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(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE YEAST YNG1 PROTEIN IN COMPLEX WITH H3(1-9)K4ME3 PEPTIDE
 
Authors :  S. Ilin, S. D. Taverna, R. S. Rogers, J. C. Tanny, H. Lavender, H. Li, L. Baker, J. Boyle, L. P. Blair, B. T. Chait, D. J. Patel, J. D. Aitchison A. J. Tackett, C. D. Allis
Date :  15 Nov 06  (Deposition) - 03 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,P  (20x)
Keywords :  Nmr, Histone, Phd, H3K4Me3, Complex, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. D. Taverna, S. Ilin, R. S. Rogers, J. C. Tanny, H. Lavender, H. Li, L. Baker, J. Boyle, L. P. Blair, B. T. Chait, D. J. Patel, J. D. Aitchison, A. J. Tackett, C. D. Allis
Yng1 Phd Finger Binding To H3 Trimethylated At K4 Promotes Nua3 Hat Activity At K14 Of H3 And Transcription At A Subset Of Targeted Orfs
Mol. Cell V. 24 785 2006
PubMed-ID: 17157260  |  Reference-DOI: 10.1016/J.MOLCEL.2006.10.026
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN YNG1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PHD FINGER
    Gene: YNG1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: ING1 HOMOLOG 1
 
Molecule 2 - HISTONE H3
    Chains: P
    Engineered: YES
    Other Details: THE PEPTIDE H3(1-9)K4ME3 IS NATURALLY FOUND IN SACCHAROMYCES CEREVISIAE (LOCUS AAS64341 TO AAS64341).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

NMR Structure (2, 3)
No.NameCountTypeFull Name
1M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
2ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:42 , CYS A:47 , PHE A:52 , CYS A:69 , CYS A:73BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:29 , CYS A:31 , ASN A:33 , TYR A:36 , HIS A:53 , CYS A:56BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (5, 5)

NMR Structure
No.Residues
1A:29 -A:31
2A:31 -A:56
3A:42 -A:69
4A:47 -A:73
5A:69 -A:73

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL031C1YNL031C.1XIV:576052-575642411H3_YEAST1-1361361P:1-99
2.1YOR064C1YOR064C.1XV:446740-446081660YNG1_YEAST1-2192191A:24-8360

(-) 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:60
 aligned with YNG1_YEAST | Q08465 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:60
                                   162       172       182       192       202       212
           YNG1_YEAST   153 QEEVYCFCRNVSYGPMVACDNPACPFEWFHYGCVGLKQAPKGKWYCSKDCKEIANQRSKS 212
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ----PHD-2jmjA01 A:28-76                              ------- Pfam domains
         Sec.struct. author ...............ee...........ee................hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
               Transcript 2 Exon 2.1  PDB: A:24-83 UniProt: 1-219 [INCOMPLETE]           Transcript 2
                 2jmj A  24 QEEVYCFCRNVSYGPMVACDNPACPFEWFHYGCVGLKQAPKGKWYCSKDCKEIANQRSKS  83
                                    33        43        53        63        73        83


Chain P from PDB  Type:PROTEIN  Length:9
 aligned with H3_YEAST | P61830 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:9
             H3_YEAST     2 ARTKQTARK  10
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..ee..... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
               Transcript 1 Exon 1.1  Transcript 1
                 2jmj P   1 ARTkQTARK   9
                               |     
                               |     
                               4-M3L
   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 2JMJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: zf-FYVE-PHD (57)

(-) Gene Ontology  (23, 25)

NMR Structure(hide GO term definitions)
Chain A   (YNG1_YEAST | Q08465)
molecular function
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0032968    positive regulation of transcription elongation from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0033100    NuA3 histone acetyltransferase complex    A Gcn5-independent multisubunit complex that catalyzes the acetylation of histone H3. The budding yeast complex includes Sas3p, Taf30p, and Yng1p.
    GO:1990467    NuA3a histone acetyltransferase complex    A NuA3 complex that catalyzes the acetylation of Histone H3. In S. cerevisiae, this complex consists of Eaf6p, Nto1p, Sas3p, Taf14p, Yng1p and associates with H3K4me3 using Yng1p.
    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 P   (H3_YEAST | P61830)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0006333    chromatin assembly or disassembly    The formation or destruction of chromatin structures.
    GO:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    GO:0009303    rRNA transcription    The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
    GO:0043935    sexual sporulation resulting in formation of a cellular spore    The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0043505    CENP-A containing nucleosome    A form of nucleosome located only at the centromere, in which the histone H3 is replaced by the variant form CENP-A (sometimes known as CenH3).
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000788    nuclear nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order 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:0031298    replication fork protection complex    A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

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 Related Entries

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

UniProtKB/Swiss-Prot
        H3_YEAST | P61830: 1id3 1m1d 1peg 1pu9 1pua 1qsn 2cnx 2h2g 2idc 2rnw 2rnx 2rsn 3mp1 3mp6 3q33 4jjn 4kud 4psx 5d7e 5iok
        YNG1_YEAST | Q08465: 2jmi

(-) Related Entries Specified in the PDB File

2jmi PHD FINGER FRAGMENT OF YEAST YNG1 PROTEIN IN FREE STATE