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(-) Description

Title :  HISTONE FOLD HETERODIMER OF THE CHROMATIN ACCESSIBILITY COMPLEX
 
Authors :  C. Fernandez-Tornero, K. F. Hartlepp, T. Grune, A. Eberharter, P. B. Becker, C. W. Muller
Date :  03 Aug 05  (Deposition) - 09 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Chrac-14, Nucleosome Sliding, Histone Fold, Chrac-16, Dna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. F. Hartlepp, C. Fernandez-Tornero, A. Eberharter, T. Grune, C. W. Muller, P. B. Becker
The Histone Fold Subunits Of Drosophila Chrac Facilitate Nucleosome Sliding Through Dynamic Dna Interactions.
Mol. Cell. Biol. V. 25 9886 2005
PubMed-ID: 16260604  |  Reference-DOI: 10.1128/MCB.25.22.9886-9896.2005

(-) Compounds

Molecule 1 - CHRAC-14
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX2T-CHRAC14/16
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: RE59557P, CG15736-PA
 
Molecule 2 - CHRAC-16
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX2T-CHRAC14/16
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: CG32956-PA ISOFORM A, CG32956-PE, ISOFORM E

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CD3Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:57 , HIS D:57BINDING SITE FOR RESIDUE CD B1096
2AC2SOFTWAREGLU A:65 , GLU C:65 , HOH C:2004 , HOH C:2005 , HOH C:2008BINDING SITE FOR RESIDUE CD C1100
3AC3SOFTWAREHIS D:61 , ASP D:77 , HOH D:2001BINDING SITE FOR RESIDUE CD D1098

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BYM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2BYM)

(-) Exons   (0, 0)

(no "Exon" information available for 2BYM)

(-) 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:PROTEIN  Length:65
 aligned with Q9V452_DROME | Q9V452 from UniProtKB/TrEMBL  Length:140

    Alignment length:65
                                    44        54        64        74        84        94     
          Q9V452_DROME   35 TGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQK 99
               SCOP domains d2byma_ A: Chrac-16                                               SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhh..hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  2bym A 35 TGLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQK 99
                                    44        54        64        74        84        94     


Chain B from PDB  Type:PROTEIN  Length:83
 aligned with Q9V444_DROME | Q9V444 from UniProtKB/TrEMBL  Length:128

    Alignment length:83
                                    22        32        42        52        62        72        82        92   
          Q9V444_DROME   13 AVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKV 95
               SCOP domains d2bymb_ B: Chrac-14                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                  2bym B 13 AVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKV 95
                                    22        32        42        52        62        72        82        92   


Chain C from PDB  Type:PROTEIN  Length:64
 aligned with Q9V452_DROME | Q9V452 from UniProtKB/TrEMBL  Length:140

    Alignment length:64
                                    45        55        65        75        85        95    
          Q9V452_DROME   36 GLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQK 99
               SCOP domains d2bymc_ C: Chrac-16                                              SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhh.hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  2bym C 36 GLITNEVLFLMTKCTELFVRHLAGAAYTEEFGQRPGEALKYEHLSQVVNKNKNLEFLLQIVPQK 99
                                    45        55        65        75        85        95    


Chain D from PDB  Type:PROTEIN  Length:86
 aligned with Q9V444_DROME | Q9V444 from UniProtKB/TrEMBL  Length:128

    Alignment length:86
                                    21        31        41        51        61        71        81        91      
          Q9V444_DROME   12 NAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVK 97
               SCOP domains d2bymd_ D: Chrac-14                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                  2bym D 12 NAVIGRLIKEALPESASVSKEARAAIARAASVFAIFVTSSSTALAHKQNHKTITAKDILQTLTELDFESFVPSLTQDLEVYRKVVK 97
                                    21        31        41        51        61        71        81        91
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BYM)

(-) Gene Ontology  (16, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q9V452_DROME | Q9V452)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070615    nucleosome-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate. This reaction requires the presence of one or more nucleosomes.
    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.
biological process
    GO:0006974    cellular response to DNA damage stimulus    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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0042766    nucleosome mobilization    The movement of nucleosomes along a DNA fragment.
cellular component
    GO:0008623    CHRAC    An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals, Isw2 in S. cerevisiae), an ACF1 homolog, and additional small histone fold subunits (generally two of these, but Xenopus has only one and some additional non-conserved subunits). CHRAC plays roles in the regulation of RNA polymerase II transcription and in DNA replication and repair.
    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.

Chain B,D   (Q9V444_DROME | Q9V444)
molecular function
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0070615    nucleosome-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate. This reaction requires the presence of one or more nucleosomes.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0034080    CENP-A containing nucleosome assembly    The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.
    GO:0006974    cellular response to DNA damage stimulus    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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0071480    cellular response to gamma radiation    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 gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0042766    nucleosome mobilization    The movement of nucleosomes along a DNA fragment.
cellular component
    GO:0005671    Ada2/Gcn5/Ada3 transcription activator complex    A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues.
    GO:0008623    CHRAC    An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2H in mammals, Isw2 in S. cerevisiae), an ACF1 homolog, and additional small histone fold subunits (generally two of these, but Xenopus has only one and some additional non-conserved subunits). CHRAC plays roles in the regulation of RNA polymerase II transcription and in DNA replication and repair.
    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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(-) Related Entries Specified in the PDB File

2byk HISTONE FOLD HETERODIMER OF THE CHROMATIN ACCESSIBILITY COMPLEX