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A number of transcription factors contain a conserved domain of 56 amino-acid residues, sometimes known as the MADS-box domain. They are listed below:

• Serum response factor (SRF) [1], a mammalian transcription factor that binds to the Serum Response Element (SRE). This is a short sequence of dyad symmetry located 300 bp to the 5' end of the transcription initiation site of genes such as c-fos.
• Mammalian myocyte-specific enhancer factors 2A to 2D (MEF2A to MEF2D). These proteins are transcription factor which binds specifically to the MEF2 element present in the regulatory regions of many muscle-specific genes.
• Drosophila myocyte-specific enhancer factor 2 (MEF2).
• Yeast GRM/PRTF protein (gene MCM1) [2], a transcriptional regulator of mating-type-specific genes.
• Yeast arginine metabolism regulation protein I (gene ARGR1 or ARG80).
• Yeast transcription factor RLM1.
• Yeast transcription factor SMP1.
• Arabidopsis thaliana agamous protein (AG) [3], a probable transcription factor involved in regulating genes that determines stamen and carpel development in wild-type flowers. Mutations in the AG gene result in the replacement of the stamens by petals and the carpels by a new flower.
• Arabidopsis thaliana homeotic proteins Apetala1 (AP1), Apetala3 (AP3) and Pistillata (PI) which act locally to specify the identity of the floral meristem and to determine sepal and petal development [4].
• Antirrhinum majus and tobacco homeotic protein deficiens (DEFA) and globosa (GLO) [5]. Both proteins are transcription factors involved in the genetic control of flower development. Mutations in DEFA or GLO cause the transformation of petals into sepals and of stamina into carpels.
• Arabidopsis thaliana putative transcription factors AGL1 to AGL6 [6].
• Antirrhinum majus morphogenetic protein DEF H33 (squamosa).

In SRF, the conserved domain has been shown [1] to be involved in DNA-binding and dimerization. We have derived a pattern that spans the complete length of the domain. The profile also spans the length of the MADS-box.

April 2006 / Pattern revised.

PROSITE methods (with tools and information) covered by this documentation:

MADS_BOX_2, PS50066; MADS-box domain profile  (MATRIX)

Sequences known to belong to this class detected by the profile: ALL Other sequence(s) detected in Swiss-Prot: NONE.

• Domain architecture view of Swiss-Prot proteins matching PS50066 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS50066 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS50066 • Scan Swiss-Prot/TrEMBL entries against PS50066 • view ligand binding statistics

Matching PDB structures: 1C7U 1EGW 1HBX 1K6O ... [ALL]

MADS_BOX_1, PS00350; MADS-box domain signature  (PATTERN)

Consensus pattern: [RGS]-x-[RKS]-x(5)-[IL]-x-[DNGSK]-x(3)-[KR]-x(2)-T-[FY]-x-[RK](3)-x(2)-[LIVM]-x-[KE]-K-[AT]-x-[EQ]-[LIVM]-[STA]-x-L-x(4)-[LIVM]-x-[LIVM]-[LIVMT]-[LIVM]-x(6)-[LIVMFC]-x(2)-[FYLS] Sequences known to belong to this class detected by the pattern: ALL Other sequence(s) detected in Swiss-Prot: NONE.

• Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS00350 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS00350 • Scan Swiss-Prot/TrEMBL entries against PS00350 • view ligand binding statistics

Matching PDB structures: 1C7U 1EGW 1HBX 1K6O ... [ALL]

1	Authors	Norman C., Runswick M., Pollock R., Treisman R.
	Title	Isolation and properties of cDNA clones encoding SRF, a transcription factor that binds to the c-fos serum response element.
	Source	Cell 55:989-1003(1988).
	PubMed ID	3203386

2	Authors	Passmore S., Maine G.T., Elble R., Christ C., Tye B.-K.
	Title	Saccharomyces cerevisiae protein involved in plasmid maintenance is necessary for mating of MAT alpha cells.
	Source	J. Mol. Biol. 204:593-606(1988).
	PubMed ID	3066908

3	Authors	Yanofsky M.F., Ma H., Bowman J.L., Drews G.N., Feldmann K.A., Meyerowitz E.M.
	Title	The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors.
	Source	Nature 346:35-39(1990).
	PubMed ID	1973265
	DOI	10.1038/346035a0

4	Authors	Goto K., Meyerowitz E.M.
	Title	Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA.
	Source	Genes Dev. 8:1548-1560(1994).
	PubMed ID	7958839

5	Authors	Troebner W., Ramirez L., Motte P., Hue I., Huijser P., Loennig W.-E., Saedler H., Sommer H., Schwartz-Sommer Z.
	Source	EMBO J. 11:4693-4704(1992).

6	Authors	Ma H., Yanofsky M.F., Meyerowitz E.M.
	Title	AGL1-AGL6, an Arabidopsis gene family with similarity to floral homeotic and transcription factor genes.
	Source	Genes Dev. 5:484-495(1991).
	PubMed ID	1672119

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