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(-) Description

Title :  STRUCTURE OF HUMAN CIRCADIAN CLOCK PROTEIN BMAL2 C-TERMINAL PAS DOMAIN
 
Authors :  E. Wasielewski, C. Correia, F. G. Prendergast, G. Mer
Date :  10 Jan 09  (Deposition) - 13 Apr 11  (Release) - 26 Oct 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
NMR Structure *:  A  (1x)
Keywords :  Circadian Clock, Pas Domain, Transcription, Activator, Biological Rhythms, Dna-Binding, Nucleus, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Correia, E. Wasielewski, F. G. Prendergast, G. Mer
Structure Of Human Circadian Clock Protein Bmal2 C-Terminal Pas Domain
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR-LIKE PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector: PTEV
    Gene: ARNTL2, BMAL2, CLIF, MOP9
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BRAIN AND MUSCLE ARNT-LIKE 2, MEMBER OF PAS PROTEIN 9, BASIC-HELIX-LOOP-HELIX-PAS PROTEIN MOP9, CYCLE-LIKE FACTOR, CLIF

 Structural Features

(-) Chains, Units

  1
NMR Structure (10x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KDK)

(-) Sites  (0, 0)

(no "Site" information available for 2KDK)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KDK)

(-) Cis Peptide Bonds  (1, 2)

NMR Structure
No.ModelResidues
12, 3Lys A:316 -Pro A:317

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KDK)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASPS50112 PAS repeat profile.BMAL2_HUMAN178-243
378-427		  1-
A:327-376
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASPS50112 PAS repeat profile.BMAL2_HUMAN178-243
378-427		  1-
A:327-376

(-) Exons   (0, 0)

(no "Exon" information available for 2KDK)

(-) Sequences/Alignments

NMR Structure
   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:118
 aligned with BMAL2_HUMAN | Q8WYA1 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:118
                                   369       379       389       399       409       419       429       439       449       459       469        
          BMAL2_HUMAN   360 NSGEINVKPTEFITRFAVNGKFVYVDQRATAILGYLPQELLGTSCYEYFHQDDHNNLTDKHKAVLQSKEKILTDSYKFRAKDGSFVTLKSQWFSFTNPWTKELEYIVSVNTLVLGHSE 477
               SCOP domains d2kdka_ A: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------PAS_3-2kdkA01 A:330-418                                                                  -------- Pfam domains
         Sec.struct. author ..........eeeeee.....eeee.hhhhhhh...................hhhhhhhhhhhhhh....eeeeeeeee.....eeeeeeeeeeee......eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------PAS  PDB: A:327-376 UniProt: 378-427              -------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2kdk A 309 NSGEINVKPTEFITRFAVNGKFVYVDQRATAILGYLPQELLGTSCYEYFHQDDHNNLTDKHKAVLQSKEKILTDSYKFRAKDGSFVTLKSQWFSFTNPDTKELEYIVSVNTLVLGHSE 426
                                   318       328       338       348       358       368       378       388       398       408       418
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KDK)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PAS_Fold (84)

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (BMAL2_HUMAN | Q8WYA1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070888    E-box binding    Interacting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0000982    transcription factor 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 modulate transcription by RNAP II.
    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:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0009649    entrainment of circadian clock    The synchronization of a circadian rhythm to environmental time cues such as light.
    GO:0042753    positive regulation of circadian rhythm    Any process that activates or increases the frequency, rate or extent of a circadian rhythm behavior.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    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:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    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: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: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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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    Lys A:316 - Pro A:317   [ RasMol ]  
 

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