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Title :   SOLUTION STRUCTURE AND DYNAMICS OF THE DNA-BINDING DOMAIN OF MYOCYTE NUCLEAR FACTOR

Authors :   W. -J. Chuang, C. -H. Chang, W. -Y. Jeng, Y. -P. Chu

Date :   19 Sep 05 (Deposition) - 05 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Dna-Binding Domain, Winged-Helix, Forkhead, Nmr, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. -H. Chang, Y. -P. Chu, W. -Y. Jeng, W. -J. Chuang
Solution Structure And Backbone Dynamics Of The Dna-Binding Domain Of Myocyte Nuclear Factor (Foxk1)
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - FORKHEAD BOX PROTEIN K1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA-BINDING DOMAIN
	Gene	:	FOXK1
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	MYOCYTE NUCLEAR FACTOR, MNF


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2D2W)

(no "Site" information available for 2D2W)

(no "SS Bond" information available for 2D2W)

(no "Cis Peptide Bond" information available for 2D2W)

(no "SAP(SNP)/Variant" information available for 2D2W)

NMR Structure (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FORK_HEAD_1	PS00657	Fork head domain signature 1.	FOXK1_MOUSE	291-304	1	A:3-16
2	FORK_HEAD_3	PS50039	Fork head domain profile.	FOXK1_MOUSE	291-386	1	A:3-98
3	FORK_HEAD_2	PS00658	Fork head domain signature 2.	FOXK1_MOUSE	335-341	1	A:47-53

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENSMUST00000072837	1a	ENSMUSE00000590046	chr5:142877451-142877995	545	FOXK1_MOUSE	1-173	173	0	-	-
1.2	ENSMUST00000072837	2	ENSMUSE00000474194	chr5:142911095-142911280	186	FOXK1_MOUSE	173-235	63	0	-	-
1.3	ENSMUST00000072837	3	ENSMUSE00000590045	chr5:142924641-142924797	157	FOXK1_MOUSE	235-287	53	0	-	-
1.4	ENSMUST00000072837	4	ENSMUSE00000534632	chr5:142926195-142926341	147	FOXK1_MOUSE	288-336	49	1	A:1-48	48
1.5	ENSMUST00000072837	5	ENSMUSE00000473425	chr5:142927393-142927586	194	FOXK1_MOUSE	337-401	65	1	A:49-101	53
1.6	ENSMUST00000072837	6	ENSMUSE00000472392	chr5:142929463-142929629	167	FOXK1_MOUSE	401-457	57	0	-	-
1.7	ENSMUST00000072837	7	ENSMUSE00000509938	chr5:142929714-142929998	285	FOXK1_MOUSE	457-552	96	0	-	-
1.8	ENSMUST00000072837	8	ENSMUSE00000590040	chr5:142931307-142931531	225	FOXK1_MOUSE	552-627	76	0	-	-
1.9b	ENSMUST00000072837	9b	ENSMUSE00000590039	chr5:142932430-142937968	5539	FOXK1_MOUSE	627-719	93	0	-	-

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:101
 aligned with FOXK1_MOUSE | P42128 from UniProtKB/Swiss-Prot  Length:719

    Alignment length:101
                                   298       308       318       328       338       348       358       368       378       388 
          FOXK1_MOUSE   289 ESKPPYSYAQLIVQAISSAQDRQLTLSGIYAHITKHYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPASEAKLVEQAFRKRRQRGVS 389
               SCOP domains d2d2wa_ A: automated matches                                                                          SCOP domains
               CATH domains 2d2wA00 A:1-101 'winged helix' repressor DNA binding domain                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhh...ee...hhhhhhhhhh........hhhhhhhhhhhhh...ee.............ee.......hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --FORK_HEAD_1   ------------------------------FORK_HE------------------------------------------------ PROSITE (1)
                PROSITE (2) --FORK_HEAD_3  PDB: A:3-98 UniProt: 291-386                                                       --- PROSITE (2)
               Transcript 1 Exon 1.4  PDB: A:1-48 UniProt: 288-336          Exon 1.5  PDB: A:49-101 UniProt: 337-401 [INCOMPLETE] Transcript 1
                 2d2w A   1 ESKPPYSYAQLIVQAISSAQDRQLTLSGIYAHITKHYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPASEAKLVEQAFRKRRQRGVS 101
                                    10        20        30        40        50        60        70        80        90       100

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: Forkhead DNA-binding domain (17)

Protein domain: automated matches (9)

Mouse (Mus musculus) [TaxId: 10090] (2)

d2d2wa_

NMR Structure

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

House mouse (Mus musculus) (11)

2d2wA00

A:1-101

(no "Pfam Domain" information available for 2D2W)

NMR Structure(hide GO term definitions)

Chain A (FOXK1_MOUSE | P42128)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0007517	muscle organ development	The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
	GO:0045786	negative regulation of cell cycle	Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
	GO:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

NMR Structure
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	FOXK1_MOUSE \| P42128
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	FOXK1_MOUSE \| P42128	:	2a3s

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Description

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