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PDBsum entry 1kbh

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Transcription PDB id
1kbh

 

 

 

 

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Contents
Protein chains
47 a.a. *
59 a.a. *
* Residue conservation analysis
PDB id:
1kbh
Name: Transcription
Title: Mutual synergistic folding in the interaction between nuclear receptor coactivators cbp and actr
Structure: Nuclear receptor coactivator. Chain: a. Synonym: actr. Engineered: yes. Creb-binding protein. Chain: b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: actr. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse. Organism_taxid: 10090.
NMR struc: 20 models
Authors: S.J.Demarest,M.Martinez-Yamout,J.Chung,H.Chen,W.Xu,H.J.Dyson, R.M.Evans,P.E.Wright
Key ref:
S.J.Demarest et al. (2002). Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators. Nature, 415, 549-553. PubMed id: 11823864 DOI: 10.1038/415549a
Date:
06-Nov-01     Release date:   06-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9Y6Q9  (NCOA3_HUMAN) -  Nuclear receptor coactivator 3 from Homo sapiens
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1424 a.a.
47 a.a.
Protein chain
Pfam   ArchSchema ?
P45481  (CBP_MOUSE) -  Histone lysine acetyltransferase CREBBP from Mus musculus
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
2441 a.a.
59 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: Chains A, B: E.C.2.3.1.48  - histone acetyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-lysyl-[protein] + acetyl-CoA = N6-acetyl-L-lysyl-[protein] + CoA + H+
L-lysyl-[protein]
+ acetyl-CoA
= N(6)-acetyl-L-lysyl-[protein]
+ CoA
+ H(+)
   Enzyme class 2: Chain B: E.C.2.3.1.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1038/415549a Nature 415:549-553 (2002)
PubMed id: 11823864  
 
 
Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators.
S.J.Demarest, M.Martinez-Yamout, J.Chung, H.Chen, W.Xu, H.J.Dyson, R.M.Evans, P.E.Wright.
 
  ABSTRACT  
 
Nuclear hormone receptors are ligand-activated transcription factors that regulate the expression of genes that are essential for development, reproduction and homeostasis. The hormone response is mediated through recruitment of p160 receptor coactivators and the general transcriptional coactivator CBP/p300, which function synergistically to activate transcription. These coactivators exhibit intrinsic histone acetyltransferase activity, function in the remodelling of chromatin, and facilitate the recruitment of RNA polymerase II and the basal transcription machinery. The activities of the p160 coactivators are dependent on CBP. Both coactivators are essential for proper cell-cycle control, differentiation and apoptosis, and are implicated in cancer and other diseases. To elucidate the molecular basis of assembling the multiprotein activation complex, we undertook a structural and thermodynamic analysis of the interaction domains of CBP and the activator for thyroid hormone and retinoid receptors. Here we show that although the isolated domains are intrinsically disordered, they combine with high affinity to form a cooperatively folded helical heterodimer. Our study uncovers a unique mechanism, called 'synergistic folding', through which p160 coactivators recruit CBP/p300 to allow transmission of the hormonal signal to the transcriptional machinery.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: Solution structure of the ACTR -CBP complex. ACTR is pink and CBP blue in all figures. a, Stereo view showing best-fit superposition of backbone heavy atoms within the structured region. Residues at the boundaries of the structured region are numbered. b, Ribbon representation, in the same orientation as a. Helices A 1 -3 and C 1 -3, and the polyglutamine (polyQ) stretch in CBP are labelled. c, Surface representation of CBP domain, showing the hydrophobic groove formed by C 1 and C 3 that accommodates helix A 1 of ACTR. The orientation is the same as in a and b. Bulky hydrophobic residues from A 1 embedded within the groove are labelled. d, Surface representation of CBP domain, rotated to show the hydrophobic cleft that binds helix A 2 of ACTR. The interactions between A 3 and C 3 are also shown. Bulky hydrophobic residues of ACTR that form the molecular interface are labelled, as is Asp 1068, which participates in the buried salt bridge.
Figure 3.
Figure 3: Conserved interactions in the ACTR -CBP complex. a, Sequence alignment of the CBP binding domain of human ACTR(1018 -1088) and a representative set of p160 coactivators. b, Sequence alignment of the ACTR binding domain of murine CBP with other members of the CBP/p300 family. Conserved hydrophobic residues (green), conserved acidic residues (red), conserved basic residues (blue), and other conserved residues (orange) are indicated (h, human; m, murine, x, Xenopus laevis; d, Drosophila; dr, Danio rerio; c, Caenorhabditis elegans). c, -X-X- - and - -X-X- hydrophobic contact map defining the interface between ACTR and CBP ( denotes hydrophobic residue). The four -X-X- - motifs that comprise the hydrophobic core are enclosed by a green box. The buried intermolecular salt bridge is indicated. d, Close-up of the salt bridge between Arg 2105 and Asp 1068 salt bridge. The solvent-accessible surface of ACTR is shown.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2002, 415, 549-553) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21347390 D.Ruggiero, C.Dalmasso, T.Nutile, R.Sorice, L.Dionisi, M.Aversano, P.Bröet, A.L.Leutenegger, C.Bourgain, and M.Ciullo (2011).
Genetics of VEGF serum variation in human isolated populations of cilento: importance of VEGF polymorphisms.
  PLoS One, 6, e16982.  
21234644 M.Kjaergaard, S.Brander, and F.M.Poulsen (2011).
Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH.
  J Biomol NMR, 49, 139-149.  
20174674 A.B.Sigalov (2010).
Protein intrinsic disorder and oligomericity in cell signaling.
  Mol Biosyst, 6, 451-461.  
20308326 E.Herbig, L.Warfield, L.Fish, J.Fishburn, B.A.Knutson, B.Moorefield, D.Pacheco, and S.Hahn (2010).
Mechanism of Mediator recruitment by tandem Gcn4 activation domains and three Gal11 activator-binding domains.
  Mol Cell Biol, 30, 2376-2390.  
20556825 M.Kjaergaard, A.B.Nørholm, R.Hendus-Altenburger, S.F.Pedersen, F.M.Poulsen, and B.B.Kragelund (2010).
Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II?
  Protein Sci, 19, 1555-1564.  
20616042 M.Kjaergaard, K.Teilum, and F.M.Poulsen (2010).
Conformational selection in the molten globule state of the nuclear coactivator binding domain of CBP.
  Proc Natl Acad Sci U S A, 107, 12535-12540.
PDB code: 2kkj
20007729 Z.Dosztányi, B.Mészáros, and I.Simon (2010).
Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins.
  Brief Bioinform, 11, 225-243.  
19679084 A.del Sol, C.J.Tsai, B.Ma, and R.Nussinov (2009).
The origin of allosteric functional modulation: multiple pre-existing pathways.
  Structure, 17, 1042-1050.  
19412530 B.Mészáros, I.Simon, and Z.Dosztányi (2009).
Prediction of protein binding regions in disordered proteins.
  PLoS Comput Biol, 5, e1000376.  
19490121 D.S.Libich, M.Schwalbe, S.Kate, H.Venugopal, J.K.Claridge, P.J.Edwards, K.Dutta, and S.M.Pascal (2009).
Intrinsic disorder and coiled-coil formation in prostate apoptosis response factor 4.
  FEBS J, 276, 3710-3728.  
19357310 J.C.Ferreon, C.W.Lee, M.Arai, M.A.Martinez-Yamout, H.J.Dyson, and P.E.Wright (2009).
Cooperative regulation of p53 by modulation of ternary complex formation with CBP/p300 and HDM2.
  Proc Natl Acad Sci U S A, 106, 6591-6596.  
19214187 J.M.Wojciak, M.A.Martinez-Yamout, H.J.Dyson, and P.E.Wright (2009).
Structural basis for recruitment of CBP/p300 coactivators by STAT1 and STAT2 transactivation domains.
  EMBO J, 28, 948-958.
PDB codes: 2ka4 2ka6
19157855 P.E.Wright, and H.J.Dyson (2009).
Linking folding and binding.
  Curr Opin Struct Biol, 19, 31-38.  
19260013 P.Tompa, M.Fuxreiter, C.J.Oldfield, I.Simon, A.K.Dunker, and V.N.Uversky (2009).
Close encounters of the third kind: disordered domains and the interactions of proteins.
  Bioessays, 31, 328-335.  
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  J Biol Chem, 284, 7542-7552.  
19391622 S.H.Bae, H.J.Dyson, and P.E.Wright (2009).
Prediction of the rotational tumbling time for proteins with disordered segments.
  J Am Chem Soc, 131, 6814-6821.  
19678741 Y.B.Shi (2009).
Dual functions of thyroid hormone receptors in vertebrate development: the roles of histone-modifying cofactor complexes.
  Thyroid, 19, 987-999.  
19434099 Y.Sato, A.Ding, R.A.Heimeier, A.F.Yousef, J.S.Mymryk, P.G.Walfish, and Y.B.Shi (2009).
The adenoviral E1A protein displaces corepressors and relieves gene repression by unliganded thyroid hormone receptors in vivo.
  Cell Res, 19, 783-792.  
18400374 A.Ishizuya-Oka, and Y.B.Shi (2008).
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  Mol Cell Endocrinol, 288, 71-78.  
18698566 A.Miyagi, Y.Tsunaka, T.Uchihashi, K.Mayanagi, S.Hirose, K.Morikawa, and T.Ando (2008).
Visualization of intrinsically disordered regions of proteins by high-speed atomic force microscopy.
  Chemphyschem, 9, 1859-1866.  
18627125 C.A.Galea, Y.Wang, S.G.Sivakolundu, and R.W.Kriwacki (2008).
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  Biochemistry, 47, 7598-7609.  
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An allosteric circuit in caspase-1.
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PDB codes: 2h4w 2h4y 2h51 2h54
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19008886 M.Fuxreiter, P.Tompa, I.Simon, V.N.Uversky, J.C.Hansen, and F.J.Asturias (2008).
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Structural diversity in p160/CREB-binding protein coactivator complexes.
  J Biol Chem, 281, 14787-14795.
PDB code: 2c52
16649994 P.Y.Liu, T.Y.Hsieh, W.Y.Chou, and S.M.Huang (2006).
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  FEBS J, 273, 2172-2183.  
16923966 Q.Feng, P.Yi, J.Wong, and B.W.O'Malley (2006).
Signaling within a coactivator complex: methylation of SRC-3/AIB1 is a molecular switch for complex disassembly.
  Mol Cell Biol, 26, 7846-7857.  
16452926 R.Métivier, G.Reid, and F.Gannon (2006).
Transcription in four dimensions: nuclear receptor-directed initiation of gene expression.
  EMBO Rep, 7, 161-167.  
16894158 S.R.Loftus, D.Walker, M.J.Maté, D.A.Bonsor, R.James, G.R.Moore, and C.Kleanthous (2006).
Competitive recruitment of the periplasmic translocation portal TolB by a natively disordered domain of colicin E9.
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16287116 V.Receveur-Bréchot, J.M.Bourhis, V.N.Uversky, B.Canard, and S.Longhi (2006).
Assessing protein disorder and induced folding.
  Proteins, 62, 24-45.  
16507364 Y.Nominé, M.Masson, S.Charbonnier, K.Zanier, T.Ristriani, F.Deryckère, A.P.Sibler, D.Desplancq, R.A.Atkinson, E.Weiss, G.Orfanoudakis, B.Kieffer, and G.Travé (2006).
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  Mol Cell, 21, 665-678.
PDB code: 2fk4
15901728 B.D.Paul, D.R.Buchholz, L.Fu, and Y.B.Shi (2005).
Tissue- and gene-specific recruitment of steroid receptor coactivator-3 by thyroid hormone receptor during development.
  J Biol Chem, 280, 27165-27172.  
16154084 B.Y.Qin, C.Liu, H.Srinath, S.S.Lam, J.J.Correia, R.Derynck, and K.Lin (2005).
Crystal structure of IRF-3 in complex with CBP.
  Structure, 13, 1269-1277.  
16076839 C.Rochette-Egly (2005).
Dynamic combinatorial networks in nuclear receptor-mediated transcription.
  J Biol Chem, 280, 32565-32568.  
15738986 H.J.Dyson, and P.E.Wright (2005).
Intrinsically unstructured proteins and their functions.
  Nat Rev Mol Cell Biol, 6, 197-208.  
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MOZ-TIF2 inhibits transcription by nuclear receptors and p53 by impairment of CBP function.
  Mol Cell Biol, 25, 988.  
16094445 W.Xu (2005).
Nuclear receptor coactivators: the key to unlock chromatin.
  Biochem Cell Biol, 83, 418-428.  
15731352 Y.H.Lee, S.A.Coonrod, W.L.Kraus, M.A.Jelinek, and M.R.Stallcup (2005).
Regulation of coactivator complex assembly and function by protein arginine methylation and demethylimination.
  Proc Natl Acad Sci U S A, 102, 3611-3616.  
15221992 H.Hong, C.Kao, M.H.Jeng, J.N.Eble, M.O.Koch, T.A.Gardner, S.Zhang, L.Li, C.X.Pan, Z.Hu, G.T.MacLennan, and L.Cheng (2004).
Aberrant expression of CARM1, a transcriptional coactivator of androgen receptor, in the development of prostate carcinoma and androgen-independent status.
  Cancer, 101, 83-89.  
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p300 regulates the synergy of steroidogenic factor-1 and early growth response-1 in activating luteinizing hormone-beta subunit gene.
  J Biol Chem, 279, 7832-7839.  
15318225 M.J.Wood, G.Storz, and N.Tjandra (2004).
Structural basis for redox regulation of Yap1 transcription factor localization.
  Nature, 430, 917-921.
PDB code: 1sse
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Interaction of the TAZ1 domain of the CREB-binding protein with the activation domain of CITED2: regulation by competition between intrinsically unstructured ligands for non-identical binding sites.
  J Biol Chem, 279, 3042-3049.
PDB code: 1r8u
14691235 S.J.Demarest, S.Deechongkit, H.J.Dyson, R.M.Evans, and P.E.Wright (2004).
Packing, specificity, and mutability at the binding interface between the p160 coactivator and CREB-binding protein.
  Protein Sci, 13, 203-210.  
14722092 S.Matsuda, J.C.Harries, M.Viskaduraki, P.J.Troke, K.B.Kindle, C.Ryan, and D.M.Heery (2004).
A Conserved alpha-helical motif mediates the binding of diverse nuclear proteins to the SRC1 interaction domain of CBP.
  J Biol Chem, 279, 14055-14064.  
12732728 B.D.Nguyen, K.L.Abbott, K.Potempa, M.S.Kobor, J.Archambault, J.Greenblatt, P.Legault, and J.G.Omichinski (2003).
NMR structure of a complex containing the TFIIF subunit RAP74 and the RNA polymerase II carboxyl-terminal domain phosphatase FCP1.
  Proc Natl Acad Sci U S A, 100, 5688-5693.
PDB code: 1onv
14555998 B.Zagrovic, and V.S.Pande (2003).
Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties.
  Nat Struct Biol, 10, 955-961.  
12515863 H.Wang, and S.Chong (2003).
Visualization of coupled protein folding and binding in bacteria and purification of the heterodimeric complex.
  Proc Natl Acad Sci U S A, 100, 478-483.  
12885766 K.Brown, Y.Chen, T.M.Underhill, J.S.Mymryk, and J.Torchia (2003).
The coactivator p/CIP/SRC-3 facilitates retinoic acid receptor signaling via recruitment of GCN5.
  J Biol Chem, 278, 39402-39412.  
12676584 K.Deguchi, P.M.Ayton, M.Carapeti, J.L.Kutok, C.S.Snyder, I.R.Williams, N.C.Cross, C.K.Glass, M.L.Cleary, and D.G.Gilliland (2003).
MOZ-TIF2-induced acute myeloid leukemia requires the MOZ nucleosome binding motif and TIF2-mediated recruitment of CBP.
  Cancer Cell, 3, 259-271.  
14555995 K.Takahasi, N.N.Suzuki, M.Horiuchi, M.Mori, W.Suhara, Y.Okabe, Y.Fukuhara, H.Terasawa, S.Akira, T.Fujita, and F.Inagaki (2003).
X-ray crystal structure of IRF-3 and its functional implications.
  Nat Struct Biol, 10, 922-927.
PDB code: 1j2f
12486728 M.Albrecht, D.Hoffmann, B.O.Evert, I.Schmitt, U.Wüllner, and T.Lengauer (2003).
Structural modeling of ataxin-3 reveals distant homology to adaptins.
  Proteins, 50, 355-370.  
12736264 R.J.Simpson, E.D.Cram, R.Czolij, J.M.Matthews, M.Crossley, and J.P.Mackay (2003).
CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions.
  J Biol Chem, 278, 28011-28018.
PDB code: 1p7a
14604535 R.Linding, L.J.Jensen, F.Diella, P.Bork, T.J.Gibson, and R.B.Russell (2003).
Protein disorder prediction: implications for structural proteomics.
  Structure, 11, 1453-1459.  
12824398 R.Linding, R.B.Russell, V.Neduva, and T.J.Gibson (2003).
GlobPlot: Exploring protein sequences for globularity and disorder.
  Nucleic Acids Res, 31, 3701-3708.  
14675539 R.Métivier, G.Penot, M.R.Hübner, G.Reid, H.Brand, M.Kos, and F.Gannon (2003).
Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter.
  Cell, 115, 751-763.  
12825087 S.Bhattacharya, and P.J.Ratcliffe (2003).
ExCITED about HIF.
  Nat Struct Biol, 10, 501-503.  
12771138 Y.Liang, F.Du, S.Sanglier, B.R.Zhou, Y.Xia, A.Van Dorsselaer, C.Maechling, M.C.Kilhoffer, and J.Haiech (2003).
Unfolding of rabbit muscle creatine kinase induced by acid. A study using electrospray ionization mass spectrometry, isothermal titration calorimetry, and fluorescence spectroscopy.
  J Biol Chem, 278, 30098-30105.  
12727881 Z.Q.Huang, J.Li, L.M.Sachs, P.A.Cole, and J.Wong (2003).
A role for cofactor-cofactor and cofactor-histone interactions in targeting p300, SWI/SNF and Mediator for transcription.
  EMBO J, 22, 2146-2155.  
11893728 D.Burakov, L.A.Crofts, C.P.Chang, and L.P.Freedman (2002).
Reciprocal recruitment of DRIP/mediator and p160 coactivator complexes in vivo by estrogen receptor.
  J Biol Chem, 277, 14359-14362.  
12507421 F.Picard, M.Géhin, J.Annicotte, S.Rocchi, M.F.Champy, B.W.O'Malley, P.Chambon, and J.Auwerx (2002).
SRC-1 and TIF2 control energy balance between white and brown adipose tissues.
  Cell, 111, 931-941.  
12209130 J.R.Tata (2002).
Signalling through nuclear receptors.
  Nat Rev Mol Cell Biol, 3, 702-710.  
11955428 K.P.Hoeflich, and M.Ikura (2002).
Calmodulin in action: diversity in target recognition and activation mechanisms.
  Cell, 108, 739-742.  
12271132 M.M.Dedmon, C.N.Patel, G.B.Young, and G.J.Pielak (2002).
FlgM gains structure in living cells.
  Proc Natl Acad Sci U S A, 99, 12681-12684.  
12192059 M.S.Qutob, R.N.Bhattacharjee, E.Pollari, S.P.Yee, and J.Torchia (2002).
Microtubule-dependent subcellular redistribution of the transcriptional coactivator p/CIP.
  Mol Cell Biol, 22, 6611-6626.  
12205094 N.K.Goto, T.Zor, M.Martinez-Yamout, H.J.Dyson, and P.E.Wright (2002).
Cooperativity in transcription factor binding to the coactivator CREB-binding protein (CBP). The mixed lineage leukemia protein (MLL) activation domain binds to an allosteric site on the KIX domain.
  J Biol Chem, 277, 43168-43174.  
12368089 P.Tompa (2002).
Intrinsically unstructured proteins.
  Trends Biochem Sci, 27, 527-533.  
11959977 S.A.Dames, M.Martinez-Yamout, R.N.De Guzman, H.J.Dyson, and P.E.Wright (2002).
Structural basis for Hif-1 alpha /CBP recognition in the cellular hypoxic response.
  Proc Natl Acad Sci U S A, 99, 5271-5276.
PDB code: 1l8c
11959990 S.J.Freedman, Z.Y.Sun, F.Poy, A.L.Kung, D.M.Livingston, G.Wagner, and M.J.Eck (2002).
Structural basis for recruitment of CBP/p300 by hypoxia-inducible factor-1 alpha.
  Proc Natl Acad Sci U S A, 99, 5367-5372.
PDB code: 1l3e
12208951 T.Kino, A.Gragerov, O.Slobodskaya, M.Tsopanomichalou, G.P.Chrousos, and G.N.Pavlakis (2002).
Human immunodeficiency virus type 1 (HIV-1) accessory protein Vpr induces transcription of the HIV-1 and glucocorticoid-responsive promoters by binding directly to p300/CBP coactivators.
  J Virol, 76, 9724-9734.  
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