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PDBsum entry 1mnm

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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   ArchSchema ?
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     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.
 
  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 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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20724380 W.Wu, X.Huang, J.Cheng, Z.Li, S.de Folter, Z.Huang, X.Jiang, H.Pang, and S.Tao (2011).
Conservation and evolution in and among SRF- and MEF2-type MADS domains and their binding sites.
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The tumor suppressor p53: from structures to drug discovery.
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20385083 J.Leatherwood, and B.Futcher (2010).
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.
  Genes Dev, 24, 893-903.  
20385087 Z.Darieva, A.Clancy, R.Bulmer, E.Williams, A.Pic-Taylor, B.A.Morgan, and A.D.Sharrocks (2010).
A competitive transcription factor binding mechanism determines the timing of late cell cycle-dependent gene expression.
  Mol Cell, 38, 29-40.  
19360118 G.Freckleton, S.I.Lippman, J.R.Broach, and S.Tavazoie (2009).
Microarray profiling of phage-display selections for rapid mapping of transcription factor-DNA interactions.
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19305407 J.R.Hesselberth, X.Chen, Z.Zhang, P.J.Sabo, R.Sandstrom, A.P.Reynolds, R.E.Thurman, S.Neph, M.S.Kuehn, W.S.Noble, S.Fields, and J.A.Stamatoyannopoulos (2009).
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting.
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Impact of DNA-binding position variants on yeast gene expression.
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19289051 S.Balasubramanian, F.Xu, and W.K.Olson (2009).
DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences.
  Biophys J, 96, 2245-2260.  
19233144 S.Yoon, and A.G.Hinnebusch (2009).
Mcm1p binding sites in ARG1 positively regulate Gcn4p binding and SWI/SNF recruitment.
  Biochem Biophys Res Commun, 381, 123-128.  
19686662 Y.Yonetani, and H.Kono (2009).
Sequence dependencies of DNA deformability and hydration in the minor groove.
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18466303 J.Lee, M.Oh, H.Park, and I.Lee (2008).
SOC1 translocated to the nucleus by interaction with AGL24 directly regulates leafy.
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18271625 X.Y.Li, S.MacArthur, R.Bourgon, D.Nix, D.A.Pollard, V.N.Iyer, A.Hechmer, L.Simirenko, M.Stapleton, C.L.Luengo Hendriks, H.C.Chu, N.Ogawa, W.Inwood, V.Sementchenko, A.Beaton, R.Weiszmann, S.E.Celniker, D.W.Knowles, T.Gingeras, T.P.Speed, M.B.Eisen, and M.D.Biggin (2008).
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm.
  PLoS Biol, 6, e27.  
18075577 J.Kuriyan, and D.Eisenberg (2007).
The origin of protein interactions and allostery in colocalization.
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17510955 K.Takano, Y.Katagiri, A.Mukaiyama, H.Chon, H.Matsumura, Y.Koga, and S.Kanaya (2007).
Conformational contagion in a protein: structural properties of a chameleon sequence.
  Proteins, 68, 617-625.
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?
  Bioessays, 29, 1095-1104.  
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.
  Mol Cell Biol, 26, 4134-4148.  
  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.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 340-345.
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.
  Eukaryot Cell, 5, 1957-1968.  
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.
  Eukaryot Cell, 4, 1808-1819.  
  16511069 J.Jeyakanthan, E.Inagaki, C.Kuroishi, and T.H.Tahirov (2005).
Structure of PIN-domain protein PH0500 from Pyrococcus horikoshii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 463-468.
PDB codes: 1v96 1ye5
15332082 A.Reményi, H.R.Schöler, and M.Wilmanns (2004).
Combinatorial control of gene expression.
  Nat Struct Mol Biol, 11, 812-815.  
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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15173185 E.N.Andreishcheva, J.P.Kunkel, T.R.Gemmill, and R.B.Trimble (2004).
Five genes involved in biosynthesis of the pyruvylated Galbeta1,3-epitope in Schizosaccharomyces pombe N-linked glycans.
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15289616 S.Yoon, C.K.Govind, H.Qiu, S.J.Kim, J.Dong, and A.G.Hinnebusch (2004).
Recruitment of the ArgR/Mcm1p repressor is stimulated by the activator Gcn4p: a self-checking activation mechanism.
  Proc Natl Acad Sci U S A, 101, 11713-11718.  
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.
  J Biol Chem, 279, 3758-3765.
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.
  Nature, 422, 730-734.
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.
  BMC Evol Biol, 3, 19.  
12888520 C.Van Slyke, and E.J.Grayhack (2003).
The essential transcription factor Reb1p interacts with the CLB2 UAS outside of the G2/M control region.
  Nucleic Acids Res, 31, 4597-4607.  
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.
  Mol Cell Biol, 23, 450-461.  
12784213 J.Aishima, and C.Wolberger (2003).
Insights into nonspecific binding of homeodomains from a structure of MATalpha2 bound to DNA.
  Proteins, 51, 544-551.  
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.
  Nucleic Acids Res, 31, 2279-2288.  
14573865 K.Ikeda, and J.Higo (2003).
Free-energy landscape of a chameleon sequence in explicit water and its inherent alpha/beta bifacial property.
  Protein Sci, 12, 2542-2548.  
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.
  Plant J, 33, 47-59.  
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.
  Mol Cell Biol, 22, 5741-5752.  
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.
  Structure, 10, 961-971.
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.
  Mol Cell Biol, 22, 430-441.  
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.
  J Pept Res, 59, 34-43.  
12466549 J.Aishima, R.K.Gitti, J.E.Noah, H.H.Gan, T.Schlick, and C.Wolberger (2002).
A Hoogsteen base pair embedded in undistorted B-DNA.
  Nucleic Acids Res, 30, 5244-5252.
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.
  Mol Cell Biol, 22, 4607-4621.  
12242287 K.Murai, and R.Treisman (2002).
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.
  Mol Cell Biol, 22, 7083-7092.  
11959501 S.K.Burley, and K.Kamada (2002).
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.
  Nucleic Acids Res, 30, 1182-1191.  
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.
  EMBO J, 19, 400-409.  
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.
  EMBO J, 19, 3069-3079.  
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.
  EMBO J, 19, 5875-5883.  
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
  10892803 M.Altman, P.Lee, A.Rich, and S.Zhang (2000).
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.
  Genome Biol, 1, REVIEWS001.  
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.
  Proc Natl Acad Sci U S A, 97, 3901-3906.  
10727231 S.Deb, S.Bandyopadhyay, and S.Roy (2000).
DNA sequence dependent and independent conformational changes in multipartite operator recognition by lambda-repressor.
  Biochemistry, 39, 3377-3383.  
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.
  Mol Cell Biol, 20, 1.  
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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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9890883 A.Scaloni, M.Monti, R.Acquaviva, G.Tell, G.Damante, S.Formisano, and P.Pucci (1999).
Topology of the thyroid transcription factor 1 homeodomain-DNA complex.
  Biochemistry, 38, 64-72.  
10449733 B.S.Wang, and C.O.Pabo (1999).
Dimerization of zinc fingers mediated by peptides evolved in vitro from random sequences.
  Proc Natl Acad Sci U S A, 96, 9568-9573.  
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.
  Genes Dev, 13, 2650-2657.
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
10047576 L.Chen (1999).
Combinatorial gene regulation by eukaryotic transcription factors.
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10375516 S.Khorasanizadeh, and F.Rastinejad (1999).
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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Quantitative evaluation of the chicken lysozyme epitope in the HyHEL-10 Fab complex: free energies and kinetics.
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9742392 A.Travers (1998).
Transcription: activation by cooperating conformations.
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Combinatorial transcription factors.
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Mcm1 regulates donor preference controlled by the recombination enhancer in Saccharomyces mating-type switching.
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9748284 D.Meierhans, and R.K.Allemann (1998).
The N-terminal methionine is a major determinant of the DNA binding specificity of MEF-2C.
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9819228 E.P.Newberry, T.Latifi, and D.A.Towler (1998).
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.
  Annu Rev Genet, 32, 561-599.  
9724964 J.E.Haber (1998).
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.
  Cold Spring Harb Symp Quant Biol, 63, 447-457.  
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.
  J Biol Chem, 273, 10506-10514.  
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.