Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HAT DOMAIN OF THE HUMAN MOZ PROTEIN
 
Authors :  M. A. Holbert, T. Sikorski, D. Snowflack, R. Marmorstein
Date :  19 Sep 07  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Coenzyme A Binding Domain, Zinc-Finger, Helix-Turn-Helix, Activator, Acyltransferase, Chromatin Regulator, Metal-Binding, Nucleus, Phosphorylation, Proto-Oncogene, Repressor, Transcription, Transcription Regulation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Holbert, T. Sikorski, J. Carten, D. Snowflack, S. Hodawadekar, R. Marmorstein
The Human Monocytic Leukemia Zinc Finger Histone Acetyltransferase Domain Contains Dna-Binding Activity Implicated In Chromatin Targeting.
J. Biol. Chem. V. 282 36603 2007
PubMed-ID: 17925393  |  Reference-DOI: 10.1074/JBC.M705812200

(-) Compounds

Molecule 1 - HISTONE ACETYLTRANSFERASE MYST3
    ChainsA
    EC Number2.3.1.48, 2.3.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentHAT DOMAIN
    GeneMYST3, MOZ, RUNXBP2, ZNF220
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMYST PROTEIN 3, MOZ, YBF2/SAS3, SAS2 AND TIP60 PROTEIN 3, RUNT-RELATED TRANSCRIPTION FACTOR-BINDING PROTEIN 2, MONOCYTIC LEUKEMIA ZINC FINGER PROTEIN, ZINC FINGER PROTEIN 220

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACO1Ligand/IonACETYL COENZYME *A
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:540 , CYS A:543 , HIS A:556 , CYS A:560BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREPHE A:600 , LEU A:601 , SER A:645 , CYS A:646 , ILE A:647 , MET A:648 , ILE A:649 , GLN A:654 , ARG A:655 , LYS A:656 , GLY A:657 , TYR A:658 , GLY A:659 , ARG A:660 , GLU A:680 , LEU A:683 , SER A:684 , LEU A:686 , LEU A:689 , SER A:690BINDING SITE FOR RESIDUE ACO A 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RC4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Cys A:508 -Pro A:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RC4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RC4)

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003969301bENSE00001247926chr8:41909505-4190941987KAT6A_HUMAN-00--
1.2bENST000003969302bENSE00001611634chr8:41907225-41907094132KAT6A_HUMAN-00--
1.3bENST000003969303bENSE00002107560chr8:41906820-41905896925KAT6A_HUMAN1-2002000--
1.4ENST000003969304ENSE00000818786chr8:41845081-41844973109KAT6A_HUMAN201-237370--
1.5ENST000003969305ENSE00000692308chr8:41839472-41839357116KAT6A_HUMAN237-275390--
1.6ENST000003969306ENSE00000692307chr8:41838445-4183836482KAT6A_HUMAN276-303280--
1.7ENST000003969307ENSE00000692300chr8:41836295-41836160136KAT6A_HUMAN303-348460--
1.8bENST000003969308bENSE00000818785chr8:41834845-41834526320KAT6A_HUMAN348-4551080--
1.9bENST000003969309bENSE00001128473chr8:41832340-41832222119KAT6A_HUMAN455-494400--
1.11ENST0000039693011ENSE00001128468chr8:41812929-41812814116KAT6A_HUMAN495-533391A:507-53327
1.12ENST0000039693012ENSE00000692227chr8:41806881-41806740142KAT6A_HUMAN533-580481A:533-58048
1.13ENST0000039693013ENSE00001762740chr8:41805430-41805269162KAT6A_HUMAN581-634541A:581-63454
1.14ENST0000039693014ENSE00000692210chr8:41804202-4180410994KAT6A_HUMAN635-666321A:635-66632
1.15ENST0000039693015ENSE00000818792chr8:41801497-41801266232KAT6A_HUMAN666-743781A:666-73873
1.16aENST0000039693016aENSE00000692156chr8:41800518-41800311208KAT6A_HUMAN743-812701A:748-77932
1.17ENST0000039693017ENSE00000692153chr8:41798962-41798360603KAT6A_HUMAN813-10132010--
1.18ENST0000039693018ENSE00001040899chr8:41795086-41794774313KAT6A_HUMAN1014-11181050--
1.19bENST0000039693019bENSE00001247935chr8:41792385-417869975389KAT6A_HUMAN1118-20048870--

(-) 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:264
 aligned with KAT6A_HUMAN | Q92794 from UniProtKB/Swiss-Prot  Length:2004

    Alignment length:273
                                   516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776   
          KAT6A_HUMAN   507 RCPSVIEFGKYEIHTWYSSPYPQEYSRLPKLYLCEFCLKYMKSRTILQQHMKKCGWFHPPANEIYRKNNISVFEVDGNVSTIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVLTQNDVKGCHLVGYFSKEKHCQQKYNVSCIMILPQYQRKGYGRFLIDFSYLLSKREGQAGSPEKPLSDLGRLSYMAYWKSVILECLYHQNDKQISIKKLSKLTGICPQDITSTLHHLRMLDFRSDQFVIIRREKLIQDHMAKLQLNLRPVDVDPECLRWTPV 779
               SCOP domains d2rc4a1 A:507-779 Histone acetyltransferase MYST3                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee....eee.......hhhhhh..eee..........hhhhhhhh...........eeeeee..eeeeeee...hhhhhhhhhhhhhh.............eeeeeeeeee..eeeeeeeeeee..........eeee.hhhh..hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhh.....---------..hhhhhhhhhhhhh.......hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  PDB: A:507-533  -----------------------------------------------Exon 1.13  PDB: A:581-634 UniProt: 581-634            Exon 1.14  PDB: A:635-666       ----------------------------------------------------------------------------Exon 1.16a  PDB: A:748-779            Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.12  PDB: A:533-580 UniProt: 533-580      -------------------------------------------------------------------------------------Exon 1.15  PDB: A:666-738 UniProt: 666-743 [INCOMPLETE]                       ------------------------------------ Transcript 1 (2)
                 2rc4 A 507 RCPSVIEFGKYEIHTWYSSPYPQEYSRLPKLYLCEFCLKYMKSRTILQQHMKKCGWFHPPANEIYRKNNISVFEVDGNVSTIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVLTQNDVKGCHLVGYFSKEKHCQQKYNVSCIMILPQYQRKGYGRFLIDFSYLLSKREGQAGSPEKPLSDLGRLSYMAYWKSVILECLYHQNDKQISIKKLSKLTGICPQDITSTLHHLRMLD---------RREKLIQDHMAKLQLNLRPVDVDPECLRWTPV 779
                                   516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736 |       - |     756       766       776   
                                                                                                                                                                                                                                                                 738       748                               

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RC4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RC4)

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KAT6A_HUMAN | Q92794)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016407    acetyltransferase activity    Catalysis of the transfer of an acetyl group to an acceptor molecule.
    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: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: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).
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006323    DNA packaging    Any process in which DNA and associated proteins are formed into a compact, orderly structure.
    GO:0048513    animal organ development    Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0090398    cellular senescence    A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest.
    GO:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0030099    myeloid cell differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006473    protein acetylation    The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    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:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0070776    MOZ/MORF histone acetyltransferase complex    A histone acetyltransferase complex that has histone H3 acetyltransferase and coactivator activities. Subunits of the human complex include MYST3/MOZ, MYST4/MORF, ING5, EAF6 and one of BRPF1, BRD1/BRPF2 and BRPF3.
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:508 - Pro A:509   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2rc4
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KAT6A_HUMAN | Q92794
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.3.1.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
  2.3.1.48
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  KAT6A_HUMAN | Q92794
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        KAT6A_HUMAN | Q927941m36 2ln0 2ozu 3v43 4ljn 4lk9 4lka 4llb 5b75 5b76 5b77 5b78

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2RC4)