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(-) Description

Title :  SIR2-S-ALKYLAMIDATE COMPLEX CRYSTAL STRUCTURE
 
Authors :  W. F. Hawse, K. G. Hoff, D. Fatkins, A. Daines, O. V. Zubkova, V. L. Schramm, W. Zheng, C. Wolberger
Date :  22 May 08  (Deposition) - 30 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Rossmann Fold, Nad Dependent Deacetylase, Cytoplasm, Hydrolase, Metal-Binding, Nad, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. F. Hawse, K. G. Hoff, D. G. Fatkins, A. Daines, O. V. Zubkova, V. L. Schramm, W. Zheng, C. Wolberger
Structural Insights Into Intermediate Steps In The Sir2 Deacetylation Reaction.
Structure V. 16 1368 2008
PubMed-ID: 18786399  |  Reference-DOI: 10.1016/J.STR.2008.05.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NAD-DEPENDENT DEACETYLASE
    Chains: A
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL-21(DE3)
    Expression System Vector Type: PLASMID
    Gene: NPDA, TM_0490
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: REGULATORY PROTEIN SIR2 HOMOLOG
 
Molecule 2 - S-ALKYLAMIDATE INTERMEDIATE
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FZN1Mod. Amino Acid(2S)-2-AMINO-6-{[(1Z)-1-{[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]SULFANYL}ETHYLIDENE]AMINO}HEXANOIC ACID
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:21 , ALA A:22 , GLY A:23 , THR A:26 , PRO A:27 , ASP A:32 , PHE A:33 , GLN A:98 , HIS A:116 , ILE A:159 , PHE A:161 , PHE A:162 , GLY A:163 , GLU A:164 , LEU A:166 , GLY A:188 , SER A:189 , SER A:190 , TYR A:194 , ASN A:214 , LEU A:215 , MET A:230 , ASP A:231 , LYS C:10 , LEU C:12BINDING SITE FOR RESIDUE FZN C 11
2AC2SOFTWARECYS A:124 , CYS A:127 , CYS A:148 , CYS A:151BINDING SITE FOR RESIDUE ZN A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D81)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:194 -Pro A:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D81)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIRTUINPS50305 Sirtuin catalytic domain profile.NPD_THEMA4-246  1A:4-246

(-) Exons   (0, 0)

(no "Exon" information available for 3D81)

(-) 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:235
 aligned with NPD_THEMA | Q9WYW0 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
            NPD_THEMA     1 MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDFRGPNGIYKKYSQNVFDIDFFYSHPEEFYRFAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKKVIELHGNVEEYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVFFGENLPQDALREAIGLSSRASLMIVLGSSLVVYPAAELPLITVRSGGKLVIVNLGETPFDDIATLKYNMDVVEFARRVMEEGGIS 246
               SCOP domains d3d81a_ A: NAD-dependent deacetyl           ase NpdA                                                                                                                                                                                                   SCOP domains
               CATH domains 3d81A01 TPP-binding domain   3d81           A02 A:30-75,A:117-165          3d81A01 A:1-29,A:76-116,A:166-246        3d81A02 A:30-75,A:117-165                        3d81A01 A:1-29,A:76-116,A:166-246 TPP-binding domain                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..eeeee.hhhhhhhh....-----------....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeee....hhhhhh....eee..eeeeeeee.....eeehhhhhhhhhhh...........eeeee.......hhhhhhhhhhhhhhh.eeeee.....eehhhhhhhhhhhh..eeeee............eee..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---SIRTUIN  PDB: A:4-246 UniProt: 4-246                                                                                                                                                                                                                PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d81 A   1 MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDF-----------QNVFDIDFFYSHPEEFYRFAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKKVIELHGNVEEYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVFFGENLPQDALREAIGLSSRASLMIVLGSSLVVYPAAELPLITVRSGGKLVIVNLGETPFDDIATLKYNMDVVEFARRVMEEGGIS 246
                                    10        20        30  |      -    |   50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
                                                           33          45                                                                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author .....ee. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 3d81 C   7 SRHKkLMF  14
                                |   
                               11-FZN
   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 3D81)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NPD_THEMA | Q9WYW0)
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:0034979    NAD-dependent protein deacetylase activity    Catalysis of the removal of one or more acetyl groups from a protein, requiring NAD.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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.

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  3d81
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  3.5.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        NPD_THEMA | Q9WYW0: 1yc5 2h2d 2h2f 2h2g 2h2h 2h2i 2h4f 2h4h 2h4j 2h59 3d4b 3jr3 3pdh 4buz 4bv2

(-) Related Entries Specified in the PDB File

3d4b