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(-) Description

Title :  PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX
 
Authors :  T. Shimizu, A. Toumoto, K. Ihara, M. Shimizu, Y. Kyogoku, N. Ogawa, Y. Oshima, T. Hakoshima
Date :  27 Nov 97  (Deposition) - 18 Mar 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription Factor, Basic Helix Loop Helix, Complex (Transcription Factor/Dna), Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Shimizu, A. Toumoto, K. Ihara, M. Shimizu, Y. Kyogoku, N. Ogawa, Y. Oshima, T. Hakoshima
Crystal Structure Of Pho4 Bhlh Domain-Dna Complex: Flanking Base Recognition.
Embo J. V. 16 4689 1997
PubMed-ID: 9303313  |  Reference-DOI: 10.1093/EMBOJ/16.15.4689
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*CP*TP*CP*AP*CP*AP*CP*GP*TP*GP*GP*GP*AP*CP*TP*AP*G )-3')
    Chains: C
    Engineered: YES
    Fragment: UPSTREAM ACTIVATION SITE P2
    Synonym: UASP2(17)
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*CP*TP*AP*GP*TP*CP*CP*CP*AP*CP*GP*TP*GP*TP*GP*AP*G )-3')
    Chains: D
    Engineered: YES
    Fragment: UPSTREAM ACTIVATION SITE P2
    Synonym: UASP2(17)
    Synthetic: YES
 
Molecule 3 - PROTEIN (PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: DNA BINDING DOMAIN
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: BHLH

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1A0A)

(-) Sites  (0, 0)

(no "Site" information available for 1A0A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A0A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A0A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A0A)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BHLHPS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile.PHO4_YEAST250-306
 		  2A:1-56
B:1-56

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YFR034C1YFR034C.1VI:225946-225008939PHO4_YEAST1-3123122A:0-62
B:0-62		63
63

(-) 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:PROTEIN  Length:63
 aligned with PHO4_YEAST | P07270 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:63
                                   259       269       279       289       299       309   
           PHO4_YEAST   250 DKRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNVST 312
               SCOP domains d1a0aa_ A: Pho4 B/HLH domain                                    SCOP domains
               CATH domains 1a0aA00 A:0-62 MYOD Basic-Helix-Loop-Helix Domain, subunit B    CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE BHLH  PDB: A:1-56 UniProt: 250-306                       ------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:0-62 UniProt: 1-312 [INCOMPLETE]               Transcript 1
                 1a0a A   0 MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST  62
                                     9        19        29        39        49        59   


Chain B from PDB  Type:PROTEIN  Length:63
 aligned with PHO4_YEAST | P07270 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:63
                                   259       269       279       289       299       309   
           PHO4_YEAST   250 DKRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNVST 312
               SCOP domains d1a0ab_ B: Pho4 B/HLH domain                                    SCOP domains
               CATH domains 1a0aB00 B:0-62 MYOD Basic-Helix-Loop-Helix Domain, subunit B    CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh........hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE BHLH  PDB: B:1-56 UniProt: 250-306                       ------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:0-62 UniProt: 1-312 [INCOMPLETE]               Transcript 1
                 1a0a B   0 MKRESHKHAEQARRNRLAVALHELASLIPAEWKQQNVSAAPSKATTVEAACRYIRHLQQNGST  62
                                     9        19        29        39        49        59   


Chain C from PDB  Type:DNA  Length:17
                                                 
                 1a0a C   1 CTCACACGTGGGACTAG  17
                                    10       


Chain D from PDB  Type:DNA  Length:17
                                                 
                 1a0a D   1 CTAGTCCCACGTGTGAG  17
                                    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)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A0A)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PHO4_YEAST | P07270)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    DNA-binding transcription factor activity    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    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.
biological process
    GO:0016036    cellular response to phosphate starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of phosphate.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0045937    positive regulation of phosphate metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates.
    GO:0045944    positive regulation of transcription by RNA polymerase II    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PHO4_YEAST | P07270: 3w3x

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