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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SIRT2 IN COMPLEX WITH ADPR AND EX-243
 
Authors :  T. Rumpf, S. Gerhardt, O. Einsle, M. Jung
Date :  14 Aug 15  (Deposition) - 02 Dec 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Human Sirtuin 2, Inhibitor Complex, Deacylase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Rumpf, S. Gerhardt, O. Einsle, M. Jung
Seeding For Sirtuins: Microseed Matrix Seeding To Obtain Crystals Of Human Sirt3 And Sirt2 Suitable For Soaking.
Acta Crystallogr. , Sect. F V. 71 1498 2015
PubMed-ID: 26625292  |  Reference-DOI: 10.1107/S2053230X15019986

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
    Chains: A, B
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 56-356
    Gene: SIRT2, SIR2L, SIR2L2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: GLY1 ORIGINATES FROM TEV CLEAVAGE SITE HIS2/MET3 ORIGINATE FROM NDEI RESTRICTION SITE OF THE VECTOR
    Synonym: SIRTUIN 2, REGULATORY PROTEIN SIR2 HOMOLOG 2,SIR2-LIKE PROTEIN 2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1AR62Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGENPHOSPHATE
2OCZ4Ligand/Ion(1S)-6-CHLORO-2,3,4,9-TETRAHYDRO-1H-CARBAZOLE-1-CARBOXAMIDE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4ZN2Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:195 , CYS A:200 , CYS A:221 , CYS A:224binding site for residue ZN A 401
2AC2SOFTWAREGLY A:84 , ALA A:85 , GLY A:86 , THR A:89 , ASP A:95 , PHE A:96 , ARG A:97 , TYR A:104 , GLN A:167 , HIS A:187 , PHE A:235 , GLY A:261 , THR A:262 , SER A:263 , VAL A:266 , ASN A:286 , LYS A:287 , GLU A:288 , GLY A:322 , GLU A:323 , CYS A:324 , OCZ A:404 , HOH A:537 , HOH A:543 , HOH A:545 , HOH A:566binding site for residue AR6 A 402
3AC3SOFTWAREPHE A:131 , LEU A:138 , TYR A:139 , PRO A:140 , GLY A:141 , PHE A:190 , OCZ A:404 , HOH A:551binding site for residue OCZ A 403
4AC4SOFTWAREPRO A:94 , PHE A:96 , PHE A:119 , GLN A:167 , ASN A:168 , ILE A:169 , ASP A:170 , ILE A:232 , AR6 A:402 , OCZ A:403 , HOH A:558binding site for residue OCZ A 404
5AC5SOFTWARECYS B:195 , CYS B:200 , CYS B:221 , CYS B:224binding site for residue ZN B 401
6AC6SOFTWAREGLY B:84 , ALA B:85 , GLY B:86 , THR B:89 , ASP B:95 , PHE B:96 , ARG B:97 , TYR B:104 , GLN B:167 , HIS B:187 , PHE B:235 , GLY B:261 , THR B:262 , SER B:263 , VAL B:266 , ASN B:286 , LYS B:287 , GLU B:288 , GLY B:322 , GLU B:323 , CYS B:324 , OCZ B:404 , HOH B:504 , HOH B:507 , HOH B:521binding site for residue AR6 B 402
7AC7SOFTWAREPHE B:131 , ALA B:135 , LEU B:138 , TYR B:139 , GLY B:141 , PHE B:190 , OCZ B:404binding site for residue OCZ B 403
8AC8SOFTWAREPHE B:96 , PHE B:119 , GLN B:167 , ASN B:168 , ILE B:169 , ASP B:170 , ILE B:232 , AR6 B:402 , OCZ B:403 , HOH B:569binding site for residue OCZ B 404
9AC9SOFTWARETHR B:89 , ILE B:93 , PRO B:94 , ASP B:95 , SER B:98 , LYS B:287 , HOH B:503 , HOH B:529binding site for residue PEG B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D7P)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:267 -Pro A:268
2Gln B:267 -Pro B:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D7P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D7P)

(-) Exons   (0, 0)

(no "Exon" information available for 5D7P)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh.....eeeee.hhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.......eeehhhhhhhhhh............eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..............................eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7p A  54 HMERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353  


Chain B from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh......eeeee.hhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.......eeehhhhhhhhh.............eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..............................eeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d7p B  56 ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDA 354
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345
   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  (0, 0)

(no "SCOP Domain" information available for 5D7P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D7P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D7P)

(-) Gene Ontology  (117, 117)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:267 - Pro A:268   [ RasMol ]  
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 Related Entries

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UniProtKB/Swiss-Prot
        SIR2_HUMAN | Q8IXJ6: 1j8f 3zgo 3zgv 4l3o 4r8m 4rmg 4rmh 4rmi 4rmj 4x3o 4x3p 4y6l 4y6o 4y6q 5d7o 5d7q 5dy4 5dy5 5fyq 5g4c 5mar 5mat

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