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(-) Description

Title :  STRUCTURAL DIFFERENCES IN THE DNA BINDING DOMAINS OF HUMAN P53 AND ITS C. ELEGANS ORTHOLOG CEP-1: STRUCTURE OF C. ELEGANS CEP-1
 
Authors :  Y. Huyen, P. D. Jeffrey, W. B. Derry, J. H. Rothman, N. P. Pavletich, E. S. Stavridi, T. D. Halazonetis
Date :  30 Apr 04  (Deposition) - 20 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna-Binding Domain, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Huyen, P. D. Jeffrey, W. B. Derry, J. H. Rothman, N. P. Pavletich, E. S. Stavridi, T. D. Halazonetis
Structural Differences In The Dna Binding Domains Of Human P53 And Its C. Elegans Ortholog Cep-1.
Structure V. 12 1237 2004
PubMed-ID: 15242600  |  Reference-DOI: 10.1016/J.STR.2004.05.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - C.ELEGANS P53 TUMOR SUPPRESSOR-LIKE TRANSCRIPTION FACTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentDNA BINDING DOMAIN
    Organism ScientificCAENORHABDITIS ELEGANS
    Organism Taxid6239
    SynonymCEP-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:307 , HIS A:310 , CYS A:361 , CYS A:365BINDING SITE FOR RESIDUE ZN A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T4W)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:317 -Pro A:318

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T4W)

(-) Exons   (0, 0)

(no "Exon" information available for 1T4W)

(-) 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:196
 aligned with CEP1_CAEEL | Q20646 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:196
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412      
           CEP1_CAEEL   223 EKWMEIDVLKQKVAKSSDMAFAISSEHEKYLWTKMGCLVPIQVKWKLDKRHFNSNLSLRIRFVKYDKKENVEYAIRNPRSDVMKCRSHTEREQHFPFDSFFYIRNSEHEFSYSAEKGSTFTLIMYPGAVQANFDIIFMCQEKCLDLDDRRKTMCLAVFLDDENGNEILHAYIKQVRIVAYPRRDWKNFCEREDAKQ 418
               SCOP domains d1t4wa_ A: Transcription factor CEP-1                                                                                                                                                                SCOP domains
               CATH domains 1t4wA00 A:223-418  [code=2.60.40.720, no name defined]                                                                                                                                               CATH domains
               Pfam domains CEP1-DNA_bind-1t4wA01 A:223-418                                                                                                                                                                      Pfam domains
         Sec.struct. author ..eeeeeehhhhhh....eeeee.....eeeee.....eeeeeeee..........eeeeeeeee....hhhhhh.........hhhhhhh.........eeee....eeeee.....eeeee......eeeeeeee..hhhhhhhhhhh.eeeeeeeee.....eeeeeeeeeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t4w A 223 EKWMEIDVLKQKVAKSSDMAFAISSEHEKYLWTKMGCLVPIQVKWKLDKRHFNSNLSLRIRFVKYDKKENVEYAIRNPRSDVMKCRSHTEREQHFPFDSFFYIRNSEHEFSYSAEKGSTFTLIMYPGAVQANFDIIFMCQEKCLDLDDRRKTMCLAVFLDDENGNEILHAYIKQVRIVAYPRRDWKNFCEREDAKQ 418
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412      

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P53-like (54)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CEP1_CAEEL | Q20646)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0042771    intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0045132    meiotic chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle.
    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:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (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:0042594    response to starvation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
    GO:0042770    signal transduction in response to DNA damage    A cascade of processes induced by the detection of DNA damage within a cell.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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)

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        CEP1_CAEEL | Q206462rp5

(-) Related Entries Specified in the PDB File

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