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(-) Description

Title :  HUMAN CHROMODOMAIN Y-LIKE PROTEIN
 
Authors :  J. Min, H. Wu, T. Antoshenko, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)
Date :  28 Apr 06  (Deposition) - 09 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Chromodomain Y-Like Protein, Structural Genomics, Structural Genomics Consortium, Sgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Antoshenko, J. Min, H. Wu, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
The Crystal Structure Of Human Chromodomain Y-Like Protein.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHROMODOMAIN Y-LIKE PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CDYL, CDYL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CDY-LIKE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2GTR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (5, 15)

Asymmetric/Biological Unit (5, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003289081bENSE00001241571chr6:4706393-470648593CDYL1_HUMAN-00--
1.2aENST000003289082aENSE00002154059chr6:4715975-4716115141CDYL1_HUMAN1-35350--
1.4ENST000003289084ENSE00001979662chr6:4734996-473507883CDYL1_HUMAN35-62280--
1.9dENST000003289089dENSE00001979701chr6:4891947-4892613667CDYL1_HUMAN63-2852230--
1.11bENST0000032890811bENSE00001972080chr6:4935749-4936005257CDYL1_HUMAN285-370863A:3-33
B:4-33
C:3-33		31
30
31
1.12ENST0000032890812ENSE00001991020chr6:4937799-4937971173CDYL1_HUMAN371-428583A:34-91
B:34-91
C:34-91		58
58
58
1.13bENST0000032890813bENSE00001960715chr6:4943780-4943990211CDYL1_HUMAN428-498713A:91-161
B:91-161
C:91-161		71
71
71
1.14ENST0000032890814ENSE00001962725chr6:4952500-4952643144CDYL1_HUMAN499-546483A:162-209
B:162-209
C:162-209		48
48
48
1.15eENST0000032890815eENSE00001930193chr6:4954132-49557811650CDYL1_HUMAN547-598523A:210-260
B:210-261
C:210-252		51
52
43

(-) 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:258
 aligned with CDYL1_HUMAN | Q9Y232 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:258
                                   349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589        
          CDYL1_HUMAN   340 RYRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQSALSTAAADDSKLVLLSAVGSVFCCGLDFIYFIRRLTDDRKRESTKMAEAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSTVMFPKIMGGASANEMLLSGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEESKALVRCNMKMELEQANERECEVLKKIWGSAQGMDSMLKYLQRKIDE 597
               SCOP domains d2gtra_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeee........eehhhhhhhhhhhhhhhhhh....eeeee.......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...eehhhhhhhhhh.eeeee...eee............hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.11b  PDB: A:3-33        Exon 1.12  PDB: A:34-91 UniProt: 371-428                  ----------------------------------------------------------------------Exon 1.14  PDB: A:162-209 UniProt: 499-546      Exon 1.15e  PDB: A:210-260 UniProt: 547-598         Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.13b  PDB: A:91-161 UniProt: 428-498                             --------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2gtr A   3 RYRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQSALSTAAADDSKLVLLSAVGSVFCCGLDFIYFIRRLTDDRKRESTKMAEAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSTVMFPKIMGGASANEMLLSGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEESKALVRCNMKMELEQANERECEVLKKIWGSAQGMDSMLKYLQRKIDE 260
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252        


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with CDYL1_HUMAN | Q9Y232 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:258
                                   350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590        
          CDYL1_HUMAN   341 YRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQSALSTAAADDSKLVLLSAVGSVFCCGLDFIYFIRRLTDDRKRESTKMAEAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSTVMFPKIMGGASANEMLLSGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEESKALVRCNMKMELEQANERECEVLKKIWGSAQGMDSMLKYLQRKIDEF 598
               SCOP domains d2gtrb_ B: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..eeeeee..........hhhhhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...eehhhhhhhhhh.eeeee...eee..hhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.11b  PDB: B:4-33       Exon 1.12  PDB: B:34-91 UniProt: 371-428                  ----------------------------------------------------------------------Exon 1.14  PDB: B:162-209 UniProt: 499-546      Exon 1.15e  PDB: B:210-261 UniProt: 547-598          Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------Exon 1.13b  PDB: B:91-161 UniProt: 428-498                             ---------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2gtr B   4 YRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQSALSTAAADDSKLVLLSAVGSVFCCGLDFIYFIRRLTDDRKRESTKMAEAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSTVMFPKIMGGASANEMLLSGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEESKALVRCNMKMELEQANERECEVLKKIWGSAQGMDSMLKYLQRKIDEF 261
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253        


Chain C from PDB  Type:PROTEIN  Length:250
 aligned with CDYL1_HUMAN | Q9Y232 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:250
                                   349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589
          CDYL1_HUMAN   340 RYRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQSALSTAAADDSKLVLLSAVGSVFCCGLDFIYFIRRLTDDRKRESTKMAEAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSTVMFPKIMGGASANEMLLSGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEESKALVRCNMKMELEQANERECEVLKKIWGSAQGMDSMLK 589
               SCOP domains d2gtrc_ C: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeee..........hhhhhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeee...eehhhhhhhhhh.eeeee...eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh....eee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11b  PDB: C:3-33        Exon 1.12  PDB: C:34-91 UniProt: 371-428                  ----------------------------------------------------------------------Exon 1.14  PDB: C:162-209 UniProt: 499-546      Exon 1.15e  PDB: C:210-252 UniProt: 547-598 Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------Exon 1.13b  PDB: C:91-161 UniProt: 428-498                             ------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2gtr C   3 RYRDIVVRKQDGFTHILLSTKSSENNSLNPEVMREVQSALSTAAADDSKLVLLSAVGSVFCCGLDFIYFIRRLTDDRKRESTKMAEAIRNFVNTFIQFKKPIIVAVNGPAIGLGASILPLCDVVWANEKAWFQTPYTTFGQSPDGCSTVMFPKIMGGASANEMLLSGRKLTAQEACGKGLVSQVFWPGTFTQEVMVRIKELASCNPVVLEESKALVRCNMKMELEQANERECEVLKKIWGSAQGMDSMLK 252
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CDYL1_HUMAN | Q9Y232)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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: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: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:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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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  2gtr
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 Related Entries

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

UniProtKB/Swiss-Prot
        CDYL1_HUMAN | Q9Y232: 2dnt

(-) Related Entries Specified in the PDB File

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