PUT3/YKL015W Summary Help

Standard Name PUT3
Systematic Name YKL015W
Feature Type ORF, Verified
Description Transcriptional activator; binds specific gene recruitment sequences and is required for DNA zip code-mediated targeting of genes to nuclear periphery; regulates proline utilization genes, constitutively binds PUT1 and PUT2 promoters as a dimer, undergoes conformational change to form active state; binds other promoters only under activating conditions; differentially phosphorylated in presence of different nitrogen sources; has a Zn(2)-Cys(6) binuclear cluster domain (1, 2, 3, 4, 5, 6 and see Summary Paragraph)
Name Description Proline UTilization
Chromosomal Location
ChrXI:408544 to 411483 | ORF Map | GBrowse
Genetic position: -5 cM
Gene Ontology Annotations All PUT3 GO evidence and references
  View Computational GO annotations for PUT3
Molecular Function
Manually curated
Biological Process
Manually curated
Cellular Component
Manually curated
Targets 54 genes
Regulators 11 genes
Classical genetics
Large-scale survey
34 total interaction(s) for 31 unique genes/features.
Physical Interactions
  • Affinity Capture-MS: 3
  • Biochemical Activity: 1
  • Co-crystal Structure: 2
  • Protein-RNA: 1
  • Reconstituted Complex: 1
  • Two-hybrid: 5

Genetic Interactions
  • Dosage Lethality: 1
  • Negative Genetic: 13
  • Phenotypic Enhancement: 1
  • Positive Genetic: 6

Expression Summary
Length (a.a.) 979
Molecular Weight (Da) 111,413
Isoelectric Point (pI) 5.15
Phosphorylation PhosphoGRID | PhosphoPep Database
sequence information
ChrXI:408544 to 411483 | ORF Map | GBrowse
Genetic position: -5 cM
Last Update Coordinates: 2011-02-03 | Sequence: 1996-07-31
Subfeature details
Most Recent Updates
Coordinates Sequence
CDS 1..2940 408544..411483 2011-02-03 1996-07-31
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 SGDIDS000001498

Proline is an amino acid that is not only required for protein synthesis but can also serve as a nitrogen source. Although proline is the least-preferred nitrogen source for many lab strains of S. cerevisiae, it is the most abundant source of nitrogen in grapes, the natural environment of wild yeast (2). When more optimal sources of nitrogen are unavailable, S. cerevisiae cells degrade proline into glutamate via the proline utilization pathway, shown here (7, 8). In the mitochondria, proline is first converted into delta-1-pyrroline-5-carboxylate (P5C) by the PUT1 gene product, proline oxidase (EC Then, P5C is processed by the delta-1-pyrroline-5-carboxylate dehydrogenase (EC Put2p into glutamate (7).

PUT3 encodes a pathway-specific transcriptional activator that is responsible for regulating PUT1 and PUT2 expression (8). It is a member of the Zn(II)2Cys6 family of transcription factors that has thus far been identified exclusively in fungi (9, 10). As a dimer, Put3p asymmetrically binds to a 16-bp promoter sequence, CGG-N10-CCG, called UASPUT (11, 1). Although Put3p is constitutively bound to the PUT1 and PUT2 promoters, it is maximally active for upregulation of the PUT genes only in the presence of proline and in the absence of preferred sources of nitrogen (2, 12). Put3p regulates transcription by undergoing differential phosphorylation as a function of nitrogen source quality--hyperphosphorylation of Put3p is correlated with growth on non-preferred nitrogen sources (2). Additionally, epitope-tagging and proteolysis experiments indicate that Put3p also undergoes conformational changes in response to proline (5). Mutants lacking Put3p activity are unable to grow on proline as their sole nitrogen source (4). However, there is experimental evidence indicating that in the absence of Put3p, the Gal4p transcriptional activator is able to bind to the UASPUT and upregulate PUT2 expression (13).

Last updated: 2005-09-07 Contact SGD

References cited on this page View Complete Literature Guide for PUT3
1) Siddiqui AH and Brandriss MC  (1989) The Saccharomyces cerevisiae PUT3 activator protein associates with proline-specific upstream activation sequences. Mol Cell Biol 9(11):4706-12
2) Huang HL and Brandriss MC  (2000) The regulator of the yeast proline utilization pathway is differentially phosphorylated in response to the quality of the nitrogen source. Mol Cell Biol 20(3):892-9
3) des Etages SA, et al.  (1996) Functional analysis of the PUT3 transcriptional activator of the proline utilization pathway in Saccharomyces cerevisiae. Genetics 142(4):1069-82
4) Brandriss MC  (1987) Evidence for positive regulation of the proline utilization pathway in Saccharomyces cerevisiae. Genetics 117(3):429-35
5) Des Etages SA, et al.  (2001) Conformational changes play a role in regulating the activity of the proline utilization pathway-specific regulator in Saccharomyces cerevisiae. Mol Microbiol 40(4):890-9
6) Brickner DG, et al.  (2012) Transcription factor binding to a DNA zip code controls interchromosomal clustering at the nuclear periphery. Dev Cell 22(6):1234-46
7) Brandriss MC and Magasanik B  (1979) Genetics and physiology of proline utilization in Saccharomyces cerevisiae: enzyme induction by proline. J Bacteriol 140(2):498-503
8) Brandriss MC and Magasanik B  (1979) Genetics and physiology of proline utilization in Saccharomyces cerevisiae: mutation causing constitutive enzyme expression. J Bacteriol 140(2):504-7
9) Walters KJ, et al.  (1997) Structure and mobility of the PUT3 dimer. Nat Struct Biol 4(9):744-50
10) Todd RB and Andrianopoulos A  (1997) Evolution of a fungal regulatory gene family: the Zn(II)2Cys6 binuclear cluster DNA binding motif. Fungal Genet Biol 21(3):388-405
11) Swaminathan K, et al.  (1997) Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster. Nat Struct Biol 4(9):751-9
12) Axelrod JD, et al.  (1991) Proline-independent binding of PUT3 transcriptional activator protein detected by footprinting in vivo. Mol Cell Biol 11(1):564-7
13) D'Alessio M and Brandriss MC  (2000) Cross-pathway regulation in Saccharomyces cerevisiae: activation of the proline utilization pathway by Ga14p in vivo. J Bacteriol 182(13):3748-53
14) Badis G, et al.  (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6):878-87
15) Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66