PDBsum entry 1mnm

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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
Protein chains
85 a.a. *
77 a.a. *
Waters ×53
* Residue conservation analysis
PDB id:
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)
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
03-Nov-97     Release date:   18-Mar-98    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P11746  (MCM1_YEAST) -  Pheromone receptor transcription factor
286 a.a.
85 a.a.
Protein chains
Pfam   ArchSchema ?
P0CY08  (MTAL2_YEAST) -  Mating-type protein ALPHA2
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     DNA binding     4 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.
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 an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20625780 S.Hong, and S.Yoon (2011).
Mcm1p binding sites in the ARG1 promoter positively regulate ARG1 transcription and S. cerevisiae growth in the absence of arginine and Gcn4p.
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King of the castle: competition between repressors and activators on the Mcm1 platform.
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20388728 Y.Xie, E.M.Rubenstein, T.Matt, and M.Hochstrasser (2010).
SUMO-independent in vivo activity of a SUMO-targeted ubiquitin ligase toward a short-lived transcription factor.
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20385087 Z.Darieva, A.Clancy, R.Bulmer, E.Williams, A.Pic-Taylor, B.A.Morgan, and A.D.Sharrocks (2010).
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19233144 S.Yoon, and A.G.Hinnebusch (2009).
Mcm1p binding sites in ARG1 positively regulate Gcn4p binding and SWI/SNF recruitment.
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Sequence dependencies of DNA deformability and hydration in the minor groove.
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SOC1 translocated to the nucleus by interaction with AGL24 directly regulates leafy.
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Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.
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PDB codes: 2df5 2dfe 2dff 2dfh 2dfi
17935152 S.Meier, and S.Ozbek (2007).
A biological cosmos of parallel universes: does protein structural plasticity facilitate evolution?
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17006507 A.E.Tsong, B.B.Tuch, H.Li, and A.D.Johnson (2006).
Evolution of alternative transcriptional circuits with identical logic.
  Nature, 443, 415-420.  
16705166 A.I.Zaromytidou, F.Miralles, and R.Treisman (2006).
MAL and ternary complex factor use different mechanisms to contact a common surface on the serum response factor DNA-binding domain.
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  16582480 K.Kitano, F.Yusa, and T.Hakoshima (2006).
Structure of dimerized radixin FERM domain suggests a novel masking motif in C-terminal residues 295-304.
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PDB code: 2d2q
17041190 P.J.Riggle, and C.A.Kumamoto (2006).
Transcriptional regulation of MDR1, encoding a drug efflux determinant, in fluconazole-resistant Candida albicans strains through an Mcm1p binding site.
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16278448 D.S.Abraham, and A.K.Vershon (2005).
N-terminal arm of Mcm1 is required for transcription of a subset of genes involved in maintenance of the cell wall.
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Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.
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PDB codes: 1v96 1ye5
15332082 A.Reményi, H.R.Schöler, and M.Wilmanns (2004).
Combinatorial control of gene expression.
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15118075 E.A.Carr, J.Mead, and A.K.Vershon (2004).
Alpha1-induced DNA bending is required for transcriptional activation by the Mcm1-alpha1 complex.
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Recruitment of the ArgR/Mcm1p repressor is stimulated by the activator Gcn4p: a self-checking activation mechanism.
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14583607 Y.W.Chen, M.D.Allen, D.B.Veprintsev, J.Löwe, and M.Bycroft (2004).
The structure of the AXH domain of spinocerebellar ataxin-1.
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PDB code: 1oa8
12700764 A.Han, F.Pan, J.C.Stroud, H.D.Youn, J.O.Liu, and L.Chen (2003).
Sequence-specific recruitment of transcriptional co-repressor Cabin1 by myocyte enhancer factor-2.
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PDB code: 1n6j
12946282 A.M.Moses, D.Y.Chiang, M.Kellis, E.S.Lander, and M.B.Eisen (2003).
Position specific variation in the rate of evolution in transcription factor binding sites.
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The essential transcription factor Reb1p interacts with the CLB2 UAS outside of the G2/M control region.
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12509445 F.L.Lim, A.Hayes, A.G.West, A.Pic-Taylor, Z.Darieva, B.A.Morgan, S.G.Oliver, and A.D.Sharrocks (2003).
Mcm1p-induced DNA bending regulates the formation of ternary transcription factor complexes.
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12784213 J.Aishima, and C.Wolberger (2003).
Insights into nonspecific binding of homeodomains from a structure of MATalpha2 bound to DNA.
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12711672 J.Boros, F.L.Lim, Z.Darieva, A.Pic-Taylor, R.Harman, B.A.Morgan, and A.D.Sharrocks (2003).
Molecular determinants of the cell-cycle regulated Mcm1p-Fkh2p transcription factor complex.
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14573865 K.Ikeda, and J.Higo (2003).
Free-energy landscape of a chameleon sequence in explicit water and its inherent alpha/beta bifacial property.
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14580198 K.J.Hwang, B.Xiang, J.M.Gruschus, K.Y.Nam, K.T.No, M.Nirenberg, and J.A.Ferretti (2003).
Distortion of the three-dimensional structure of the vnd/NK-2 homeodomain bound to DNA induced by an embryonically lethal A35T point mutation.
  Biochemistry, 42, 12522-12531.
PDB code: 1qry
12825085 K.T.Forest, and M.S.Filutowicz (2003).
Remodeling of replication initiator proteins.
  Nat Struct Biol, 10, 496-498.
PDB code: 1hkq
12548619 W.Flader, B.Wellenzohn, R.H.Winger, A.Hallbrucker, E.Mayer, and K.R.Liedl (2003).
Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA.
  Biopolymers, 68, 139-149.  
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.
  Curr Opin Struct Biol, 12, 107-114.  
12138185 A.Jamai, E.Dubois, A.K.Vershon, and F.Messenguy (2002).
Swapping functional specificity of a MADS box protein: residues required for Arg80 regulation of arginine metabolism.
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12121651 A.Ke, J.R.Mathias, A.K.Vershon, and C.Wolberger (2002).
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.
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PDB code: 1k61
12052870 J.Mead, A.R.Bruning, M.K.Gill, A.M.Steiner, T.B.Acton, and A.K.Vershon (2002).
Interactions of the Mcm1 MADS box protein with cofactors that regulate mating in yeast.
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Interaction of serum response factor (SRF) with the Elk-1 B box inhibits RhoA-actin signaling to SRF and potentiates transcriptional activation by Elk-1.
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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.
  Mol Cell, 8, 937-946.  
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.  
11328878 X.Wang, and R.T.Simpson (2001).
Chromatin structure mapping in Saccharomyces cerevisiae in vivo with DNase I.
  Nucleic Acids Res, 29, 1943-1950.  
11726497 Y.Tanaka, O.Nureki, H.Kurumizaka, S.Fukai, S.Kawaguchi, M.Ikuta, J.Iwahara, T.Okazaki, and S.Yokoyama (2001).
Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA.
  EMBO J, 20, 6612-6618.
PDB code: 1hlv
10654939 C.E.Ducker, and R.T.Simpson (2000).
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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10856250 E.Gillitzer, G.Chen, and A.Stenlund (2000).
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.
  J Virol, 74, 1506-1512.  
11060038 I.M.Gavin, M.P.Kladde, and R.T.Simpson (2000).
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.
  EMBO J, 19, 2615-2628.
PDB code: 1c7u
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Conformational behavior of ionic self-complementary peptides.
  Protein Sci, 9, 1095-1105.  
  11104519 N.M.Luscombe, S.E.Austin, H.M.Berman, and J.M.Thornton (2000).
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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10727231 S.Deb, S.Bandyopadhyay, and S.Roy (2000).
DNA sequence dependent and independent conformational changes in multipartite operator recognition by lambda-repressor.
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10594003 T.B.Acton, J.Mead, A.M.Steiner, and A.K.Vershon (2000).
Scanning mutagenesis of Mcm1: residues required for DNA binding, DNA bending, and transcriptional activation by a MADS-box protein.
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Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers.
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Topology of the thyroid transcription factor 1 homeodomain-DNA complex.
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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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10410794 C.Wolberger (1999).
Multiprotein-DNA complexes in transcriptional regulation.
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10541551 D.Chasman, K.Cepek, P.A.Sharp, and C.O.Pabo (1999).
Crystal structure of an OCA-B peptide bound to an Oct-1 POU domain/octamer DNA complex: specific recognition of a protein-DNA interface.
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PDB code: 1cqt
10219246 J.A.Hirsch, C.Schubert, V.V.Gurevich, and P.B.Sigler (1999).
The 2.8 A crystal structure of visual arrestin: a model for arrestin's regulation.
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PDB code: 1cf1
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Combinatorial gene regulation by eukaryotic transcription factors.
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Transcription factors: the right combination for the DNA lock.
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The yeast a1 and alpha2 homeodomain proteins do not contribute equally to heterodimeric DNA binding.
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Transcription: activation by cooperating conformations.
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Reciprocal regulation of osteocalcin transcription by the homeodomain proteins Msx2 and Dlx5.
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9928492 J.E.Haber (1998).
Mating-type gene switching in Saccharomyces cerevisiae.
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A locus control region regulates yeast recombination.
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9914185 L.J.Maher (1998).
Mechanisms of DNA bending.
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10384309 M.Wahi, K.Komachi, and A.D.Johnson (1998).
Gene regulation by the yeast Ssn6-Tup1 corepressor.
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9634693 T.K.Kerppola (1998).
Transcriptional cooperativity: bending over backwards and doing the flip.
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Interaction of transcription factors with serum response factor. Identification of the Elk-1 binding surface.
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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.