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(-) Description

Title :  HUMAN GCN5 ACETYLTRANSFERASE
 
Authors :  A. Dong, G. Bernstein, A. Schuetz, T. Antoshenko, H. Wu, P. Loppnau, M. Sundstrom, C. Arrowsmith, A. Edwards, A. Bochkarev, A. Plotnikov, Structural Genomics Consortium (Sgc)
Date :  16 Mar 05  (Deposition) - 29 Mar 05  (Release) - 20 May 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A
Keywords :  Gcn5, Acetyltransferase, Sgc, Structural Genomics, Structural Genomics Consortium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Schuetz, G. Bernstein, A. Dong, T. Antoshenko, H. Wu, P. Loppnau, A. Bochkarev, A. N. Plotnikov
Crystal Structure Of A Binary Complex Between Human Gcn5 Histone Acetyltransferase Domain And Acetyl Coenzyme A
Proteins V. 68 403 2007
PubMed-ID: 17410582  |  Reference-DOI: 10.1002/PROT.21407
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GENERAL CONTROL OF AMINO ACID SYNTHESIS PROTEIN 5-LIKE 2
    Chains: A
    EC Number: 2.3.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 497-662
    Gene: GCN5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE ACETYLTRANSFERASE GCN5, HSGCN5, STAF97

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACO1Ligand/IonACETYL COENZYME *A

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:502 , ALA A:512 , ASN A:513 , ARG A:515 , TRP A:519 , GLN A:530 , LEU A:531 , ILE A:576 , VAL A:577 , PHE A:578 , CYS A:579 , ALA A:580 , VAL A:581 , GLN A:586 , VAL A:587 , LYS A:588 , GLY A:589 , TYR A:590 , GLY A:591 , THR A:592 , THR A:612 , TYR A:613 , ASP A:615 , TYR A:617 , GLY A:620 , TYR A:621 , LYS A:624 , HOH A:1002 , HOH A:1008 , HOH A:1013 , HOH A:1024 , HOH A:1033 , HOH A:1036 , HOH A:1044BINDING SITE FOR RESIDUE ACO A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z4R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z4R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z4R)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GNATPS51186 Gcn5-related N-acetyltransferase (GNAT) domain profile.KAT2A_HUMAN503-656  1A:503-656

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002259161aENSE00001233454chr17:40273376-40272984393KAT2A_HUMAN1-1131130--
1.2ENST000002259162ENSE00000724857chr17:40272847-40272724124KAT2A_HUMAN114-155420--
1.3ENST000002259163ENSE00001629884chr17:40272388-40272243146KAT2A_HUMAN155-203490--
1.4ENST000002259164ENSE00000724850chr17:40272137-4027204890KAT2A_HUMAN204-233300--
1.5ENST000002259165ENSE00000724846chr17:40271736-40271555182KAT2A_HUMAN234-294610--
1.6aENST000002259166aENSE00000724842chr17:40271454-40271263192KAT2A_HUMAN294-358650--
1.7ENST000002259167ENSE00000724837chr17:40270421-40270315107KAT2A_HUMAN358-394370--
1.8ENST000002259168ENSE00000724835chr17:40270035-40269925111KAT2A_HUMAN394-431380--
1.9ENST000002259169ENSE00000724833chr17:40269832-40269696137KAT2A_HUMAN431-476460--
1.10ENST0000022591610ENSE00000724830chr17:40269614-40269406209KAT2A_HUMAN477-546701A:496-54651
1.11ENST0000022591611ENSE00001618772chr17:40269179-40269053127KAT2A_HUMAN546-588431A:546-58843
1.12ENST0000022591612ENSE00000724825chr17:40267851-40267741111KAT2A_HUMAN589-625371A:589-62537
1.13ENST0000022591613ENSE00000865274chr17:40267053-40266910144KAT2A_HUMAN626-673481A:626-65833
1.14ENST0000022591614ENSE00000724821chr17:40266622-40266508115KAT2A_HUMAN674-712390--
1.15ENST0000022591615ENSE00000724818chr17:40266412-4026637637KAT2A_HUMAN712-724130--
1.16ENST0000022591616ENSE00000724813chr17:40266300-4026623764KAT2A_HUMAN724-745220--
1.17ENST0000022591617ENSE00000724809chr17:40266102-4026601885KAT2A_HUMAN746-774290--
1.18bENST0000022591618bENSE00001842471chr17:40265860-40265126735KAT2A_HUMAN774-837640--

(-) 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:163
 aligned with KAT2A_HUMAN | Q92830 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:163
                                   505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655   
          KAT2A_HUMAN   496 RGIIEFHVIGNSLTPKANRRVLLWLVGLQNVFSHQLPRMPKEYIARLVFDPKHKTLALIKDGRVIGGICFRMFPTQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHIKHNILYFLTYADEYAIGYFKKQGFSKDIKVPKSRYLGYIKDYEGATLMECELNPR 658
               SCOP domains -d1z4ra1 A:497-658 Catalytic domain of GCN5 histone acetyltransferase                                                                                               SCOP domains
               CATH domains 1z4rA00 A:496-658  [code=3.40.630.30, no name defined]                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------Acetyltransf_1-1z4rA01 A:553-628                                            ------------------------------ Pfam domains
         Sec.struct. author ...eeeeee........hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh....eeeeeee..eeeeeeeeeee....eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhh.ee.....hhhhhh.........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------GNAT  PDB: A:503-656 UniProt: 503-656                                                                                                                     -- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:496-546 UniProt: 477-546         ------------------------------------------Exon 1.12  PDB: A:589-625            Exon 1.13  PDB: A:626-658         Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.11  PDB: A:546-588 UniProt: 546-588 ---------------------------------------------------------------------- Transcript 1 (2)
                 1z4r A 496 SGIIEFHVIGNSLTPKANRRVLLWLVGLQNVFSHQLPRMPKEYIARLVFDPKHKTLALIKDGRVIGGICFRMFPTQGFTEIVFCAVTSNEQVKGYGTHLMNHLKEYHIKHNILYFLTYADEYAIGYFKKQGFSKDIKVPKSRYLGYIKDYEGATLMECELNPR 658
                                   505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655
   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  (57, 57)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KAT2A_HUMAN | Q92830)
molecular function
    GO:0010484    H3 histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone H3 = CoA + acetyl-histone H3.
    GO:0008080    N-acetyltransferase activity    Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
    GO:0016407    acetyltransferase activity    Catalysis of the transfer of an acetyl group to an acceptor molecule.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0043997    histone acetyltransferase activity (H4-K12 specific)    Catalysis of the reaction: acetyl-CoA + histone H4 L-lysine (position 12) = CoA + histone H4 N6-acetyl-L-lysine (position 12).
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    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:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    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:0071929    alpha-tubulin acetylation    The addition of an acetyl group to the lysine 40 residue of alpha-tubulin.
    GO:0055007    cardiac muscle cell differentiation    The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:1990090    cellular response to nerve growth factor stimulus    A 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 nerve growth factor stimulus.
    GO:0071356    cellular response to tumor necrosis factor    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 tumor necrosis factor stimulus.
    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:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0044154    histone H3-K14 acetylation    The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 14 of the histone.
    GO:0043983    histone H4-K12 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 12 of the histone.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0016578    histone deubiquitination    The modification of histones by removal of ubiquitin groups.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0048312    intracellular distribution of mitochondria    Any process that establishes the spatial arrangement of mitochondria within the cell.
    GO:0022037    metencephalon development    The process whose specific outcome is the progression of the metencephalon over time, from its formation to the mature structure.
    GO:0030901    midbrain development    The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0031346    positive regulation of cell projection organization    Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0035948    positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of gluconeogenesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0035066    positive regulation of histone acetylation    Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:2000679    positive regulation of transcription regulatory region DNA binding    Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding.
    GO:1903146    regulation of mitophagy    Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
    GO:0031647    regulation of protein stability    Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
    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:0031667    response to nutrient levels    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0001756    somitogenesis    The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
    GO:0021537    telencephalon development    The process whose specific outcome is the progression of the telencephalon over time, from its formation to the mature structure. The telencephalon is the paired anteriolateral division of the prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0030914    STAGA complex    A large multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. The composition is similar to that of the SAGA complex; for example, the human complex contains the transcription-transformation cofactor TRRAP, hGCN5L acetylase, novel human ADA-like and SPT-like cofactors, and a subset of TAFs.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0000123    histone acetyltransferase complex    A protein complex that possesses histone acetyltransferase activity.
    GO:0072686    mitotic spindle    A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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.
    GO:0033276    transcription factor TFTC complex    A protein complex that does not contain either a TATA-binding protein (TBP) or a TBP-like factor, but is composed of several TAFIIs and other proteins, including a histone acetyltransferase. This complex is able to nucleate transcription initiation by RNA polymerase II, can mediate transcriptional activation, and has histone acetyltransferase activity.

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        KAT2A_HUMAN | Q92830: 1f68 3d7c 5h84 5h86

(-) Related Entries Specified in the PDB File

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