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(-) Description

Title :  STRUCTURAL BASIS FOR NICOTINAMIDE INHIBITION AND BASE EXCHANGE IN SIR2 ENZYMES
 
Authors :  R. Marmorstein, B. D. Sanders
Date :  21 Dec 06  (Deposition) - 27 Feb 07  (Release) - 11 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Zn Binding Protein, Rossmann Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. D. Sanders, K. Zhao, J. T. Slama, R. Marmorstein
Structural Basis For Nicotinamide Inhibition And Base Exchange In Sir2 Enzymes.
Mol. Cell V. 25 463 2007
PubMed-ID: 17289592  |  Reference-DOI: 10.1016/J.MOLCEL.2006.12.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NAD-DEPENDENT DEACETYLASE HST2
    Chains: A
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET
    Expression System Strain: DE3 BL-21 GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HST2 CATALYTIC CORE DOMAIN, RESIDUES 1-294
    Gene: HST2
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: HOMOLOGOUS TO SIR2 PROTEIN 2
 
Molecule 2 - H4 PEPTIDE
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1A1R1Ligand/Ion5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
2ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
3NCA1Ligand/IonNICOTINAMIDE
4ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1A1R1Ligand/Ion5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
2ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
3NCA1Ligand/IonNICOTINAMIDE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1A1R2Ligand/Ion5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
2ALY2Mod. Amino AcidN(6)-ACETYLLYSINE
3NCA2Ligand/IonNICOTINAMIDE
4ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
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 , PHE A:44 , ARG A:45 , GLU A:64 , GLN A:115 , 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 , NCA A:3721 , HOH A:3732 , HOH A:3744 , HOH A:3756 , HOH A:3816 , ALY B:16 , HIS B:18BINDING SITE FOR RESIDUE A1R A 1001
3AC3SOFTWAREPHE A:44 , PHE A:67 , PHE A:184 , A1R A:1001 , HOH A:3748 , HOH A:3774 , ALY B:16BINDING SITE FOR RESIDUE NCA A 3721

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OD9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 2OD9)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIRTUINPS50305 Sirtuin catalytic domain profile.HST2_YEAST13-286  1A:13-286
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIRTUINPS50305 Sirtuin catalytic domain profile.HST2_YEAST13-286  1A:13-286
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIRTUINPS50305 Sirtuin catalytic domain profile.HST2_YEAST13-286  2A:13-286

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL015C1YPL015C.1XVI:526880-5258071074HST2_YEAST1-3573571A:1-293 (gaps)293

(-) Sequences/Alignments

Asymmetric 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:291
 aligned with HST2_YEAST | P53686 from UniProtKB/Swiss-Prot  Length:357

    Alignment length:296
                               1                                                                                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287      
           HST2_YEAST     - ---MSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITTSGKHPQQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTA 293
               SCOP domains d2od9a_ A: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2od9A01 A:-2-37,A:94-134,A:190-293      2od9A02 A:38-93,A:135-189 SIR2/SIRT2 'Small Domain'     2od9A01 A:-2-37,A:94-134,A:190-293       2od9A02 A:38-93,A:135-189 SIR2/SIRT2 'Small Domain'    2od9A01 A:-2-37,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.....eehhhhhhhhh.................eeeee.......hhhhhhhhhhhhhhhhhhh..-----...eeeee.......hhhhhhhhh.....eeee.....hhhhhh.....eee..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------SIRTUIN  PDB: A:13-286 UniProt: 13-286                                                                                                                                                                                                                                            ------- PROSITE
               Transcript 1 ---Exon 1.1  PDB: A:1-293 (gaps) UniProt: 1-357 [INCOMPLETE]                                                                                                                                                                                                                                             Transcript 1
                 2od9 A  -2 MASMSVSTASTEMSVRKIAAHMKSNPNAKVIFMVGAGISTSCGIPDFRSPGTGLYHNLARLKLPYPEAVFDVDFFQSDPLPFYTLAKELYPGNFRPSKFHYLLKLFQDKDVLKRVYTQNIDTLERQAGVKDDLIIEAHGSFAHCHCIGCGKVYPPQVFKSKLAEHPIKDFVKCDVCGELVKPAIVFFGEDLPDSFSETWLNDSEWLREKITT-----QQPLVIVVGTSLAVYPFASLPEEIPRKVKRVLCNLETVGDFKANKRPTDLIVHQYSDEFAEQLVEELGWQEDFEKILTA 293
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207 |     217       227       237       247       257       267       277       287      
                                                                                                                                                                                                                                             209   215                                                                              


Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 2od9 B  12 KGGAkRH  18
                                |  
                               16-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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OD9)

(-) Gene Ontology  (18, 18)

Asymmetric 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HST2_YEAST | P53686: 1q14 1q17 1q1a 1szc 1szd 2od2 2od7 2qqf 2qqg

(-) Related Entries Specified in the PDB File

1szc YHST2 BOUND TO CARBA-NAD+ AND AN ACETYLATED H4 PEPTIDE
1szd WILDTYPE YHST2 BOUND TO ADP-RIBOSE AND AN ACETYLATED H4 PEPTIDE
2od2 STRUCTURAL BASIS FOR NICOTINAMIDE INHIBITION AND BASE EXCHANGE IN SIR2 ENZYMES
2od7 CRYSTAL STRUCTURE OF YHST2 BOUND TO THE INTERMEDIATE ANALOGUE ADP-HPD, AND AND ACEYLATED H4 PEPTIDE