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(-) Description

Title :  CRYSTAL STRUCTURE OF SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND NAD
 
Authors :  M. Gertz, N. T. T. Nguyen, M. Weyand, C. Steegborn
Date :  24 Jun 13  (Deposition) - 17 Jul 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Gertz, F. Fischer, G. T. T. Nguyen, M. Lakshminarasimhan, M. Schutkowski, M. Weyand, C. Steegborn
Ex-527 Inhibits Sirtuins By Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism
Proc. Natl. Acad. Sci. Usa V. 110 E2772 2013
PubMed-ID: 23840057  |  Reference-DOI: 10.1073/PNAS.1303628110

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
    Chains: A
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVFT3S
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 116-399
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSIRT3, REGULATORY PROTEIN SIR2 HOMOLOG 3, SIR2-LIKE PROTEIN 3, SIRT3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 9)

Asymmetric/Biological Unit (8, 9)
No.NameCountTypeFull Name
1APR1Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
2CL1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4NA1Ligand/IonSODIUM ION
5NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
6NO31Ligand/IonNITRATE ION
7OCZ1Ligand/Ion(1S)-6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-1- CARBOXAMIDE
8ZN1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:145 , ALA A:146 , GLY A:147 , THR A:150 , ASP A:156 , PHE A:157 , ARG A:158 , TYR A:165 , PHE A:180 , HIS A:248 , VAL A:292 , PHE A:294 , GLY A:319 , THR A:320 , SER A:321 , VAL A:324 , ASN A:344 , ARG A:345 , GLY A:364 , ASP A:365 , VAL A:366 , GOL A:1397 , HOH A:2010 , HOH A:2016 , HOH A:2052 , HOH A:2102 , HOH A:2123BINDING SITE FOR RESIDUE NAD A1392
2AC2SOFTWAREGLY A:145 , ALA A:146 , GLY A:147 , THR A:150 , ASP A:156 , PHE A:157 , ARG A:158 , HIS A:248 , PHE A:294 , GLY A:319 , THR A:320 , SER A:321 , VAL A:324 , ASN A:344 , ARG A:345 , GLY A:364 , ASP A:365 , VAL A:366 , HOH A:2010 , HOH A:2016 , HOH A:2051 , HOH A:2102BINDING SITE FOR RESIDUE APR A1393
3AC3SOFTWAREPRO A:155 , PHE A:157 , PHE A:180 , GLN A:228 , ASN A:229 , ILE A:230 , ASP A:231 , ILE A:291 , VAL A:292 , HOH A:2011BINDING SITE FOR RESIDUE OCZ A1394
4AC4SOFTWARECYS A:256 , CYS A:259 , CYS A:280 , CYS A:283BINDING SITE FOR RESIDUE ZN A1395
5AC5SOFTWAREHIS A:248 , LEU A:298 , VAL A:324 , GLU A:325 , PRO A:326 , PHE A:327 , GOL A:1397BINDING SITE FOR RESIDUE NO3 A1396
6AC6SOFTWAREHIS A:248 , VAL A:292 , PHE A:294 , GLY A:295 , GLU A:296 , LEU A:298 , NAD A:1392 , NO3 A:1396 , GOL A:1398 , HOH A:2093 , HOH A:2123 , HOH A:2124BINDING SITE FOR RESIDUE GOL A1397
7AC7SOFTWAREASN A:207 , GLY A:295 , PRO A:326 , GOL A:1397 , HOH A:2014 , HOH A:2044 , HOH A:2093BINDING SITE FOR RESIDUE GOL A1398
8AC8SOFTWAREGLU A:325 , SER A:329 , PRO A:350BINDING SITE FOR RESIDUE NA A1399
9AC9SOFTWAREGLY A:349 , PRO A:350 , TRP A:353BINDING SITE FOR RESIDUE CL A1400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BV3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:325 -Pro A:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051978V208ISIR3_HUMANPolymorphism11246020AV208I
2UniProtVAR_051979G369SSIR3_HUMANPolymorphism3020901AG369S
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIRTUINPS50305 Sirtuin catalytic domain profile.SIR3_HUMAN126-382  1A:126-382

(-) Exons   (0, 0)

(no "Exon" information available for 4BV3)

(-) 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:270
 aligned with SIR3_HUMAN | Q9NTG7 from UniProtKB/Swiss-Prot  Length:399

    Alignment length:270
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391
           SIR3_HUMAN   122 KLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRET 391
               SCOP domains d4bv3a_ A: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....eeeee.hhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....eee...hhhhhhh............eeeee.......hhhhhhhhhhhhhh.eeeee.......hhhhhhhh......eeeee....hhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------- SAPs(SNPs)
                    PROSITE ----SIRTUIN  PDB: A:126-382 UniProt: 126-382                                                                                                                                                                                                                         --------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bv3 A 122 KLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRET 391
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391
   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  (0, 0)

(no "CATH Domain" information available for 4BV3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BV3)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SIR3_HUMAN | Q9NTG7)
molecular function
    GO:0003950    NAD+ ADP-ribosyltransferase activity    Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
    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: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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009060    aerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
    GO:0070932    histone H3 deacetylation    The modification of histone H3 by the removal of one or more acetyl groups.
    GO:0007005    mitochondrion organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
    GO:2000757    negative regulation of peptidyl-lysine acetylation    Any process that stops, prevents or reduces the frequency, rate or extent of peptidyl-lysine acetylation.
    GO:0034983    peptidyl-lysine deacetylation    The removal of an acetyl group from an acetylated lysine residue in a peptide or protein.
    GO:0006471    protein ADP-ribosylation    The transfer, from NAD, of ADP-ribose to protein amino acids.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SIR3_HUMAN | Q9NTG7: 3glr 3gls 3glt 3glu 4bn4 4bn5 4bvb 4bve 4bvf 4bvg 4bvh 4c78 4c7b 4fvt 4fz3 4hd8 4jsr 4jt8 4jt9 4o8z 4v1c 5bwn 5bwo 5d7n

(-) Related Entries Specified in the PDB File

4buz SIR2 COMPLEX STRUCTURE MIXTURE OF EX-527 INHIBITOR AND REACTION PRODUCTS OR OF REACTION SUBSTRATES P53 PEPTIDE AND NAD
4bv2 CRYSTAL STRUCTURE OF SIR2 IN COMPLEX WITH EX-527 AND 2'-O-ACETYL-ADP-RIBOSE
4bvb CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND ADP-RIBOSE
4bve CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2- PEPTIDE
4bvf CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THIOALKYLIMIDATE FORMED FROM THIO-ACETYL-LYSINE ACS2- PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX- 527
4bvg CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE ALKYLIMIDATE FORMED FROM ACETYL-LYSINE ACS2- PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX- 527
4bvh CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND 2'-O-ACETYL-ADP-RIBOSE