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(-) Description

Title :  STRUCTURE OF THE PLANT TRANSCRIPTIONAL REGULATOR PBF-2
 
Authors :  D. Desveaux, J. Allard, N. Brisson, J. Sygusch
Date :  26 Feb 02  (Deposition) - 26 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pbf-2, Single Strand Dna Binding Protein, Plant, Whirly, Transcriptionnal Activator, Cyclic C4 Symmetry (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Desveaux, J. Allard, N. Brisson, J. Sygusch
A New Family Of Plant Transcription Factors Displays A Novel Ssdna-Binding Surface.
Nat. Struct. Biol. V. 9 512 2002
PubMed-ID: 12080340  |  Reference-DOI: 10.1038/NSB814
(for further references see the PDB file header)

(-) Compounds

Molecule 1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21
    Expression System Plasmid: PET21A
    Expression System Taxid: 562
    Fragment: RESIDUES 68-273
    Organism Common: POTATO
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
    Other Details: P24: PLANT TRANSCRIPTIONAL REGULATOR PBF-2
    Synonym: PBF-2

 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 1L3A)

(-) Sites  (0, 0)

(no "Site" information available for 1L3A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L3A)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr D:89 -Pro D:90

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L3A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L3A)

(-) Exons   (0, 0)

(no "Exon" information available for 1L3A)

(-) 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:166
 aligned with WHY1_SOLTU | Q9LL85 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:166
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248      
           WHY1_SOLTU    89 TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGAKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPE 254
               SCOP domains d1l3aa_ A: Plant transcriptional regulator PBF-2                                                                                                                       SCOP domains
               CATH domains 1l3aA00 A:89-254 Transcriptional Coactivator Pc4; Chain A                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeee...eeeeeeee..eeee....eeeeee..eeeeeeee.......hhhhheeeeehhhhhhhhhh......eeeee............eeeeeeee.....eeeeeeeeeehhhheeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l3a A  89 TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPE 254
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248      


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with WHY1_SOLTU | Q9LL85 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:183
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268   
           WHY1_SOLTU    89 TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGAKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPEDASRSNNANPRSGAELE 271
               SCOP domains d1l3ab_ B: Plant transcriptional regulator PBF-2                                                                                                                                        SCOP domains
               CATH domains 1l3aB00 B:89-271 Transcriptional Coactivator Pc4; Chain A                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeeee..eeeeeeee..eeee.....eeeee..eeeeeeee.......hhhhheeeeehhhhhhhhhh......eeeee...........eeeeeeeee.....eeeeeeeeee....eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.....-------------.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l3a B  89 TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPE-------------AELE 271
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248     |   -       268   
                                                                                                                                                                                               254           268   


Chain C from PDB  Type:PROTEIN  Length:182
 aligned with WHY1_SOLTU | Q9LL85 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:193
                                                                                                                                                                                                                   274       
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268     |   -   
           WHY1_SOLTU    89 TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGAKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPEDASRSNNANPRSGAELEWNR-------   -
               SCOP domains d1l3ac_ C: Plant transcriptional regulator PBF-2                                                                                                                                                  SCOP domains
               CATH domains 1l3aC00 C:89-281 Transcriptional Coactivator Pc4; Chain A                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeee...eeeeeeee..eeee.....eeeee..eeeeeeeeeee..ee.hhhheeeeehhhhhhhhhh......eeeee...........eeeeeeeee.....eeeeeeeeee.....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.....-----------.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l3a C  89 TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPE-----------SGAELEWNLEHHHHHH 281
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248     |   -       268       278   
                                                                                                                                                                                               254         266               


Chain D from PDB  Type:PROTEIN  Length:171
 aligned with WHY1_SOLTU | Q9LL85 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:183
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268   
           WHY1_SOLTU    89 TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGAKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPEDASRSNNANPRSGAELE 271
               SCOP domains d1l3ad_ D: Plant transcriptional regulator PBF-2                                                                                                                                        SCOP domains
               CATH domains 1l3aD00 D:89-271 Transcriptional Coactivator Pc4; Chain A                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeee...eeeeeeee..eeee.hhh.eeeee..eeeeeeee.......hhhhheeeeehhhhhhhhhh......eeeee...........eeeeeeeee.....eeeeeeeeee.hhheeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.....------------..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l3a D  89 TPKVFVGYSIYKGKAALTVEPRSPEFSPLDSGAFKLSREGMVMLQFAPAAGVRQYDWSRKQVFSLSVTEIGSIISLGTKDSCEFFHDPNKGRSDEGRVRKVLKVEPLPDGSGHFFNLSVQNKLINLDENIYIPVTKAEFAVLVSAFNFVMPYLLGWHTAVNSFKPE------------GAELE 271
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248     |   -       268   
                                                                                                                                                                                               254          267
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1L3A)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (WHY1_SOLTU | Q9LL85)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    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.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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    Thr D:89 - Pro D:90   [ RasMol ]  
 

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 Related Entries

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