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(-) Description

Title :  CRYSTAL STRUCTURE OF TETRAHYMENA GCN5 WITH BOUND COENZYME A AND A PHOSPHORYLATED, 19-RESIDUE HISTONE H3 PEPTIDE
 
Authors :  A. Clements, A. N. Poux, W. S. Lo, L. Pillus, S. L. Berger, R. Marmorstein
Date :  24 Jun 03  (Deposition) - 23 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Histone Acetyltransferase, Gcn5-Related N-Acetyltransferase, Coa-Binding Protein, Ternary Complex, Transferase/Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Clements, A. N. Poux, W. S. Lo, L. Pillus, S. L. Berger, R. Marmorstein
Structural Basis For Histone And Phospho-Histone Binding By The Gcn5 Histone Acetyltransferase
Mol. Cell V. 12 461 2003
PubMed-ID: 14536085  |  Reference-DOI: 10.1016/S1097-2765(03)00288-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HAT A1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PRSETA
    Expression System Strain: BL-21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 48-210
    Organism Scientific: TETRAHYMENA THERMOPHILA
    Organism Taxid: 5911
 
Molecule 2 - HISTONE H3
    Chains: B
    Engineered: YES
    Fragment: RESIDUES 305-323
    Other Details: SER 310 IS PHOSPHORYLATED
    Other Details - Source: THIS PROTEIN NATURALLY OCCURS IN SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:76 , LEU A:77 , LEU A:126 , ALA A:127 , VAL A:128 , GLN A:133 , VAL A:134 , ARG A:135 , GLY A:136 , GLY A:138 , THR A:139 , GLN A:152 , PHE A:164 , TYR A:168 , HOH A:410 , HOH A:415 , HOH A:459 , LYS B:314 , GLN B:319BINDING SITE FOR RESIDUE COA A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H3_1PS00322 Histone H3 signature 1.H3_KLULA15-21  1B:314-320
H3_YEAST15-21  1B:314-320

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL031C1YNL031C.1XIV:576052-575642411H3_YEAST1-1361361B:305-32319

(-) 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:162
 aligned with Q27198_TETTH | Q27198 from UniProtKB/TrEMBL  Length:418

    Alignment length:162
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
         Q27198_TETTH    49 LDFDILTNDGTHRNMKLLIDLKNIFSRQLPKMPKEYIVKLVLDRHHESMVILKNKQKVIGGICFRQYKPQRFAEVAFLAVTANEQVRGYGTRLMNKFKDHMQKQNIEYLLTYADNFAIGYFKKQGFTKEHRMPQEKWKGYIKDYDGGTLMECYIHPYVDYGN 210
               SCOP domains d1puaa_ A: Catalytic domain of GCN5 histone acetyltransferase                                                                                                      SCOP domains
               CATH domains 1puaA00 A:49-210  [code=3.40.630.30, no name defined]                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------Acetyltransf_1-1puaA01 A:100-175                                            ----------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...eeeeeeee...eeeeeeeeeee....eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhh........hhhhhh.........eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pua A  49 LDFDILTNDGTHRNMKLLIDLKNIFSRQLPKMPKEYIVKLVFDRHHESMVILKNKQKVIGGICFRQYKPQRFAEVAFLAVTANEQVRGYGTRLMNKFKDHMQKQNIEYLLTYADNFAIGYFKKQGFTKEHRMPQEKWKGYIKDYDGGTLMECYIHPYVDYGR 210
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  


Chain B from PDB  Type:PROTEIN  Length:19
 aligned with H3_KLULA | P61831 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:19
                                    15         
             H3_KLULA     6 QTARKSTGGKAPRKQLASK  24
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ................... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                PROSITE (2) ---------HISTONE--- PROSITE (2)
                 Transcript ------------------- Transcript
                 1pua B 305 QTARKsTGGKAPRKQLASK 323
                                 | 314         
                                 |             
                               310-SEP         


Chain B from PDB  Type:PROTEIN  Length:19
 aligned with H3_YEAST | P61830 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:19
                                    15         
             H3_YEAST     6 QTARKSTGGKAPRKQLASK  24
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ................... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ---------HISTONE--- PROSITE
               Transcript 1 Exon 1.1            Transcript 1
                 1pua B 305 QTARKsTGGKAPRKQLASK 323
                                 | 314         
                               310-SEP
   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)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Acetyltrans (109)

(-) Gene Ontology  (14, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q27198_TETTH | Q27198)
molecular function
    GO:0008080    N-acetyltransferase activity    Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.

Chain B   (H3_KLULA | P61831)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    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.

Chain B   (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_KLULA | P61831: 1m1d 1peg 1pu9
        H3_YEAST | P61830: 1id3 1m1d 1peg 1pu9 1qsn 2cnx 2h2g 2idc 2jmj 2rnw 2rnx 2rsn 3mp1 3mp6 3q33 4jjn 4kud 4psx 5d7e 5iok
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        Q27198_TETTH | Q27198: 1m1d 1pu9 1q2c 1q2d 1qsn 1qsr 1qst 5gcn

(-) Related Entries Specified in the PDB File

1m1d TETRAHYMENA GCN5 WITH BOUND BISUBSTRATE ANALOG INHIBITOR
1pu9 CRYSTAL STRUCTURE OF TETRAHYMENA GCN5 WITH BOUND COENZYME A AND A 19-RESIDUE HISTONE H3 PEPTIDE
1qsn CRYSTAL STRUCTURE OF TETRAHYMENA GCN5 WITH BOUND COENZYME A AND HISTONE H3 PEPTIDE
1qsr CRYSTAL STRUCTURE OF TETRAHYMENA GCN5 WITH BOUND ACETYL- COENZYME A
1qst CRYSTAL STRUCTURE OF TETRAHYMENA GCN5