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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
1mnm
Jmol
Contents
Protein chains
85 a.a. *
77 a.a. *
DNA/RNA
Waters ×53
* Residue conservation analysis
PDB id:
1mnm
Name: Transcription/DNA
Title: Yeast matalpha2/mcm1/DNA ternary transcription complex crystal structure
Structure: DNA (ste6 operator DNA). Chain: e. Engineered: yes. DNA (ste6 operator DNA). Chain: f. Engineered: yes. Protein (mcm1 transcriptional regulator). Chain: a, b. Fragment: residues 1 - 100.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.25Å     R-factor:   0.240     R-free:   0.285
Authors: T.J.Richmond S.Tan
Key ref:
S.Tan and T.J.Richmond (1998). Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature, 391, 660-666. PubMed id: 9490409 DOI: 10.1038/35563
Date:
03-Nov-97     Release date:   18-Mar-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P11746  (MCM1_YEAST) -  Pheromone receptor transcription factor
Seq:
Struc: 		286 a.a.
85 a.a.
Protein chains
Pfam  
P0CY08  (MTAL2_YEAST) -  Mating-type protein ALPHA2
Seq:
Struc: 		210 a.a.
77 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     protein binding     5 terms  

 

 
DOI no: 10.1038/35563 Nature 391:660-666 (1998)
PubMed id: 9490409  
 
 
Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex.
S.Tan, T.J.Richmond.
 
  ABSTRACT  
 
The structure of a complex containing the homeodomain repressor protein MATalpha2 and the MADS-box transcription factor MCM1 bound to DNA has been determined by X-ray crystallography at 2.25 A resolution. It reveals the protein-protein interactions responsible for cooperative binding of MATalpha2 and MCM1 to DNA. The otherwise flexible amino-terminal extension of the MATalpha2 homeodomain forms a beta-hairpin that grips the MCM1 surface through parallel beta-strand hydrogen bonds and close-packed, predominantly hydrophobic, side chains. DNA bending induced by MCM1 brings the two proteins closer together, facilitating their interaction. An unusual feature of the complex is that an eight-amino-acid sequence adopts an alpha-helical conformation in one of two copies of the MATalpha2 monomer and a beta-strand conformation in the other. This 'chameleon' sequence of MATalpha2 may be important for recognizing natural operator sites.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 2-MCM1 interactions. a, b, Cis and trans 2/MCM1 interactions in ribbon representation; selected side chains are shown. c, d, Surface representation of cis and trans 2/MCM1 interactions showing the complementarity of 2 and MCM1 surfaces (prepared in GRASP42). The view is slightly rotated compared with that in a and b in order to show better the hydrophobic cavity filled by 2 Phe 116 and hydrophobic channel occupied by Gln 121. 		Figure 4.
Figure 4 Model for the interaction of 2 and MCM1 on 31 bp of STE6 UAS. The -chameleon structure and the equivalent region in the 2-bp-spaced 2 model are shown in red. The 2/MCM1/STE6 DNA model is based on the MCM1 dimer, cis (3-bp-spaced) 2 and respective DNA coordinates from the crystal structure. The 2-bp-spaced 2 and remaining DNA were modelled by rotating the equivalent fragments from the crystal structure about the P-box pseudodyad axis before translating and rotating to account for the 1-bp shift of the 2-binding site.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 391, 660-666) copyright 1998.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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PDB codes: 2df5 2dfe 2dff 2dfh 2dfi
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PDB codes: 1v96 1ye5
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12825085 K.T.Forest, and M.S.Filutowicz (2003).
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12548619 W.Flader, B.Wellenzohn, R.H.Winger, A.Hallbrucker, E.Mayer, and K.R.Liedl (2003).
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12943540 Y.Yang, L.Fanning, and T.Jack (2003).
The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins, APETALA3 and PISTILLATA.
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11839497 A.J.Warren (2002).
Eukaryotic transcription factors.
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Structural and thermodynamic characterization of the DNA binding properties of a triple alanine mutant of MATalpha2.
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PDB code: 1le8
11756540 B.Mai, S.Miles, and L.L.Breeden (2002).
Characterization of the ECB binding complex responsible for the M/G(1)-specific transcription of CLN3 and SWI4.
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11906605 C.Y.Ho, M.Smith, M.E.Houston, J.G.Adamson, and R.S.Hodges (2002).
A possible mechanism for partitioning between homo- and heterodimerization of the yeast homeodomain proteins MATa1 and MATalpha2.
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A Hoogsteen base pair embedded in undistorted B-DNA.
  Nucleic Acids Res, 30, 5244-5252.
PDB code: 1k61
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Transcription factor complexes.
  Curr Opin Struct Biol, 12, 225-230.  
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
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11741530 C.W.Garvie, and C.Wolberger (2001).
Recognition of specific DNA sequences.
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11779502 C.W.Garvie, J.Hagman, and C.Wolberger (2001).
Structural studies of Ets-1/Pax5 complex formation on DNA.
  Mol Cell, 8, 1267-1276.
PDB codes: 1k78 1k79 1k7a
11369849 H.Zhao, M.H.Chen, Z.M.Shen, P.C.Kahn, and P.N.Lipke (2001).
Environmentally induced reversible conformational switching in the yeast cell adhesion protein alpha-agglutinin.
  Protein Sci, 10, 1113-1123.  
11406578 M.Hassler, and T.J.Richmond (2001).
The B-box dominates SAP-1-SRF interactions in the structure of the ternary complex.
  EMBO J, 20, 3018-3028.
PDB code: 1hbx
11406412 S.Khorasanizadeh, and F.Rastinejad (2001).
Nuclear-receptor interactions on DNA-response elements.
  Trends Biochem Sci, 26, 384-390.  
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Chromatin structure mapping in Saccharomyces cerevisiae in vivo with DNase I.
  Nucleic Acids Res, 29, 1943-1950.  
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Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.
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PDB code: 1hlv
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The organized chromatin domain of the repressed yeast a cell-specific gene STE6 contains two molecules of the corepressor Tup1p per nucleosome.
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Separate domains in E1 and E2 proteins serve architectural and productive roles for cooperative DNA binding.
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10627562 G.Chen, and A.Stenlund (2000).
Two patches of amino acids on the E2 DNA binding domain define the surface for interaction with E1.
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Tup1p represses Mcm1p transcriptional activation and chromatin remodeling of an a-cell-specific gene.
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10835359 K.Huang, J.M.Louis, L.Donaldson, F.L.Lim, A.D.Sharrocks, and G.M.Clore (2000).
Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors.
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PDB code: 1c7u
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Conformational behavior of ionic self-complementary peptides.
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An overview of the structures of protein-DNA complexes.
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10759558 R.L.Smith, and A.D.Johnson (2000).
A sequence resembling a peroxisomal targeting sequence directs the interaction between the tetratricopeptide repeats of Ssn6 and the homeodomain of alpha 2.
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DNA sequence dependent and independent conformational changes in multipartite operator recognition by lambda-repressor.
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Scanning mutagenesis of Mcm1: residues required for DNA binding, DNA bending, and transcriptional activation by a MADS-box protein.
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10449733 B.S.Wang, and C.O.Pabo (1999).
Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences.
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Mechanisms of DNA bending.
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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 codes are shown on the right.