes
Classical genetics
reduction of function
Large-scale survey
24 total interaction(s) for 10 unique genes/features.
Physical Interactions
  • Affinity Capture-Western: 1
  • Biochemical Activity: 2
  • Co-crystal Structure: 4
  • Reconstituted Complex: 12
  • Two-hybrid: 1

Genetic Interactions
  • Dosage Lethality: 1
  • Dosage Rescue: 2
  • Phenotypic Enhancement: 1

Expression Summary
Length (a.a.) 210
Molecular Weight (Da) 24,282
Isoelectric Point (pI) 10.24
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrIII:200178 to 199546 | ORF Map | GBrowse
Note: this feature is encoded on the Crick strand.
This feature is contained within: MATALPHA
Last Update Coordinates: 2011-02-03 | Sequence: 1997-01-28
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..633 200178..199546 2011-02-03 1997-01-28
Retrieve sequences
Analyze Sequence
S288C only
S288C vs. other species
S288C vs. other strains
External Links All Associated Seq | Entrez Gene | Entrez RefSeq Protein | MIPS | Search all NCBI (Entrez) | UniProtKB
Primary SGDIDS000000635

alpha2 is one of two genes encoded by the alpha mating type cassette in S. cerevisiae. The mating type of S. cerevisiae is determined by the genetic composition of the MAT locus (4, 5, 6). Haploids of the a mating type express the genes a1 and a2 from the MAT locus while haploids of the alpha mating type express alpha1 and alpha2 from MAT (4, 5, 6). Some of the cells within a given colony are capable of switching mating type by changing the genetic composition of the MAT locus (7); more information on mating type switching can be found in the summary paragraph for MAT and references cited therein. Diploid cells are normally heterozygous (a/alpha) at the MAT locus (4, 5, 6).

alpha2 encodes a homeodomain protein involved in transcriptional regulation of mating type-specific genes (5, 6). In MATalpha haploid cells, alpha2p associates with the transcription factor Mcm1p to repress transcription of a-specific genes (5, 6). alpha2p binds DNA as a homodimer; Mcm1p determines the DNA-binding affinity and specificity of the complex (8, 9, 10, 11, 12, 5, 6). Transcriptional repression of a-specific genes also involves the repressors Ssn6p and Tup1p, which interact with alpha2p (13, 14, 15). alpha2p and Mcm1p also play a role in donor preference in mating type switching (16, 17, 7).

In a/alpha diploid cells, alpha2p interacts with another homeodomain protein, a1p, to bind DNA as a heterodimer to repress transcription of haploid-specific genes (18, 5, 19, 6, 20, 21, 22). The interaction between a1p and alpha2p stabilizes both proteins, and alters their DNA binding specificities (18, 20, 23, 24). Transcriptional repression of a-specific genes by alpha2p and Mcm1p also occurs in dipoloid cells(6).

Note: The maps and sequences within SGD reflect the fact that a MATalpha strain was used in the systematic sequencing project. Accordingly, there are two copies of the alpha1 and alpha2 genes; one pair (MATalpha1/YCR040W and MATalpha2/YCR039C) corresponds to the MAT locus, and the other (HMLalpha1/YCL066W and HMLalpha2/YCL067C) to the HML locus. There are ORFs assigned to the copies of a1 and a2 found at HMR (HMRa1/YCR097W) and (HMRa2/YCR096C); locus entries are included for MAT, MATa1 and MATa2 but they do not have ORFs associated with them. There are GenBank sequences available from all of the locus pages describing a1, a2, alpha1, and alpha2; the Genbank accession for the MATa cassette is V01313.

Last updated: 2004-11-05 Contact SGD

References cited on this page View Complete Literature Guide for MATALPHA2
1) Nasmyth KA, et al.  (1981) A position effect in the control of transcription at yeast mating type loci. Nature 289(5795):244-50
2) Porter SD and Smith M  (1986) Homoeo-domain homology in yeast MAT alpha 2 is essential for repressor activity. Nature 320(6064):766-8
3) Siliciano PG and Tatchell K  (1986) Identification of the DNA sequences controlling the expression of the MAT alpha locus of yeast. Proc Natl Acad Sci U S A 83(8):2320-4
4) Herskowitz I  (1983) Cellular differentiation, cell lineages, and transposable genetic cassettes in yeast. Curr Top Dev Biol 18:1-14
5) Herskowitz I  (1989) A regulatory hierarchy for cell specialization in yeast. Nature 342(6251):749-57
6) Herskowitz I, et al.  (1992) "Mating-type determination and mating-type interconversion in Saccharomyces cerevisiae." Pp. 583-656 in The Molecular and Cellular Biology of the Yeast Saccharomyces: Gene Expression, edited by Jones EW, Pringle JR and Broach JR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
7) Haber JE  (1998) Mating-type gene switching in Saccharomyces cerevisiae. Annu Rev Genet 32:561-99
8) Vershon AK and Johnson AD  (1993) A short, disordered protein region mediates interactions between the homeodomain of the yeast alpha 2 protein and the MCM1 protein. Cell 72(1):105-12
9) Murphy MR, et al.  (1993) DNA-protein interactions at the S.cerevisiae alpha 2 operator in vivo. Nucleic Acids Res 21(14):3295-300
10) Smith DL and Johnson AD  (1992) A molecular mechanism for combinatorial control in yeast: MCM1 protein sets the spacing and orientation of the homeodomains of an alpha 2 dimer. Cell 68(1):133-42
11) Tan S and Richmond TJ  (1998) Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature 391(6668):660-6
12) Zhong H, et al.  (1999) Identification of target sites of the alpha2-Mcm1 repressor complex in the yeast genome. Genome Res 9(11):1040-7
13) Herschbach BM, et al.  (1994) Transcriptional repression directed by the yeast alpha 2 protein in vitro. Nature 370(6487):309-11
14) Smith RL, et al.  (1995) The tetratricopeptide repeats of Ssn6 interact with the homeo domain of alpha 2. Genes Dev 9(23):2903-10
15) Komachi K and Johnson AD  (1997) Residues in the WD repeats of Tup1 required for interaction with alpha2. Mol Cell Biol 17(10):6023-8
16) Szeto L, et al.  (1997) Alpha2p controls donor preference during mating type interconversion in yeast by inactivating a recombinational enhancer of chromosome III. Genes Dev 11(15):1899-911
17) Wu C, et al.  (1998) Mcm1 regulates donor preference controlled by the recombination enhancer in Saccharomyces mating-type switching. Genes Dev 12(11):1726-37
18) Goutte C and Johnson AD  (1988) a1 protein alters the DNA binding specificity of alpha 2 repressor. Cell 52(6):875-82
19) Dranginis AM  (1990) Binding of yeast a1 and alpha 2 as a heterodimer to the operator DNA of a haploid-specific gene. Nature 347(6294):682-5
20) Goutte C and Johnson AD  (1993) Yeast a1 and alpha 2 homeodomain proteins form a DNA-binding activity with properties distinct from those of either protein. J Mol Biol 233(3):359-71
21) Goutte C and Johnson AD  (1994) Recognition of a DNA operator by a dimer composed of two different homeodomain proteins. EMBO J 13(6):1434-42
22) Li T, et al.  (1998) Crystal structure of the MATa1/MATalpha2 homeodomain heterodimer in complex with DNA containing an A-tract. Nucleic Acids Res 26(24):5707-18
23) Johnson PR, et al.  (1998) Degradation signal masking by heterodimerization of MATalpha2 and MATa1 blocks their mutual destruction by the ubiquitin-proteasome pathway. Cell 94(2):217-27
24) Stark MR, et al.  (1999) A trans-acting peptide activates the yeast a1 repressor by raising its DNA-binding affinity. EMBO J 18(6):1621-9
25) Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66