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(-) Description

Title :  CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA
 
Authors :  Y. Fujii, T. Shimizu, T. Toda, M. Yanagida, T. Hakoshima
Date :  25 Aug 00  (Deposition) - 02 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Biol. Unit 3:  I,J  (1x)
Keywords :  Basic Leucine Zipper, Protein-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fujii, T. Shimizu, T. Toda, M. Yanagida, T. Hakoshima
Structural Basis For The Diversity Of Dna Recognition By Bzip Transcription Factors.
Nat. Struct. Biol. V. 7 889 2000
PubMed-ID: 11017199  |  Reference-DOI: 10.1038/82822
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')
    Chains: A, B, C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - TRANSCRIPTION FACTOR PAP1
    Chains: E, F, G, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LEUCINE ZIPPER DOMAIN
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Synonym: AP-1-LIKE TRANSCRIPTION FACTOR

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): AB  EF    
Biological Unit 2 (1x):   CD  GH  
Biological Unit 3 (1x):         IJ

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1GD2)

(-) Sites  (0, 0)

(no "Site" information available for 1GD2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GD2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GD2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GD2)

(-) PROSITE Motifs  (2, 7)

Asymmetric Unit (2, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BZIPPS50217 Basic-leucine zipper (bZIP) domain profile.AP1_SCHPO76-139
 
 		  3E:76-139
G:76-139
H:76-139
2BZIP_BASICPS00036 Basic-leucine zipper (bZIP) domain signature.AP1_SCHPO81-96
 
 
 		  4E:81-96
F:81-96
G:81-96
H:81-96
Biological Unit 1 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BZIPPS50217 Basic-leucine zipper (bZIP) domain profile.AP1_SCHPO76-139
 
 		  1E:76-139
-
-
2BZIP_BASICPS00036 Basic-leucine zipper (bZIP) domain signature.AP1_SCHPO81-96
 
 
 		  2E:81-96
F:81-96
-
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BZIPPS50217 Basic-leucine zipper (bZIP) domain profile.AP1_SCHPO76-139
 
 		  2-
G:76-139
H:76-139
2BZIP_BASICPS00036 Basic-leucine zipper (bZIP) domain signature.AP1_SCHPO81-96
 
 
 		  2-
-
G:81-96
H:81-96
Biological Unit 3 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BZIPPS50217 Basic-leucine zipper (bZIP) domain profile.AP1_SCHPO76-139
 
 		  0-
-
-
2BZIP_BASICPS00036 Basic-leucine zipper (bZIP) domain signature.AP1_SCHPO81-96
 
 
 		  0-
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1GD2)

(-) Sequences/Alignments

Asymmetric 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
                                             
                 1gd2 A  -7 AGGTTACGTAACC   6
                                  || 3   
                                 -1|     
                                   1     


Chain B from PDB  Type:DNA  Length:13
                                             
                 1gd2 B  -7 AGGTTACGTAACC   6
                                  || 3   
                                 -1|     
                                   1     


Chain C from PDB  Type:DNA  Length:13
                                             
                 1gd2 C  -7 AGGTTACGTAACC   6
                                  || 3   
                                 -1|     
                                   1     


Chain D from PDB  Type:DNA  Length:13
                                             
                 1gd2 D  -7 AGGTTACGTAACC   6
                                  || 3   
                                 -1|     
                                   1     


Chain E from PDB  Type:PROTEIN  Length:65
 aligned with AP1_SCHPO | Q01663 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:65
                                    84        94       104       114       124       134     
            AP1_SCHPO    75 DQEPSSKRKAQNRAAQRAFRKRKEDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRIL 139
               SCOP domains d1gd2e_ E: PAP1                                                   SCOP domains
               CATH domains 1gd2E00 E:75-139  [code=1.20.5.170, no name defined]              CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -BZIP  PDB: E:76-139 UniProt: 76-139                              PROSITE (1)
                PROSITE (2) ------BZIP_BASIC      ------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------- Transcript
                 1gd2 E  75 DQEPSSKRKAQNRAAQRAFRKRKEDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRIL 139
                                    84        94       104       114       124       134     


Chain F from PDB  Type:PROTEIN  Length:64
 aligned with AP1_SCHPO | Q01663 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:64
                                    86        96       106       116       126       136    
            AP1_SCHPO    77 EPSSKRKAQNRAAQRAFRKRKEDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRILK 140
               SCOP domains d1gd2f_ F: PAP1                                                  SCOP domains
               CATH domains 1gd2F00 F:77-140  [code=1.20.5.170, no name defined]             CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BZIP  PDB: - UniProt: 76-139                                   - PROSITE (1)
                PROSITE (2) ----BZIP_BASIC      -------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------- Transcript
                 1gd2 F  77 EPSSKRKAQNRAAQRAFRKRKEDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRILK 140
                                    86        96       106       116       126       136    


Chain G from PDB  Type:PROTEIN  Length:64
 aligned with AP1_SCHPO | Q01663 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:64
                                    85        95       105       115       125       135    
            AP1_SCHPO    76 QEPSSKRKAQNRAAQRAFRKRKEDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRIL 139
               SCOP domains d1gd2g_ G: PAP1                                                  SCOP domains
               CATH domains 1gd2G00 G:76-139  [code=1.20.5.170, no name defined]             CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BZIP  PDB: G:76-139 UniProt: 76-139                              PROSITE (1)
                PROSITE (2) -----BZIP_BASIC      ------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------- Transcript
                 1gd2 G  76 QEPSSKRKAQNRAAQRAFRKRKEDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRIL 139
                                    85        95       105       115       125       135    


Chain H from PDB  Type:PROTEIN  Length:64
 aligned with AP1_SCHPO | Q01663 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:64
                                    85        95       105       115       125       135    
            AP1_SCHPO    76 QEPSSKRKAQNRAAQRAFRKRKEDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRIL 139
               SCOP domains d1gd2h_ H: PAP1                                                  SCOP domains
               CATH domains 1gd2H00 H:76-139  [code=1.20.5.170, no name defined]             CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BZIP  PDB: H:76-139 UniProt: 76-139                              PROSITE (1)
                PROSITE (2) -----BZIP_BASIC      ------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------- Transcript
                 1gd2 H  76 QEPSSKRKAQNRAAQRAFRKRKEDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRIL 139
                                    85        95       105       115       125       135    


Chain I from PDB  Type:PROTEIN  Length:40
 aligned with AP1_SCHPO | Q01663 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:59
                                    91       101       111       121       131         
            AP1_SCHPO    82 RKAQNRAAQRAFRKRKEDHLKALETQVVTLKELHSSTTLENDQLRQKVRQLEEELRILK 140
               SCOP domains d1gd2i                 _ I: PAP1                            SCOP domains
               CATH domains 1gd2I0                 0 I:82-140  [code=1.20  .5.170, no n CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ......-----------------.hhhhhhhhhhhhhhhhhhhhh--hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BZIP  PDB: - UniProt: 76-139                              - PROSITE (1)
                PROSITE (2) BZIP_BASIC     -------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------- Transcript
                 1gd2 I  82 RKAQNR-----------------ETQVVTLKELHSSTTLENDQLR--VRQLEEELRILK 140
                                 |   -         -   |   111       121    |  131         
                                87               105                  126  |           
                                                                         129           


Chain J from PDB  Type:PROTEIN  Length:11
 aligned with AP1_SCHPO | Q01663 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:11
                                   115 
            AP1_SCHPO   106 TQVVTLKELHS 116
               SCOP domains d1gd2j_ J:  SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                PROSITE (1) BZIP  PDB:  PROSITE (1)
                PROSITE (2) ----------- PROSITE (2)
                 Transcript ----------- Transcript
                 1gd2 J 106 TQVVTLKELHS 116
                                   115
   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, 6)

Asymmetric Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GD2)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain E,F,G,H,I,J   (AP1_SCHPO | Q01663)
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: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:0071313    cellular response to caffeine    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 a caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.
    GO:0070301    cellular response to hydrogen peroxide    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 a hydrogen peroxide (H2O2) stimulus.
    GO:0034599    cellular response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    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:0061408    positive regulation of transcription from RNA polymerase II promoter in response to heat stress    Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0061404    positive regulation of transcription from RNA polymerase II promoter in response to increased salt    Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of detection of, or exposure to, an increase in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
    GO:0036252    positive regulation of transcription from RNA polymerase II promoter in response to menadione    Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a menadione stimulus. Menadione (also called vitamin K3) is a naphthoquinone having a methyl substituent at the 2-position.
    GO:0036091    positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress    Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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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  AP1_SCHPO | Q01663
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