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(-) Description

Title :  HUMAN SIRT2 IN COMPLEX WITH MYRISTOYLATED PEPTIDE (TNF-ALPHAK20MYR)
 
Authors :  N. Kudo, A. Ito, M. Yoshida
Date :  13 Feb 15  (Deposition) - 06 Jan 16  (Release) - 06 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Sirtuin, Sirt, Nad-Dependent Deacetylase, Myristoylated Lysine, Hydrolase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Feldman, K. E. Dittenhafer-Reed, N. Kudo, J. N. Thelen, A. Ito, M. Yoshida, J. M. Denu
Kinetic And Structural Basis For Acyl-Group Selectivity And Nad(+) Dependence In Sirtuin-Catalyzed Deacylation.
Biochemistry V. 54 3037 2015
PubMed-ID: 25897714  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00150

(-) 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: PGEX-4T3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 52-291, 304-356
    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 - PEPTIDE LEU-PRO-LYS-MYK-THR-GLY-GLY
    Chains: C, D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1MYK2Mod. Amino AcidN~6~-TETRADECANOYL-L-LYSINE
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MYK1Mod. Amino AcidN~6~-TETRADECANOYL-L-LYSINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MYK1Mod. Amino AcidN~6~-TETRADECANOYL-L-LYSINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:195 , CYS A:200 , CYS A:221 , CYS A:224binding site for residue ZN A 501
2AC2SOFTWARECYS B:195 , CYS B:200 , CYS B:221 , CYS B:224binding site for residue ZN B 501
3AC3SOFTWAREPHE A:96 , PHE A:119 , HIS A:187 , VAL A:233 , PHE A:235 , GLY A:236 , GLU A:237 , SER A:238 , LEU A:239 , GLN A:267 , PRO A:268 , LEU C:7 , PRO C:8 , THR C:11 , HOH C:101 , HOH C:102binding site for Di-peptide LYS C 9 and MYK C 10
4AC4SOFTWAREPHE A:96 , PHE A:119 , HIS A:187 , VAL A:233 , PHE A:235 , GLY A:236 , GLU A:237 , LEU A:239 , VAL A:266 , GLN A:267 , LYS C:9 , GLY C:12 , HOH C:101 , HOH C:102 , HOH C:104binding site for Di-peptide MYK C 10 and THR C 11
5AC5SOFTWAREPHE B:96 , PHE B:143 , HIS B:187 , PHE B:190 , VAL B:233 , PHE B:235 , GLY B:236 , GLU B:237 , SER B:238 , LEU B:239 , GLN B:267 , PRO B:268 , LEU D:3 , PRO D:4 , THR D:7 , HOH D:101 , HOH D:102binding site for Di-peptide LYS D 5 and MYK D 6
6AC6SOFTWAREPHE B:96 , PHE B:143 , HIS B:187 , PHE B:190 , VAL B:233 , PHE B:235 , GLY B:236 , GLU B:237 , LEU B:239 , VAL B:266 , GLN B:267 , LYS D:5 , GLY D:8 , HOH D:101binding site for Di-peptide MYK D 6 and THR D 7

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y6O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 4Y6O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y6O)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y6O)

(-) 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:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.....eeeee.hhhhhhhh......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.......eeehhhhhhhhhhh...........eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee................eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6o A  57 RLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    66        76        86        96||     114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    || 308       318       328       338       348       
                                                                   97|                                                                                                                                                                                    289|                                                   
                                                                   106                                                                                                                                                                                     304                                                   


Chain B from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhh.....eeeee.hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.......eeehhhhhhhhhh............eeeee.......hhhhhhhhhhhh....eeeee.....eehhhhhhhhh.....eeeee.................eeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4y6o B  55 KERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    64        74        84        94  ||   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286   ||  309       319       329       339       349      
                                                                     97|                                                                                                                                                                                 290|                                                   
                                                                     110                                                                                                                                                                                  304                                                   


Chain C from PDB  Type:PROTEIN  Length:7
                                       
               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
                 4y6o C   7 LPKxTGG  13
                               |   
                              10-MYK


Chain D from PDB  Type:PROTEIN  Length:7
                                       
               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
                 4y6o D   3 LPKxTGG   9
                               |   
                               6-MYK
   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 4Y6O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y6O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y6O)

(-) Gene Ontology  (256, 264)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SIR2_HUMAN | Q8IXJ6: 1j8f 3zgo 3zgv 4l3o 4r8m 4rmg 4rmh 4rmi 4rmj 4x3o 4x3p 4y6l 4y6q 5d7o 5d7p 5d7q 5dy4 5dy5 5fyq 5g4c 5mar 5mat
        TNFA_HUMAN | P01375: 1a8m 1tnf 2az5 2e7a 2tun 2zjc 2zpx 3alq 3it8 3l9j 3wd5 4g3y 4tsv 4twt 5mu8 5tsw

(-) Related Entries Specified in the PDB File

4y6l THE SAME PROTEIN
4y6q