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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH MS-344
 
Authors :  J. R. Somoza, R. J. Skene, B. A. Katz, C. Mol, J. D. Ho, A. J. Jennings, C. Lu A. Arvai, J. J. Buggy, E. Chi, J. Tang, B. -C. Sang, E. Verner, R. Wynands E. M. Leahy, D. R. Dougan, G. Snell, M. Navre, M. W. Knuth, R. V. Swanson, D. E. Mcree, L. W. Tari
Date :  05 May 04  (Deposition) - 27 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A
Keywords :  Histone Deacetylase, Zinc Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Somoza, R. J. Skene, B. A. Katz, C. Mol, J. D. Ho, A. J. Jennings, C. Luong, A. Arvai, J. J. Buggy, E. Chi, J. Tang, B. -C. Sang, E. Verner, R. Wynands, E. M. Leahy, D. R. Dougan, G. Snell, M. Navre, M. W. Knuth, R. V. Swanson, D. E. Mcree, L. W. Tari
Structural Snapshots Of Human Hdac8 Provide Insights Into The Class I Histone Deacetylases
Structure V. 12 1325 2004
PubMed-ID: 15242608  |  Reference-DOI: 10.1016/J.STR.2004.04.012

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 8
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBACHTA
    Expression System StrainSF9
    Expression System Taxid7108
    Expression System VectorPSXB2
    Expression System Vector TypeBACULOVIRUS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHDAC8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1B3N1Ligand/Ion4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2NA2Ligand/IonSODIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:178 , HIS A:180 , ASP A:267 , B3N A:381BINDING SITE FOR RESIDUE ZN A 378
2AC2SOFTWAREASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200BINDING SITE FOR RESIDUE NA A 379
3AC3SOFTWAREPHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:480BINDING SITE FOR RESIDUE NA A 380
4AC4SOFTWARELYS A:33 , TYR A:100 , HIS A:142 , HIS A:143 , GLY A:151 , PHE A:152 , ASP A:178 , HIS A:180 , PHE A:208 , ASP A:267 , PRO A:273 , MET A:274 , GLY A:304 , TYR A:306 , ZN A:378 , HOH A:392BINDING SITE FOR RESIDUE B3N A 381

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T67)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:208 -Pro A:209
2Gly A:341 -Pro A:342
3Val A:376 -Val A:377

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069140H180RHDAC8_HUMANDisease (CDLS5)397515416AH180R
2UniProtVAR_069141T311MHDAC8_HUMANDisease (CDLS5)397515417AT311M
3UniProtVAR_069142G320RHDAC8_HUMANDisease (CDLS5)398122909AG320R
4UniProtVAR_069143H334RHDAC8_HUMANDisease (CDLS5)397515418AH334R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T67)

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003735731aENSE00001889063X:71792953-71792501453HDAC8_HUMAN1-37371A:14-3724
1.3aENST000003735733aENSE00001647366X:71791959-7179190753HDAC8_HUMAN38-55181A:38-5518
1.4aENST000003735734aENSE00000978735X:71788734-71788604131HDAC8_HUMAN55-99451A:55-99 (gaps)45
1.5aENST000003735735aENSE00001800363X:71787880-71787739142HDAC8_HUMAN99-146481A:99-14648
1.6bENST000003735736bENSE00001682124X:71715118-71715006113HDAC8_HUMAN146-184391A:146-18439
1.7bENST000003735737bENSE00001702232X:71710856-7171077978HDAC8_HUMAN184-210271A:184-21027
1.9aENST000003735739aENSE00001682340X:71708891-71708783109HDAC8_HUMAN210-246371A:210-24637
1.13bENST0000037357313bENSE00001694695X:71684581-71684409173HDAC8_HUMAN246-304591A:246-30459
1.15cENST0000037357315cENSE00001436112X:71681948-7168185495HDAC8_HUMAN304-335321A:304-33532
1.16bENST0000037357316bENSE00001435962X:71571688-71571583106HDAC8_HUMAN336-371361A:336-37136
1.18bENST0000037357318bENSE00001859665X:71549926-71549366561HDAC8_HUMAN371-37771A:371-3777

(-) 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:357
 aligned with HDAC8_HUMAN | Q9BY41 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:364
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373    
          HDAC8_HUMAN    14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
               SCOP domains d1t67a_ A: Histone deacetylase 8, HDAC8                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1t67A00 A:14-377  [code=3.40.800.20, no name defined]                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------Hist_deacetyl-1t67A01 A:21-323                                                                                                                                                                                                                                                                                 ------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhh-------...............hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhhh....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------M--------R-------------R------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:14-37 Exon 1.3a         -------------------------------------------Exon 1.5a  PDB: A:99-146 UniProt: 99-146        -------------------------------------Exon 1.7b  PDB: A:184-210  -----------------------------------Exon 1.13b  PDB: A:246-304 UniProt: 246-304                -------------------------------Exon 1.16b  PDB: A:336-371          ------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.4a  PDB: A:55-99 (gaps) UniProt: 55-99----------------------------------------------Exon 1.6b  PDB: A:146-184              -------------------------Exon 1.9a  PDB: A:210-246            ---------------------------------------------------------Exon 1.15c  PDB: A:304-335      -----------------------------------1.18b   Transcript 1 (2)
                 1t67 A  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQ-------DSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    23        33        43        53        63        73        83|       93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373    
                                                                                                 84      92                                                                                                                                                                                                                                                                                             

   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  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Arginase (56)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HDAC8_HUMAN | Q9BY41)
molecular function
    GO:0030544    Hsp70 protein binding    Interacting selectively and non-covalently with Hsp70 proteins, any of a group of heat shock proteins around 70kDa in size.
    GO:0051879    Hsp90 protein binding    Interacting selectively and non-covalently with Hsp90 proteins, any of a group of heat shock proteins around 90kDa in size.
    GO:0032041    NAD-dependent histone deacetylase activity (H3-K14 specific)    Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein.
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0006333    chromatin assembly or disassembly    The formation or destruction of chromatin structures.
    GO:0070932    histone H3 deacetylation    The modification of histone H3 by the removal of one or more acetyl groups.
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    GO:0031397    negative regulation of protein ubiquitination    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0071922    regulation of cohesin loading    Any process that modulates the frequency, rate or extent of a process in which a cohesin complex is transported to, or maintained at, a part of a chromosome that is organized into chromatin.
    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:0032204    regulation of telomere maintenance    Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HDAC8_HUMAN | Q9BY411t64 1t69 1vkg 1w22 2v5w 2v5x 3ew8 3ewf 3ezp 3ezt 3f06 3f07 3f0r 3mz3 3mz4 3mz6 3mz7 3rqd 3sff 3sfh 4qa0 4qa1 4qa2 4qa3 4qa4 4qa5 4qa6 4qa7 4rn0 4rn1 4rn2 5bwz 5d1b 5d1c 5d1d 5dc5 5dc6 5dc7 5dc8 5fcw 5ths 5tht 5thu 5thv

(-) Related Entries Specified in the PDB File

1t64 CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH TRICHOSTATIN A
1t69 CRYSTAL STRUCTURE OF HDAC8 COMPLEXED WITH SAHA