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Contents |
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* Residue conservation analysis
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Enzyme class:
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Chains A, B:
E.C.?
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Nature
376:490-498
(1995)
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PubMed id:
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Structure of serum response factor core bound to DNA.
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L.Pellegrini,
S.Tan,
T.J.Richmond.
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ABSTRACT
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The human serum response factor is a transcription factor belonging to the MADS
domain protein family with members characterized from the plant and animal
kingdoms. The X-ray crystal structure of the serum response factor core in a
specific-recognition DNA complex shows that the functions of DNA binding,
dimerization and accessory-factor interaction are compactly integrated into a
novel protein unit. The intrinsic and induced conformation of the serum response
element DNA is the principal DNA feature recognized in the specific complex.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.Neph,
J.Vierstra,
A.B.Stergachis,
A.P.Reynolds,
E.Haugen,
B.Vernot,
R.E.Thurman,
S.John,
R.Sandstrom,
A.K.Johnson,
M.T.Maurano,
R.Humbert,
E.Rynes,
H.Wang,
S.Vong,
K.Lee,
D.Bates,
M.Diegel,
V.Roach,
D.Dunn,
J.Neri,
A.Schafer,
R.S.Hansen,
T.Kutyavin,
E.Giste,
M.Weaver,
T.Canfield,
P.Sabo,
M.Zhang,
G.Balasundaram,
R.Byron,
M.J.MacCoss,
J.M.Akey,
M.A.Bender,
M.Groudine,
R.Kaul,
and
J.A.Stamatoyannopoulos
(2012).
An expansive human regulatory lexicon encoded in transcription factor footprints.
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Nature,
489,
83-90.
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S.K.Yoo,
X.Wu,
J.S.Lee,
and
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(2011).
AGAMOUS-LIKE 6 is a floral promoter that negatively regulates the FLC/MAF clade genes and positively regulates FT in Arabidopsis.
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Plant J,
65,
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Conservation and evolution in and among SRF- and MEF2-type MADS domains and their binding sites.
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Mol Biol Evol,
28,
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A.D.van Dijk,
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Conserved and variable correlated mutations in the plant MADS protein network.
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BMC Genomics,
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C.Liu,
J.Zhang,
N.Zhang,
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Z.Meng,
H.Kong,
and
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(2010).
Interactions among proteins of floral MADS-box genes in basal eudicots: implications for evolution of the regulatory network for flower development.
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Mol Biol Evol,
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Linking actin dynamics and gene transcription to drive cellular motile functions.
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On the origin of MADS-domain transcription factors.
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GORDITA (AGL63) is a young paralog of the Arabidopsis thaliana B(sister) MADS box gene ABS (TT16) that has undergone neofunctionalization.
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Plant J,
63,
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S.van Mourik,
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K.Kaufmann,
G.C.Angenent,
R.C.van Ham,
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(2010).
Continuous-time modeling of cell fate determination in Arabidopsis flowers.
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BMC Syst Biol,
4,
101.
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T.Nagata,
E.Niyada,
N.Fujimoto,
Y.Nagasaki,
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Y.Miyanoiri,
J.Murata,
K.Hiratsuka,
and
M.Katahira
(2010).
Solution structures of the trihelix DNA-binding domains of the wild-type and a phosphomimetic mutant of Arabidopsis GT-1: mechanism for an increase in DNA-binding affinity through phosphorylation.
|
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Proteins,
78,
3033-3047.
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PDB codes:
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W.Wu,
X.Shen,
and
S.Tao
(2010).
Characteristics of the CArG-SRF binding context in mammalian genomes.
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| |
Mamm Genome,
21,
104-113.
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A.L.Blaker,
J.M.Taylor,
and
C.P.Mack
(2009).
PKA-dependent phosphorylation of serum response factor inhibits smooth muscle-specific gene expression.
|
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Arterioscler Thromb Vasc Biol,
29,
2153-2160.
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K.Kaufmann,
J.M.Muiño,
R.Jauregui,
C.A.Airoldi,
C.Smaczniak,
P.Krajewski,
and
G.C.Angenent
(2009).
Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower.
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PLoS Biol,
7,
e1000090.
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R.Melzer,
and
G.Theissen
(2009).
Reconstitution of 'floral quartets' in vitro involving class B and class E floral homeotic proteins.
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Nucleic Acids Res,
37,
2723-2736.
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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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| |
Plant J,
55,
832-843.
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Y.Ito,
M.Kitagawa,
N.Ihashi,
K.Yabe,
J.Kimbara,
J.Yasuda,
H.Ito,
T.Inakuma,
S.Hiroi,
and
T.Kasumi
(2008).
DNA-binding specificity, transcriptional activation potential, and the rin mutation effect for the tomato fruit-ripening regulator RIN.
|
| |
Plant J,
55,
212-223.
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Z.Niu,
D.Iyer,
S.J.Conway,
J.F.Martin,
K.Ivey,
D.Srivastava,
A.Nordheim,
and
R.J.Schwartz
(2008).
Serum response factor orchestrates nascent sarcomerogenesis and silences the biomineralization gene program in the heart.
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Proc Natl Acad Sci U S A,
105,
17824-17829.
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J.Stepanek,
M.Vincent,
P.Y.Turpin,
D.Paulin,
S.Fermandjian,
B.Alpert,
and
C.Zentz
(2007).
C-->G base mutations in the CArG box of c-fos serum response element alter its bending flexibility. Consequences for core-SRF recognition.
|
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FEBS J,
274,
2333-2348.
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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.
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D.Iyer,
D.Chang,
J.Marx,
L.Wei,
E.N.Olson,
M.S.Parmacek,
A.Balasubramanyam,
and
R.J.Schwartz
(2006).
Serum response factor MADS box serine-162 phosphorylation switches proliferation and myogenic gene programs.
|
| |
Proc Natl Acad Sci U S A,
103,
4516-4521.
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O.G.McDonald,
B.R.Wamhoff,
M.H.Hoofnagle,
and
G.K.Owens
(2006).
Control of SRF binding to CArG box chromatin regulates smooth muscle gene expression in vivo.
|
| |
J Clin Invest,
116,
36-48.
|
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P.Prabakaran,
J.G.Siebers,
S.Ahmad,
M.M.Gromiha,
M.G.Singarayan,
and
A.Sarai
(2006).
Classification of protein-DNA complexes based on structural descriptors.
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| |
Structure,
14,
1355-1367.
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Q.Sun,
G.Chen,
J.W.Streb,
X.Long,
Y.Yang,
C.J.Stoeckert,
and
J.M.Miano
(2006).
Defining the mammalian CArGome.
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| |
Genome Res,
16,
197-207.
|
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S.L.Williams,
L.K.Parkhurst,
and
L.J.Parkhurst
(2006).
Changes in DNA bending and flexing due to tethered cations detected by fluorescence resonance energy transfer.
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| |
Nucleic Acids Res,
34,
1028-1035.
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S.de Folter,
and
G.C.Angenent
(2006).
trans meets cis in MADS science.
|
| |
Trends Plant Sci,
11,
224-231.
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Z.X.Chen,
J.G.Wu,
W.N.Ding,
H.M.Chen,
P.Wu,
and
C.H.Shi
(2006).
Morphogenesis and molecular basis on naked seed rice, a novel homeotic mutation of OsMADS1 regulating transcript level of AP3 homologue in rice.
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| |
Planta,
223,
882-890.
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|
|
A.Huet,
A.Parlakian,
M.C.Arnaud,
J.M.Glandières,
P.Valat,
S.Fermandjian,
D.Paulin,
B.Alpert,
and
C.Zentz
(2005).
Mechanism of binding of serum response factor to serum response element.
|
| |
FEBS J,
272,
3105-3119.
|
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C.René,
M.Taulan,
F.Iral,
J.Doudement,
A.L'Honoré,
C.Gerbon,
J.Demaille,
M.Claustres,
and
M.C.Romey
(2005).
Binding of serum response factor to cystic fibrosis transmembrane conductance regulator CArG-like elements, as a new potential CFTR transcriptional regulation pathway.
|
| |
Nucleic Acids Res,
33,
5271-5290.
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J.L.Asensio,
A.Albert,
D.Muñoz-Espín,
C.Gonzalez,
J.Hermoso,
L.Villar,
J.Jiménez-Barbero,
M.Salas,
and
W.J.Meijer
(2005).
Structure of the functional domain of phi29 replication organizer: insights into oligomerization and dna binding.
|
| |
J Biol Chem,
280,
20730-20739.
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PDB codes:
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J.W.Streb,
and
J.M.Miano
(2005).
AKAP12alpha, an atypical serum response factor-dependent target gene.
|
| |
J Biol Chem,
280,
4125-4134.
|
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|
A.Reményi,
H.R.Schöler,
and
M.Wilmanns
(2004).
Combinatorial control of gene expression.
|
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Nat Struct Mol Biol,
11,
812-815.
|
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|
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E.A.Carr,
J.Mead,
and
A.K.Vershon
(2004).
Alpha1-induced DNA bending is required for transcriptional activation by the Mcm1-alpha1 complex.
|
| |
Nucleic Acids Res,
32,
2298-2305.
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K.Wheaton,
and
K.Riabowol
(2004).
Protein kinase C delta blocks immediate-early gene expression in senescent cells by inactivating serum response factor.
|
| |
Mol Cell Biol,
24,
7298-7311.
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R.Escalante,
N.Iranfar,
L.Sastre,
and
W.F.Loomis
(2004).
Identification of genes dependent on the MADS box transcription factor SrfA in Dictyostelium discoideum development.
|
| |
Eukaryot Cell,
3,
564-566.
|
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|
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.
|
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PDB code:
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C.Köhler,
L.Hennig,
C.Spillane,
S.Pien,
W.Gruissem,
and
U.Grossniklaus
(2003).
The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1.
|
| |
Genes Dev,
17,
1540-1553.
|
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|
|
|
|
|
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.
|
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|
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.
|
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|
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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.
|
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L.P.Martinez-Castilla,
and
E.R.Alvarez-Buylla
(2003).
Adaptive evolution in the Arabidopsis MADS-box gene family inferred from its complete resolved phylogeny.
|
| |
Proc Natl Acad Sci U S A,
100,
13407-13412.
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R.Escalante,
N.Moreno,
and
L.Sastre
(2003).
Dictyostelium discoideum developmentally regulated genes whose expression is dependent on MADS box transcription factor SrfA.
|
| |
Eukaryot Cell,
2,
1327-1335.
|
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|
|
|
|
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.
|
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A.J.Warren
(2002).
Eukaryotic transcription factors.
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| |
Curr Opin Struct Biol,
12,
107-114.
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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.
|
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|
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|
|
D.Wang,
R.Passier,
Z.P.Liu,
C.H.Shin,
Z.Wang,
S.Li,
L.B.Sutherland,
E.Small,
P.A.Krieg,
and
E.N.Olson
(2002).
Regulation of cardiac growth and development by SRF and its cofactors.
|
| |
Cold Spring Harb Symp Quant Biol,
67,
97.
|
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|
|
E.M.Meyerowitz
(2002).
Plants compared to animals: the broadest comparative study of development.
|
| |
Science,
295,
1482-1485.
|
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|
J.L.Sepulveda,
S.Vlahopoulos,
D.Iyer,
N.Belaguli,
and
R.J.Schwartz
(2002).
Combinatorial expression of GATA4, Nkx2-5, and serum response factor directs early cardiac gene activity.
|
| |
J Biol Chem,
277,
25775-25782.
|
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|
|
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|
|
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.
|
|
|
|
|
|
|
K.U.Winter,
H.Saedler,
and
G.Theissen
(2002).
On the origin of class B floral homeotic genes: functional substitution and dominant inhibition in Arabidopsis by expression of an orthologue from the gymnosperm Gnetum.
|
| |
Plant J,
31,
457-475.
|
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|
S.Avila,
M.C.Casero,
R.Fernandez-Cantón,
and
L.Sastre
(2002).
Transactivation domains are not functionally conserved between vertebrate and invertebrate serum response factors.
|
| |
Eur J Biochem,
269,
3669-3677.
|
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|
|
S.K.Burley,
and
K.Kamada
(2002).
Transcription factor complexes.
|
| |
Curr Opin Struct Biol,
12,
225-230.
|
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|
|
|
|
G.Schratt,
B.Weinhold,
A.S.Lundberg,
S.Schuck,
J.Berger,
H.Schwarz,
R.A.Weinberg,
U.Rüther,
and
A.Nordheim
(2001).
Serum response factor is required for immediate-early gene activation yet is dispensable for proliferation of embryonic stem cells.
|
| |
Mol Cell Biol,
21,
2933-2943.
|
|
|
|
|
|
|
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:
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|
|
S.D.Hauschka
(2001).
Myocardin. a novel potentiator of SRF-mediated transcription in cardiac muscle.
|
| |
Mol Cell,
8,
1-2.
|
|
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|
|
S.S.Hook,
and
A.R.Means
(2001).
Ca(2+)/CaM-dependent kinases: from activation to function.
|
| |
Annu Rev Pharmacol Toxicol,
41,
471-505.
|
|
|
|
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|
|
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:
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|
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B.Weinhold,
G.Schratt,
S.Arsenian,
J.Berger,
K.Kamino,
H.Schwarz,
U.Rüther,
and
A.Nordheim
(2000).
Srf(-/-) ES cells display non-cell-autonomous impairment in mesodermal differentiation.
|
| |
EMBO J,
19,
5835-5844.
|
|
|
|
|
|
|
C.M.White,
O.Heidenreich,
A.Nordheim,
and
T.A.Beerman
(2000).
Evaluation of the effectiveness of DNA-binding drugs to inhibit transcription using the c-fos serum response element as a target.
|
| |
Biochemistry,
39,
12262-12273.
|
|
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|
|
J.M.Miano,
M.J.Carlson,
J.A.Spencer,
and
R.P.Misra
(2000).
Serum response factor-dependent regulation of the smooth muscle calponin gene.
|
| |
J Biol Chem,
275,
9814-9822.
|
|
|
|
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|
|
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:
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|
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K.Kvint,
C.Hosbond,
A.Farewell,
O.Nybroe,
and
T.Nyström
(2000).
Emergency derepression: stringency allows RNA polymerase to override negative control by an active repressor.
|
| |
Mol Microbiol,
35,
435-443.
|
|
|
|
|
|
|
L.D.Williams,
and
L.J.Maher
(2000).
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