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(-) Description

Title :  SIR2 HOMOLOGUES (D102G/F159A/R170A) MUTANT-2'-O-ACETYL ADP RIBOSE COMPLEX
 
Authors :  J. Chang, Y. Cho
Date :  24 Jun 02  (Deposition) - 08 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Ligand Complex, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Chang, H. C. Kim, K. Y. Hwang, J. W. Lee, S. P. Jackson, S. D. Bell, Y. Cho
Structural Basis For The Nad-Dependent Deacetylase Mechanism Of Sir2
J. Biol. Chem. V. 277 34489 2003
PubMed-ID: 12091395  |  Reference-DOI: 10.1074/JBC.M205460200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SILENT INFORMATION REGULATOR 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: SG13009 [PREP 4]
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1OAD2Ligand/Ion2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:124 , CYS A:127 , CYS A:145 , CYS A:148BINDING SITE FOR RESIDUE ZN A 999
2AC2SOFTWARECYS B:124 , CYS B:127 , CYS B:145 , CYS B:148 , SER B:150BINDING SITE FOR RESIDUE ZN B 999
3AC3SOFTWAREGLY A:20 , ALA A:21 , GLY A:22 , GLU A:26 , THR A:31 , PHE A:32 , ARG A:33 , GLN A:98 , HIS A:116 , VAL A:157 , GLY A:185 , THR A:186 , SER A:187 , VAL A:190 , ASN A:211 , PRO A:212 , LYS A:228 , ALA A:229 , LYS A:247 , HOH B:2002 , HOH B:2087BINDING SITE FOR RESIDUE OAD B 1001
4AC4SOFTWAREGLY B:20 , ALA B:21 , GLY B:22 , GLU B:26 , THR B:31 , PHE B:32 , ARG B:33 , GLN B:98 , HIS B:116 , VAL B:157 , GLY B:185 , THR B:186 , SER B:187 , VAL B:190 , ASN B:211 , PRO B:212 , ASP B:213 , LYS B:228 , ALA B:229 , LYS B:247 , HOH B:2003 , HOH B:2027 , HOH B:2076BINDING SITE FOR RESIDUE OAD B 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M2N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:191 -Pro A:192
2Gln B:191 -Pro B:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M2N)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SIRTUINPS50305 Sirtuin catalytic domain profile.NPD1_ARCFU3-245
 		  2A:3-245
B:3-245

(-) Exons   (0, 0)

(no "Exon" information available for 1M2N)

(-) 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:249
 aligned with NPD1_ARCFU | O28597 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:249
                                                                                                                                                                                                                                                                              245    
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    |    
           NPD1_ARCFU     1 MDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDDLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWFGEMLPPDVLDRAMREVERADVIIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALS----   -
               SCOP domains d1m2na_ A: AF1676, Sir2 homolog (Sir2-AF1?)                                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..eeeee.hhhhhhhh.....hhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eee...................eeeee.........hhhhhhhhhhh...eeeee.......hhhhhhhhhhh...eeeee......hhhhh.eee..hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SIRTUIN  PDB: A:3-245 UniProt: 3-245                                                                                                                                                                                                               ---- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m2n A   1 MDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDGLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWAGEMLPPDVLDAAMREVERADVIIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALSLKLN 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with NPD1_ARCFU | O28597 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:249
                                                                                                                                                                                                                                                                              245    
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    |    
           NPD1_ARCFU     1 MDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDDLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWFGEMLPPDVLDRAMREVERADVIIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALS----   -
               SCOP domains d1m2nb_ B: AF1676, Sir2 homolog (Sir2-AF1?)                                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------SIR2-1m2nB01 B:20-192                                                                                                                                                        --------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------SIR2-1m2nB02 B:20-192                                                                                                                                                        --------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhh...eeeee.hhhhhhhh.....hhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eeeeee......hhhhh...eee..eeeeeeee.....eee...................eeeee.......hhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhh..eeeee......hhhhh.eee..hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SIRTUIN  PDB: B:3-245 UniProt: 3-245                                                                                                                                                                                                               ---- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m2n B   1 MDEKLLKTIAESKYLVALTGAGVSAESGIPTFRGKDGLWNRYRPEELANPQAFAKDPEKVWKWYAWRMEKVFNAQPNKAHQAFAELERLGVLKCLITQNVDGLHERAGSRNVIHLHGSLRVVRCTSCNNSFEVESAPKIPPLPKCDKCGSLLRPGVVWAGEMLPPDVLDAAMREVERADVIIVAGTSAVVQPAASLPLIVKQRGGAIIEINPDETPLTPIADYSLRGKAGEVMDELVRHVRKALSLKLN 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1M2N)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: FAD_DHS (82)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NPD1_ARCFU | O28597)
molecular function
    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:0036054    protein-malonyllysine demalonylase activity    Catalysis of the reaction: protein-malonyllysine + H2O => protein-lysine + malonate. This reaction is the removal of a malonyl group (CO-CH2-CO) from a malonylated lysine residue of a protein or peptide.
    GO:0036055    protein-succinyllysine desuccinylase activity    Catalysis of the reaction: protein-succinyllysine + H2O => protein-lysine + succinate. This reaction is the removal of a succinyl group (CO-CH2-CH2-CO) from a succinylated lysine residue of a protein or peptide.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0036047    peptidyl-lysine demalonylation    The process of removing a malonyl group (CO-CH2-CO) from an malonylated lysine residue in a peptide or protein.
    GO:0036049    peptidyl-lysine desuccinylation    The removal of a succinyl group (CO-CH2-CH2-CO) from a succinylated lysine residue in a peptide or protein.
    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:0036048    protein desuccinylation    The removal of a succinyl group (CO-CH2-CH2-CO) from a residue in a peptide or protein.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NPD1_ARCFU | O28597: 1ici 1m2g 1m2h 1m2j 1m2k 4twi

(-) Related Entries Specified in the PDB File

1m2g 1M2G CONTAINS THE SAME PROTEIN, WILD TYPE
1m2h 1M2H CONTAINS THE SAME PROTEIN S24A MUTANT
1m2j 1M2J CONTAINS THE SAME PROTEIN H80N MUTANT
1m2k 1M2K CONTAINS THE SAME PROTEIN F159A MUTANT