2C6Y | PD0932 - JenaLib

Title :   CRYSTAL STRUCTURE OF INTERLEUKIN ENHANCER-BINDING FACTOR 1 BOUND TO DNA

Authors :   K. -L. Tsai, C. -Y. Huang, C. -H. Chang, Y. -J. Sun, W. -J. Chuang, C. -D. Hsiao

Date :   15 Nov 05 (Deposition) - 18 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Transcription Regulation, Dna-Binding Domain, Forkhead Transcription Factors, Interleukin Enhancer Binding Factor, Winged Helix, Forkhead (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. -L. Tsai, C. -Y. Huang, C. -H. Chang, Y. -J. Sun, W. -J. Chuang, C. -D. Hsiao
Crystal Structure Of The Human Foxk1A-Dna Complex And Its Implications On The Diverse Binding Specificity Of Winged Helix/Forkhead Proteins.
J. Biol. Chem. V. 281 17400 2006
PubMed-ID: 16624804 | Reference-DOI: 10.1074/JBC.M600478200

Compounds

Molecule 1 - FORKHEAD BOX PROTEIN K2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	DNA-BINDING DOMAIN, RESIDUES 251-348
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	INTERLEUKIN ENHANCER-BINDING FACTOR 1, CELLULAR TRANSCRIPTION FACTOR ILF-1

Molecule 2 - INTERLEUKIN 2 PROMOTOR
	Chains	:	C
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	5'-D(TPGPTPTPGPTPAPAPAPCPAPAP* TPAPCP*A)-3'
	Synthetic	:	YES

Molecule 3 - INTERLEUKIN 2 PROMOTOR
	Chains	:	D
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	5'-D(APTPGPTPAPTPTPGPTPTPTPAP* CPAPAP*C)-3'
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (2, 4)

Asymmetric/Biological Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000335255	1a	ENSE00002142812	chr17:80477591-80478183	593	FOXK2_HUMAN	1-140	140	0	-	-
1.3	ENST00000335255	3	ENSE00001282714	chr17:80521230-80521424	195	FOXK2_HUMAN	140-205	66	0	-	-
1.4	ENST00000335255	4	ENSE00000949826	chr17:80525930-80526077	148	FOXK2_HUMAN	205-254	50	0	-	-
1.5a	ENST00000335255	5a	ENSE00001334520	chr17:80529600-80529746	147	FOXK2_HUMAN	255-303	49	2	A:1-48 B:1-48	48 48
1.6b	ENST00000335255	6b	ENSE00001112229	chr17:80540617-80540810	194	FOXK2_HUMAN	304-368	65	2	A:49-98 B:49-96	50 48
1.7	ENST00000335255	7	ENSE00001112228	chr17:80541889-80542064	176	FOXK2_HUMAN	368-427	60	0	-	-
1.8	ENST00000335255	8	ENSE00001112227	chr17:80543780-80544076	297	FOXK2_HUMAN	427-526	100	0	-	-
1.9	ENST00000335255	9	ENSE00001112230	chr17:80544939-80545148	210	FOXK2_HUMAN	526-596	71	0	-	-
1.13c	ENST00000335255	13c	ENSE00001362311	chr17:80559179-80562483	3305	FOXK2_HUMAN	596-660	65	0	-	-

Sequences/Alignments

Asymmetric/Biological Unit

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:98
 aligned with FOXK2_HUMAN | Q01167 from UniProtKB/Swiss-Prot  Length:660

    Alignment length:98
                                   265       275       285       295       305       315       325       335       345        
          FOXK2_HUMAN   256 DSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPASESKLIEQAFRKRRPR 353
               SCOP domains d2c6ya_ A: automated matches                                                                       SCOP domains
               CATH domains 2c6yA00 A:1-98 'winged helix' repressor DNA binding domain                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.....eehhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeee...........eeeehhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --FORK_HEAD_3  PDB: A:3-98 UniProt: 258-353                                                        PROSITE (1)
                PROSITE (2) --FORK_HEAD_1   ------------------------------FORK_HE--------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.5a  PDB: A:1-48 UniProt: 255-303         Exon 1.6b  PDB: A:49-98 UniProt: 304-368           Transcript 1
                 2c6y A   1 DSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPASESKLIEQAFRKRRPR  98
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:96
 aligned with FOXK2_HUMAN | Q01167 from UniProtKB/Swiss-Prot  Length:660

    Alignment length:96
                                   265       275       285       295       305       315       325       335       345      
          FOXK2_HUMAN   256 DSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPASESKLIEQAFRKRR 351
               SCOP domains d2c6yb_ B: automated matches                                                                     SCOP domains
               CATH domains 2c6yB00 B:1-96 'winged helix' repressor DNA binding domain                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh....eehhhhhhhhhhhh.......hhhhhhhhhhhhhh..eeee...........eeeehhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --FORK_HEAD_3  PDB: B:3-96 UniProt: 258-353                                                      PROSITE (1)
                PROSITE (2) --FORK_HEAD_1   ------------------------------FORK_HE------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.5a  PDB: B:1-48 UniProt: 255-303         Exon 1.6b  PDB: B:49-96 UniProt: 304-368         Transcript 1
                 2c6y B   1 DSKPPYSYAQLIVQAITMAPDKQLTLNGIYTHITKNYPYYRTADKGWQNSIRHNLSLNRYFIKVPRSQEEPGKGSFWRIDPASESKLIEQAFRKRR  96
                                    10        20        30        40        50        60        70        80        90

Chain C from PDB  Type:DNA  Length:16
                                                
                 2c6y C   1 TGTTGTAAACAATACA  16
                                    10

Chain D from PDB  Type:DNA  Length:16
                                                
                 2c6y D   1 ATGTATTGTTTACAAC  16
                                    10

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (FOXK2_HUMAN | Q01167)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	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:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

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