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Title :   SOLUTION STRUCTURE OF THE SAM_PNT-DOMAIN OF ETS TRANSCRIPTION FACTOR PDEF (PROSTATE ETS)

Authors :   A. K. Goroncy, M. Sato, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   14 Apr 06 (Deposition) - 14 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Cell-Free Protein Synthesis, Protein Regulation, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Goroncy, M. Sato, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Sam_pnt-Domain Of Ets Transcription Factor Pdef (Prostate Ets)
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SAM POINTED DOMAIN-CONTAINING ETS TRANSCRIPTION FACTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P041108-11
	Expression System Vector Type	:	PLASMID
	Fragment	:	SAM_PNT DOMAIN(RESIDUES 8-90)
	Gene	:	SPDEF, PDEF, PSE
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	PROSTATE-DERIVED ETS FACTOR, PROSTATE EPITHELIUM- SPECIFIC ETS TRANSCRIPTION FACTOR, PROSTATE-SPECIFIC ETS


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2DKX)

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

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20	Ser A:28	-	Pro A:29

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PNT	PS51433	Pointed (PNT) domain profile.	SPDEF_HUMAN	129-213	1	A:8-90

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000374037	1	ENSE00001308802	chr6:34524091-34523706	386	SPDEF_HUMAN	-	0	0	-	-
1.2	ENST00000374037	2	ENSE00001462227	chr6:34512261-34511797	465	SPDEF_HUMAN	1-146	146	1	A:1-23 (gaps)	68
1.3	ENST00000374037	3	ENSE00000849546	chr6:34508958-34508761	198	SPDEF_HUMAN	146-212	67	1	A:23-89	67
1.4	ENST00000374037	4	ENSE00000849545	chr6:34507339-34507292	48	SPDEF_HUMAN	212-228	17	1	A:89-93 (gaps)	10
1.5	ENST00000374037	5	ENSE00001311158	chr6:34507173-34507027	147	SPDEF_HUMAN	228-277	50	1	A:94-96	3
1.6	ENST00000374037	6	ENSE00001462215	chr6:34506229-34505579	651	SPDEF_HUMAN	277-335	59	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:96
 aligned with SPDEF_HUMAN | O95238 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:168
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238        
          SPDEF_HUMAN    79 GASSREEPPEEPEQCPVIDSQAPAGSLDLVPGGLTLEEHSLEQVQSMVVGEVLKDIETACKLLNITADPMDWSPSNVQKWLLWTEHQYRLPPMGKAFQELAGKELCAMSEEQFRQRSPLGGDVLHAHLDIWKSAAWMKERTSPGAIHYCASTSEESWTDSEVDSSCSG 246
               SCOP domains d2d                  kxa_                            A: automated matches                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...------------------....---------------------------hhhhhhhhhh.....hhhhh...hhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh-----h..----------------------... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------PNT  PDB: A:8-90 UniProt: 129-213                                                    --------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:1-23 (gaps) UniProt: 1-146 [INCOMPLETE]            -----------------------------------------------------------------Exon 1.4         ------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.3  PDB: A:23-89 UniProt: 146-212                            ---------------Exon 1.5            Transcript 1 (2)
                 2dkx A   1 GSS------------------GSSG---------------------------LKDIETACKLLNITADPMDWSPSNVQKWLLWTEHQYRLPPMGKAFQELAGKELCAMSEEQFRQRSPLGGDVLHAHLDIWKSAA-----SGP----------------------SSG  96
                              |      -         - |  |    -         -         -  |     15        25        35        45        55        65        75        85    |    -| |      -         -     |  
                              3                  4  7                           8                                                                                90    91 |                     94  
                                                                                                                                                                         93

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: SAM domain-like (639)

Superfamily: SAM/Pointed domain (61)

Family: automated matches (20)

Protein domain: automated matches (20)

Human (Homo sapiens) [TaxId: 9606] (18)

d2dkxa_

(no "CATH Domain" information available for 2DKX)

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

NMR Structure(hide GO term definitions)

Chain A (SPDEF_HUMAN | O95238)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0060576	intestinal epithelial cell development	The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell of the intestine over time, from its formation to the mature structure.
	GO:0060480	lung goblet cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a lung goblet cell. A goblet cell is a cell of the epithelial lining that produces and secretes mucins.
	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:0010454	negative regulation of cell fate commitment	Any process that stops, prevents or reduces the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0010455	positive regulation of cell fate commitment	Any process that activates, maintains or increases the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
	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: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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(no "Sites" information available for 2dkx)

	Cis Peptide Bonds
		Ser A:28 - Pro A:29	[ RasMol ]

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	2dkx
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Description

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Ligands, Modified Residues, Ions (0, 0)

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Cis Peptide Bonds (1, 20)

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Exons (4, 4)

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