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protein dna_rna metals Protein-protein interface(s) links
Transcription/DNA PDB id
1zme
Jmol
Contents
Protein chains
70 a.a. *
DNA/RNA
Metals
_ZN ×4
Waters ×157
* Residue conservation analysis
PDB id:
1zme
Name: Transcription/DNA
Title: Crystal structure of put3/DNA complex
Structure: DNA (5'- d( Ap Cp Gp Gp Gp Ap Ap Gp Cp Cp Ap Ap Cp Tp Cp Cp G)-3'). Chain: a. Engineered: yes. DNA (5'-d( Ap Cp Gp Gp Ap Gp (5Iu) p Tp Gp Gp Cp Tp (5Iu)p Cp Cp Cp G)-3'). Chain: b. Engineered: yes. Proline utilization transcription activator.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Resolution:
2.50Å     R-factor:   0.208     R-free:   0.292
Authors: K.Swaminathan,R.Marmorstein
Key ref: K.Swaminathan 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, 751-759. PubMed id: 9303004 DOI: 10.1038/nsb0997-751
Date:
06-Aug-97     Release date:   16-Sep-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P25502  (PUT3_YEAST) -  Proline utilization trans-activator
Seq:
Struc: 		 
Seq:
Struc: 		979 a.a.
70 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     transcription factor activity     2 terms  

 

 
DOI no: 10.1038/nsb0997-751 Nat Struct Biol 4:751-759 (1997)
PubMed id: 9303004  
 
 
Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster.
K.Swaminathan, P.Flynn, R.J.Reece, R.Marmorstein.
 
  ABSTRACT  
 
PUT3 is a member of a family of at least 79 fungal transcription factors that contain a six-cysteine, two-zinc domain called a 'Zn2Cys6 binuclear cluster'. We have determined the crystal structure of the DNA binding region from the PUT3 protein bound to its cognate DNA target. The structure reveals that the PUT3 homodimer is bound asymmetrically to the DNA site. This asymmetry orients a beta-strand from one protein subunit into the minor groove of the DNA resulting in a partial amino acid-base pair intercalation and extensive direct and water-mediated protein interactions with the minor groove of the DNA. These interactions facilitate a sequence dependent kink at the centre of the DNA site and specify the intervening base pairs separating two DNA half-sites that are contacted in the DNA major groove. A comparison with the GAL4-DNA and PPR1-DNA complexes shows how a family of related DNA binding proteins can use a diverse set of mechanisms to discriminate between the base pairs separating conserved DNA half-sites.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20466807 M.van Dijk, and A.M.Bonvin (2010).
Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.
  Nucleic Acids Res, 38, 5634-5647.  
19854140 C.Choudhary, J.V.Olsen, C.Brandts, J.Cox, P.N.Reddy, F.D.Böhmer, V.Gerke, D.E.Schmidt-Arras, W.E.Berdel, C.Müller-Tidow, M.Mann, and H.Serve (2009).
Mislocalized activation of oncogenic RTKs switches downstream signaling outcomes.
  Mol Cell, 36, 326-339.  
18950675 J.H.Kim (2009).
DNA-binding properties of the yeast Rgt1 repressor.
  Biochimie, 91, 300-303.  
19574222 M.K.Leverentz, R.N.Campbell, Y.Connolly, A.D.Whetton, and R.J.Reece (2009).
Mutation of a phosphorylatable residue in Put3p affects the magnitude of rapamycin-induced PUT1 activation in a Gat1p-dependent manner.
  J Biol Chem, 284, 24115-24122.  
18940788 A.Spitzner, A.F.Perzlmaier, K.E.Geillinger, P.Reihl, and J.Stolz (2008).
The Proline-Dependent Transcription Factor Put3 Regulates the Expression of the Riboflavin Transporter MCH5 in Saccharomyces cerevisiae.
  Genetics, 180, 2007-2017.  
18611375 M.Hong, M.X.Fitzgerald, S.Harper, C.Luo, D.W.Speicher, and R.Marmorstein (2008).
Structural basis for dimerization in DNA recognition by Gal4.
  Structure, 16, 1019-1026.
PDB code: 3coq
17438293 A.V.Morozov, and E.D.Siggia (2007).
Connecting protein structure with predictions of regulatory sites.
  Proc Natl Acad Sci U S A, 104, 7068-7073.  
16373473 J.H.Brown (2006).
Breaking symmetry in protein dimers: designs and functions.
  Protein Sci, 15, 1.  
16533810 M.Weider, A.Machnik, F.Klebl, and N.Sauer (2006).
Vhr1p, a new transcription factor from budding yeast, regulates biotin-dependent expression of VHT1 and BIO5.
  J Biol Chem, 281, 13513-13524.  
16959962 S.MacPherson, M.Larochelle, and B.Turcotte (2006).
A fungal family of transcriptional regulators: the zinc cluster proteins.
  Microbiol Mol Biol Rev, 70, 583-604.  
15950477 C.A.Sellick, and R.J.Reece (2005).
Eukaryotic transcription factors as direct nutrient sensors.
  Trends Biochem Sci, 30, 405-412.  
15657048 K.F.Kubatzky, W.Liu, K.Goldgraben, C.Simmerling, S.O.Smith, and S.N.Constantinescu (2005).
Structural requirements of the extracellular to transmembrane domain junction for erythropoietin receptor function.
  J Biol Chem, 280, 14844-14854.  
15123673 B.Akache, S.MacPherson, M.A.Sylvain, and B.Turcotte (2004).
Complex interplay among regulators of drug resistance genes in Saccharomyces cerevisiae.
  J Biol Chem, 279, 27855-27860.  
15388966 T.Ito, S.Tani, T.Itoh, N.Tsukagoshi, M.Kato, and T.Kobayashi (2004).
Mode of AmyR binding to the CGGN8AGG sequence in the Aspergillus oryzae taaG2 promoter.
  Biosci Biotechnol Biochem, 68, 1906-1911.  
14517252 C.A.Sellick, and R.J.Reece (2003).
Modulation of transcription factor function by an amino acid: activation of Put3p by proline.
  EMBO J, 22, 5147-5153.  
12861007 J.H.Kim, J.Polish, and M.Johnston (2003).
Specificity and regulation of DNA binding by the yeast glucose transporter gene repressor Rgt1.
  Mol Cell Biol, 23, 5208-5216.  
14636581 N.Seubert, Y.Royer, J.Staerk, K.F.Kubatzky, V.Moucadel, S.Krishnakumar, S.O.Smith, and S.N.Constantinescu (2003).
Active and inactive orientations of the transmembrane and cytosolic domains of the erythropoietin receptor dimer.
  Mol Cell, 12, 1239-1250.  
11972793 D.Gómez, B.Cubero, G.Cecchetto, and C.Scazzocchio (2002).
PrnA, a Zn2Cys6 activator with a unique DNA recognition mode, requires inducer for in vivo binding.
  Mol Microbiol, 44, 585-597.  
11921102 J.Avila, C.González, N.Brito, F.Machín, M.D.Pérez, and J.M.Siverio (2002).
A second Zn(II)(2)Cys(6) transcriptional factor encoded by the YNA2 gene is indispensable for the transcriptional activation of the genes involved in nitrate assimilation in the yeast Hansenula polymorpha.
  Yeast, 19, 537-544.  
10617612 A.Hach, T.Hon, and L.Zhang (2000).
The coiled coil dimerization element of the yeast transcriptional activator Hap1, a Gal4 family member, is dispensable for DNA binding but differentially affects transcriptional activation.
  J Biol Chem, 275, 248-254.  
10629046 H.L.Huang, and M.C.Brandriss (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, 892-899.  
10850990 M.D'Alessio, and M.C.Brandriss (2000).
Cross-pathway regulation in Saccharomyces cerevisiae: activation of the proline utilization pathway by Ga14p in vivo.
  J Bacteriol, 182, 3748-3753.  
10352012 I.D.Russell, A.S.Grancell, and P.K.Sorger (1999).
The unstable F-box protein p58-Ctf13 forms the structural core of the CBF3 kinetochore complex.
  J Cell Biol, 145, 933-950.  
10092669 I.Nikolaev, F.Lenouvel, and B.Felenbok (1999).
Unique DNA binding specificity of the binuclear zinc AlcR activator of the ethanol utilization pathway in Aspergillus nidulans.
  J Biol Chem, 274, 9795-9802.  
10358080 P.C.Liu, and D.J.Thiele (1999).
Modulation of human heat shock factor trimerization by the linker domain.
  J Biol Chem, 274, 17219-17225.  
  10523674 T.Cai, T.R.Reilly, M.Cerio, and M.E.Schmitt (1999).
Mutagenesis of SNM1, which encodes a protein component of the yeast RNase MRP, reveals a role for this ribonucleoprotein endoribonuclease in plasmid segregation.
  Mol Cell Biol, 19, 7857-7869.  
9628480 D.N.Arvidson, F.Lu, C.Faber, H.Zalkin, and R.G.Brennan (1998).
The structure of PurR mutant L54M shows an alternative route to DNA kinking.
  Nat Struct Biol, 5, 436-441.
PDB code: 1vpw
9593720 J.C.Corton, E.Moreno, and S.A.Johnston (1998).
Alterations in the GAL4 DNA-binding domain can affect transcriptional activation independent of DNA binding.
  J Biol Chem, 273, 13776-13780.  
9651335 J.Noël, and B.Turcotte (1998).
Zinc cluster proteins Leu3p and Uga3p recognize highly related but distinct DNA targets.
  J Biol Chem, 273, 17463-17468.  
  9488449 J.Strauss, M.I.Muro-Pastor, and C.Scazzocchio (1998).
The regulator of nitrate assimilation in ascomycetes is a dimer which binds a nonrepeated, asymmetrical sequence.
  Mol Cell Biol, 18, 1339-1348.  
9660826 Y.Mamane, K.Hellauer, M.H.Rochon, and B.Turcotte (1998).
A linker region of the yeast zinc cluster protein leu3p specifies binding to everted repeat DNA.
  J Biol Chem, 273, 18556-18561.  
9734357 Y.Mo, B.Vaessen, K.Johnston, and R.Marmorstein (1998).
Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: insights into DNA sequence discrimination by Ets proteins.
  Mol Cell, 2, 201-212.
PDB codes: 1bc7 1bc8
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.