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(-) Description

Title :  HUMAN SIRT2 CATALYSE SHORT CHAIN FATTY ACYL LYSINE
 
Authors :  Y. Wang
Date :  09 May 16  (Deposition) - 03 May 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,E,F
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,E  (1x)
Keywords :  Hydrolase, Sirtuin Class I, Hdacs, Nad Dependent, Adpr, Acyl (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jin, B. He, X. Zhang, H. Lin, Y. Wang
Sirt2 Reverses 4-Oxononanoyl Lysine Modification On Histones.
J. Am. Chem. Soc. V. 138 12304 2016
PubMed-ID: 27610633  |  Reference-DOI: 10.1021/JACS.6B04977

(-) 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 Plasmid: PET28-SUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 34-356
    Gene: SIRT2, SIR2L, SIR2L2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: REGULATORY PROTEIN SIR2 HOMOLOG 2, SIR2-LIKE PROTEIN 2
 
Molecule 2 - SIRT2
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-SUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABEF
Biological Unit 1 (1x): A  F
Biological Unit 2 (1x):  BE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
16G42Mod. Amino Acid4-OXONONANOYL)LYSINE
2CNA2Ligand/IonCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
16G41Mod. Amino Acid4-OXONONANOYL)LYSINE
2CNA1Ligand/IonCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
16G41Mod. Amino Acid4-OXONONANOYL)LYSINE
2CNA1Ligand/IonCARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:195 , CYS A:200 , CYS A:221 , CYS A:224BINDING SITE FOR RESIDUE ZN A 1356
2AC2SOFTWAREGLY B:84 , ALA B:85 , GLY B:86 , THR B:89 , PRO B:94 , ASP B:95 , PHE B:96 , ARG B:97 , GLN B:167 , ASN B:168 , ILE B:169 , ASP B:170 , HIS B:187 , 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 , HOH B:2019 , HOH B:2027 , HOH B:2071 , HOH B:2164 , 6G4 E:4BINDING SITE FOR RESIDUE CNA B 1356
3AC3SOFTWAREGLY A:84 , ALA A:85 , GLY A:86 , THR A:89 , PRO A:94 , ASP A:95 , PHE A:96 , ARG A:97 , GLN A:167 , ASN A:168 , ILE A:169 , ASP A:170 , HIS A:187 , GLY A:261 , THR A:262 , SER A:263 , ASN A:286 , LYS A:287 , GLU A:288 , GLY A:322 , GLU A:323 , CYS A:324 , HOH A:2022 , HOH A:2029 , HOH A:2063 , 6G4 F:4BINDING SITE FOR RESIDUE CNA A 1357

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G4C)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:267 -Pro A:268
2Pro B:140 -Gly B:141
3Gln B:267 -Pro B:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G4C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G4C)

(-) Exons   (0, 0)

(no "Exon" information available for 5G4C)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               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.......eeehhhhhhhhhh............eeeee.......hhhhhhhhhhhh....eeeee........hhhhhhh......eeeee..................eeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g4c A  54 QKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    63        73        83        93     ||104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       306       316       326       336       346         
                                                                        99|                                                                                                                                                                                            292|                                                  
                                                                        101                                                                                                                                                                                             305                                                  


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh.....eeeee.hhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh......eee..eeeeeeee.......eehhhhhhhhhhh............eeeee.......hhhhhhhhhhhh....eeeee........hhhhhhhh.....eeeee...................eeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g4c B  54 QKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    63        73        83        93       103       113       123       133    || 144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       305       315       325       335       345       355
                                                                                                              138|                                                                                                                                                      293|                                                  
                                                                                                               140                                                                                                                                                       305                                                  


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               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
                 5g4c E   1 RAAkT   5
                               | 
                               4-6G4


Chain F from PDB  Type:PROTEIN  Length:5
                                     
               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
                 5g4c F   1 RAAkT   5
                               | 
                               | 
                               4-6G4
   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 5G4C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G4C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G4C)

(-) Gene Ontology  (117, 117)

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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 5d7p 5d7q 5dy4 5dy5 5fyq 5mar 5mat

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