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(-) Description

Title :  ANALYSIS OF THE 2.0A CRYSTAL STRUCTURE OF THE PROTEIN-DNA COMPLEX OF HUMAN PDEF ETS DOMAIN BOUND TO THE PROSTATE SPECIFIC ANTIGEN REGULATORY SITE
 
Authors :  Y. Wang, L. Feng, M. Said, S. Balderman, Z. Fayazi, Y. Liu, D. Ghosh, A. M. Gulick
Date :  26 Jan 05  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ets; Protein-Dna Complex; Double Helix, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wang, L. Feng, M. Said, S. Balderman, Z. Fayazi, Y. Liu, D. Ghosh, A. M. Gulick
Analysis Of The 2. 0 A Crystal Structure Of The Protein-Dna Complex Of The Human Pdef Ets Domain Bound To The Prostate Specific Antigen Regulatory Site
Biochemistry V. 44 7095 2005
PubMed-ID: 15882048  |  Reference-DOI: 10.1021/BI047352T
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENHANCER SITE OF PROSTATE SPECIFIC ANTIGEN PROMOTER REGION
    Chains: A
    Engineered: YES
    Fragment: SENSE STRAND OF E SITE
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. DNA SUBSTRATE FOR PROTEIN IS SYNTHESIZED CHEMICALLY AND PURIFIED THROUGH CHROMATOGRAPHY
    Synthetic: YES
 
Molecule 2 - ENHANCER SITE OF PROSTATE SPECIFIC ANTIGEN PROMOTER REGION
    Chains: B
    Engineered: YES
    Fragment: ANTISENSE STRAND OF E SITE
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. DNA SUBSTRATE FOR PROTEIN IS SYNTHESIZED CHEMICALLY AND PURIFIED THROUGH CHROMATOGRAPHY
    Synthetic: YES
 
Molecule 3 - SAM POINTED DOMAIN CONTAINING ETS TRANSCRIPTION FACTOR
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-GST-T-A
    Expression System Strain: BL21 (LAMBDA DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PDEF C-TERMINAL ETS DOMAIN
    Gene: PDEF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YO5)

(-) Sites  (0, 0)

(no "Site" information available for 1YO5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YO5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YO5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YO5)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ETS_DOMAIN_3PS50061 Ets-domain profile.SPDEF_HUMAN249-332  1C:249-332
2ETS_DOMAIN_1PS00345 Ets-domain signature 1.SPDEF_HUMAN251-259  1C:251-259
3ETS_DOMAIN_2PS00346 Ets-domain signature 2.SPDEF_HUMAN297-312  1C:297-312

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003740371ENSE00001308802chr6:34524091-34523706386SPDEF_HUMAN-00--
1.2ENST000003740372ENSE00001462227chr6:34512261-34511797465SPDEF_HUMAN1-1461460--
1.3ENST000003740373ENSE00000849546chr6:34508958-34508761198SPDEF_HUMAN146-212670--
1.4ENST000003740374ENSE00000849545chr6:34507339-3450729248SPDEF_HUMAN212-228170--
1.5ENST000003740375ENSE00001311158chr6:34507173-34507027147SPDEF_HUMAN228-277501C:247-27731
1.6ENST000003740376ENSE00001462215chr6:34506229-34505579651SPDEF_HUMAN277-335591C:277-33458

(-) 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:DNA  Length:13
                                             
                 1yo5 A   1 TAGCAGGATGTGT  13
                                    10   


Chain B from PDB  Type:DNA  Length:13
                                             
                 1yo5 B   1 ACACATCCTGCTA  13
                                    10   


Chain C from PDB  Type:PROTEIN  Length:88
 aligned with SPDEF_HUMAN | O95238 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:88
                                   256       266       276       286       296       306       316       326        
          SPDEF_HUMAN   247 QPIHLWQFLKELLLKPHSYGRFIRWLNKEKGIFKIEDSAQVARLWGIRKNRPAMNYDKLSRSIRQYYKKGIIRKPDISQRLVYQFVHP 334
               SCOP domains d1yo5c1 C:247-334 Sam pointed domain containing ets transcription SPDEF                  SCOP domains
               CATH domains 1yo5C00 C:247-334 'winged helix' repressor DNA binding domain                            CATH domains
               Pfam domains -Ets-1yo5C01 C:248-334                                                                   Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..eeeee....eeee.hhhhhhhhhhhhhh....hhhhhhhhhhhh.....ee........eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --ETS_DOMAIN_3  PDB: C:249-332 UniProt: 249-332                                       -- PROSITE (1)
                PROSITE (2) ----ETS_DOMAI-------------------------------------ETS_DOMAIN_2    ---------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.5  PDB: C:247-277       --------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.6  PDB: C:277-334 UniProt: 277-335 [INCOMPLETE]     Transcript 1 (2)
                 1yo5 C 247 QPIHLWQFLKELLLKPHSYGRFIRWLNKEKGIFKIEDSAQVARLWGIRKNRPAMNYDKLSRSIRQYYKKGIIRKPDISQRLVYQFVHP 334
                                   256       266       276       286       296       306       316       326
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (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.

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 Related Entries

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        SPDEF_HUMAN | O95238: 2dkx

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