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(-) Description

Title :  STRUCTURE OF THE YEAST HST2 PROTEIN DEACETYLASE IN TERNARY COMPLEX WITH 2'-O-ACETYL ADP RIBOSE AND HISTONE PEPTIDE
 
Authors :  K. Zhao, X. Chai, R. Marmorstein
Date :  18 Jul 03  (Deposition) - 18 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ternary Complex, Histone Deacetylase, 2'-O-Adp Ribose, , Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Zhao, X. Chai, R. Marmorstein
Structure Of The Yeast Hst2 Protein Deacetylase In Ternary Complex With 2'-O-Acetyl Adp Ribose And Histone Peptide.
Structure V. 11 1403 2003
PubMed-ID: 14604530  |  Reference-DOI: 10.1016/J.STR.2003.09.016
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HST2 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: C-TERMINLA DELETION OF HST2
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: HOMOLOGOUS TO SIR2 PROTEIN 2
 
Molecule 2 - HISTONE H4
    Chains: B
    Engineered: YES
    Fragment: RESIDUES 12-21
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
2OAD1Ligand/Ion2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE
3ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:143 , CYS A:146 , CYS A:170 , CYS A:173BINDING SITE FOR RESIDUE ZN A 701
2AC2SOFTWAREGLY A:32 , ALA A:33 , GLY A:34 , THR A:37 , ASP A:43 , PHE A:44 , ARG A:45 , TYR A:52 , PRO A:61 , GLN A:115 , HIS A:135 , ILE A:181 , VAL A:182 , PHE A:184 , GLY A:223 , THR A:224 , SER A:225 , VAL A:228 , ASN A:248 , LEU A:249 , GLN A:268 , TYR A:269 , SER A:270 , HOH A:1002 , HOH A:1013 , HOH A:1027 , HOH A:1124 , HOH A:1158 , HOH A:1213 , ALY B:353BINDING SITE FOR RESIDUE OAD A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q1A)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:162 -Pro A:163
2Tyr A:229 -Pro A:230

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q1A)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIRTUINPS50305 Sirtuin catalytic domain profile.HST2_YEAST13-286  1A:13-286
2HISTONE_H4PS00047 Histone H4 signature.H4_YEAST15-19  1B:351-355

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL030W1YNL030W.1XIV:576729-577040312H4_YEAST1-1031031B:349-35810
2.1YPL015C1YPL015C.1XVI:526880-5258071074HST2_YEAST1-3573571A:5-293 (gaps)289

(-) 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:285
 aligned with HST2_YEAST | P53686 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:289
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284         
           HST2_YEAST     5 TASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITTSGKHPQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTA 293
               SCOP domains d1q1aa_ A: Hst2                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1q1aA01 A:5-37,A:94-134,A:190-2931q1aA02 A:38-93,A:135-189 SIR2/SIRT2 'Small Domain'     1q1aA01 A:5-37,A:94-134,A:190-293        1q1aA02 A:38-93,A:135-189 SIR2/SIRT2 'Small Domain'    1q1aA01 A:5-37,A:94-    134,A:190-293 TPP-binding domain                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh....eeeee.hhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....ee.hhhhhhhhh................eeeee........hhhhhhhhhhhhhhhhhhhh----....eeeee.....ee..hhhhhhh....eeeee.....hhhhhh.....eee..hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------SIRTUIN  PDB: A:13-286 UniProt: 13-286                                                                                                                                                                                                                                            ------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:5-293 (gaps) UniProt: 1-357 [INCOMPLETE]                                                                                                                                                                                                                                         Transcript 2
                 1q1a A   5 TASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITT----PQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTA 293
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204    |  214       224       234       244       254       264       274       284         
                                                                                                                                                                                                                                      209  214                                                                               


Chain B from PDB  Type:PROTEIN  Length:10
 aligned with H4_YEAST | P02309 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:10
                                    22
             H4_YEAST    13 KGGAKRHRKI  22
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .....ee... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                PROSITE (2) --HISTO--- PROSITE (2)
               Transcript 1 Exon 1.1   Transcript 1
                 1q1a B 349 KGGAkRHRKI 358
                                |  358
                                |     
                              353-ALY
   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) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q1A)

(-) Gene Ontology  (30, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HST2_YEAST | P53686)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0070403    NAD+ binding    Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0017136    NAD-dependent histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from a histone.
    GO:0046970    NAD-dependent histone deacetylase activity (H4-K16 specific)    Catalysis of the reaction: histone H4 N6-acetyl-L-lysine (position 16) + H2O = histone H4 L-lysine (position 16) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 16 of the histone H4 protein.
    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:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0001300    chronological cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs when the cell is in a non-dividing, or quiescent, state.
    GO:0070933    histone H4 deacetylation    The modification of histone H4 by the removal of one or more acetyl groups.
    GO:0031939    negative regulation of chromatin silencing at telomere    Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing at telomeres.
    GO:0045950    negative regulation of mitotic recombination    Any process that inhibits or decreases the rate of DNA recombination during mitosis.
    GO:0006476    protein deacetylation    The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular 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   (H4_YEAST | P02309)
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:0034729    histone H3-K79 methylation    The modification of histone H3 by addition of a methyl group to lysine at position 79 of the histone.
    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: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.
    GO:0061587    transfer RNA gene-mediated silencing    The chromatin silencing that results in the inhibition of RNA polymerase II-transcribed genes located in the vicinity of tRNA genes.
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: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
        H4_YEAST | P02309: 1e6i 1id3 1szc 1szd 2dvq 2dvr 2e3k 2fsb 2h2h 2l5a 2qqf 2qqg 3to6 4jjn 4kud 4psx 4twi 4twj
        HST2_YEAST | P53686: 1q14 1q17 1szc 1szd 2od2 2od7 2od9 2qqf 2qqg

(-) Related Entries Specified in the PDB File

1q14 SAME APO PROTEIN
1q17 SAME PROTEIN COMPLEXED WITH ADP-RIBOSE