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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PAS REPEAT REGION OF THE DROSOPHILA CLOCK PROTEIN PERIOD
 
Authors :  O. Yildiz, M. Doi, I. Yujnovsky, L. Cardone, A. Berndt, S. Hennig, S. Schulze, C. Urbanke, P. Sassone-Corsi, E. Wolf
Date :  25 Oct 04  (Deposition) - 12 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Period, Pas Domain, Circadian Rhythm, Clock Protein, Phosphorylation, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Yildiz, M. Doi, I. Yujnovsky, L. Cardone, A. Berndt, S. Hennig, S. Schulze, C. Urbanke, P. Sassone-Corsi, E. Wolf
Crystal Structure And Interactions Of The Pas Repeat Region Of The Drosophila Clock Protein Period
Mol. Cell V. 17 69 2005
PubMed-ID: 15629718  |  Reference-DOI: 10.1016/J.MOLCEL.2004.11.022

(-) Compounds

Molecule 1 - PERIOD CIRCADIAN PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPGEX-6P2
    FragmentPAS REPEAT REGION, RESIDUES 232-599
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymCLOCK-6 PROTEIN, CLK-6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1WA9)

(-) Sites  (0, 0)

(no "Site" information available for 1WA9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WA9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WA9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WA9)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASPS50112 PAS repeat profile.PER_DROME248-297
 
399-447
 
  4A:248-294
B:248-295
A:399-447
B:399-447

(-) Exons   (0, 0)

(no "Exon" information available for 1WA9)

(-) 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:318
 aligned with PER_DROME | P07663 from UniProtKB/Swiss-Prot  Length:1224

    Alignment length:336
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566      
            PER_DROME   237 EDSFCCVISMHDGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATFASQITTGIPIAESRGSVPKDAKSTFCVMLRRYRGLKSGGFGVIGRPVSYEPFRLGLTFREAPEEARPDNYMVSNGTNMLLVICATPIKSSYKVPDEILSQKSPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYETVMKKGQTAGASFCSKPYRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVGHHRVFQGPKQCNVFEAAPTCKLKISEEAQSRNTRIKEDIVKRLAETVSRPSDTVKQEVSRRCQALASFMETLMDEVSRADL 572
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1wa9A01 A:237-373  [code=3.30.450.20, no name defined]                                                                                   1wa9A02 A:374-541  [code=3.30.450.20, no name defined]                                                                                                                  ------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.....eeee..hhhhhhh..........hhhh....hhhhhhhhh....------------...eeeeeee..................eeeeeee...........------......eeeeeeee.................eeeeeee....eeee...hhhhhh.hhhhhh...hhhh....hhhhhhhhhhhhhhhh......ee...eeee.....eeeeeeeeeeee......eeeeeeeeeeee.................hhhhh.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------PAS  PDB: A:248-294 UniProt: 248-297              -----------------------------------------------------------------------------------------------------PAS  PDB: A:399-447 UniProt: 399-447             ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wa9 A 237 EDSFCCVISMHDGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATFASQITTGI------------AKSTFCVMLRRYRGLKSGGFGVIGRPVSYEPFRLGLTFREAPEEAR------SNGTNMLLVICATPIKSSYKVPDEILSQKSPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYETVMKKGQTAGASFCSKPYRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVGHHRVFQGPKQCNVFEAAPTCKLKISEEAQSRNTRIKEDIVKRLAETVSRPSDTVKQEVSRRCQALASFMETLMDEVSRADL 572
                                   246       256       266       276       286       | -         -|      316       326       336       346     |   -  |    366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566      
                                                                                   294          307                                          352    359                                                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:319
 aligned with PER_DROME | P07663 from UniProtKB/Swiss-Prot  Length:1224

    Alignment length:341
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574 
            PER_DROME   235 VKEDSFCCVISMHDGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATFASQITTGIPIAESRGSVPKDAKSTFCVMLRRYRGLKSGGFGVIGRPVSYEPFRLGLTFREAPEEARPDNYMVSNGTNMLLVICATPIKSSYKVPDEILSQKSPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYETVMKKGQTAGASFCSKPYRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVGHHRVFQGPKQCNVFEAAPTCKLKISEEAQSRNTRIKEDIVKRLAETVSRPSDTVKQEVSRRCQALASFMETLMDEVSRADLKLE 575
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1wa9B01 B:235-373  [code=3.30.450.20, no name defined]                                                                                     1wa9B02 B:374-541  [code=3.30.450.20, no name defined]                                                                                                                  1wa9B03 B:542-575 Single helix bin CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------PAS-1wa9B01 B:381-495                                                                                              -------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------PAS-1wa9B02 B:381-495                                                                                              -------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------PAS-1wa9B03 B:381-495                                                                                              -------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------PAS-1wa9B04 B:381-495                                                                                              -------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .......eeee.....eeee.hhhhhhhh..........hhhh.hhhhhhhhhhhhhhhh.-------------..eeeeee......---------...eeeeee...eee.hhhhh...........eeee......................eeeeeee....eeee.hhhhhhh..hhhhhh...........hhhhhhhhhhhhhhhhh....ee....eeee.....eeee..eeeeee......eeeeeeeeeeee.................hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PAS  PDB: B:248-295 UniProt: 248-297              -----------------------------------------------------------------------------------------------------PAS  PDB: B:399-447 UniProt: 399-447             -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wa9 B 235 VKEDSFCCVISMHDGIVLYTTPSITDVLGYPRDMWLGRSFIDFVHLKDRATFASQITTGIP-------------STFCVMLRRYRGLK---------PVSYEPFRLGLTFREAPEEARPDNYMVSNGTNMLLVICATPIKSSYKVPDEILSQKSPKFAIRHTATGIISHVDSAAVSALGYLPQDLIGRSIMDFYHHEDLSVMKETYETVMKKGQTAGASFCSKPYRFLIQNGCYVLLETEWTSFVNPWSRKLEFVVGHHRVFQGPKQCNVFEAAPTCKLKISEEAQSRNTRIKEDIVKRLAETVSRPSDTVKQEVSRRCQALASFMETLMDEVSRADLKLE 575
                                   244       254       264       274       284       294|        -    |  314       | -       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574 
                                                                                      295           309          322       332                                                                                                                                                                                                                                                   

   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  (0, 0)

(no "SCOP Domain" information available for 1WA9)

(-) CATH Domains  (2, 5)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: PAS_Fold (84)
(-)
Family: PAS (39)
1aPAS-1wa9B01B:381-495
1bPAS-1wa9B02B:381-495
1cPAS-1wa9B03B:381-495
1dPAS-1wa9B04B:381-495

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PER_DROME | P07663)
molecular function
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0001306    age-dependent 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, where the change varies according to the age of the cell or organism.
    GO:0048148    behavioral response to cocaine    Any process that results in a change in the behavior of an organism as a result of a cocaine stimulus.
    GO:0048512    circadian behavior    The specific behavior of an organism that recurs with a regularity of approximately 24 hours.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0042745    circadian sleep/wake cycle    The cycle from wakefulness through an orderly succession of sleep states and stages that occurs on an approximately 24 hour rhythm.
    GO:0060086    circadian temperature homeostasis    Any homeostatic process in which an organism modulates its internal body temperature at different values with a regularity of approximately 24 hours.
    GO:0007620    copulation    The act of sexual union between male and female, involving the transfer of sperm.
    GO:0007619    courtship behavior    The behavioral interactions between organisms for the purpose of attracting sexual partners.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0008062    eclosion rhythm    The timing of the emergence of the adult fly from its pupal case, which usually occurs at dawn.
    GO:0009649    entrainment of circadian clock    The synchronization of a circadian rhythm to environmental time cues such as light.
    GO:0043153    entrainment of circadian clock by photoperiod    The synchronization of a circadian rhythm to photoperiod, the intermittent cycle of light (day) and dark (night).
    GO:0045475    locomotor rhythm    The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.
    GO:0007616    long-term memory    The memory process that deals with the storage, retrieval and modification of information a long time (typically weeks, months or years) after receiving that information. This type of memory is typically dependent on gene transcription regulated by second messenger activation.
    GO:0045433    male courtship behavior, veined wing generated song production    The process during wing vibration where the male insect produces a species-specific acoustic signal called a love song.
    GO:0007617    mating behavior    The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.
    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:2000678    negative regulation of transcription regulatory region DNA binding    Any process that stops, prevents or reduces the frequency, rate or extent of transcription regulatory region DNA binding.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042752    regulation of circadian rhythm    Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0045187    regulation of circadian sleep/wake cycle, sleep    Any process that modulates the frequency, rate or extent of sleep; a readily reversible state of reduced awareness and metabolic activity that occurs periodically in many animals.
    GO:1904059    regulation of locomotor rhythm    Any process that modulates the frequency, rate or extent of locomotor rhythm.
    GO:0001932    regulation of protein phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009416    response to light stimulus    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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
    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:0009266    response to temperature stimulus    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 temperature stimulus.
    GO:0007622    rhythmic behavior    The specific behavior of an organism that recur with measured regularity.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0007624    ultradian rhythm    The specific actions or reactions of an organism that recur with a regularity more frequent than every 24 hours.
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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

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        PER_DROME | P076633gec 3rty

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