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(-) Description

Title :  HUMAN SIRT2 IN COMPLEX WITH MYRISTOYLATED PEPTIDE (H3K9MYR)
 
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 52-356
    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 THR-ALA-ARG-MYK-SER-THR-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 , GLU A:137 , PHE A:143 , HIS A:187 , PHE A:190 , VAL A:233 , PHE A:235 , GLY A:236 , GLU A:237 , SER A:238 , GLN A:267 , THR C:6 , ALA C:7 , SER C:10 , HOH C:103 , HOH C:105 , HOH C:110binding site for Di-peptide ARG C 8 and MYK C 9
4AC4SOFTWAREPHE A:96 , PHE A:119 , PHE A:143 , HIS A:187 , PHE A:190 , VAL A:233 , PHE A:235 , GLY A:236 , GLU A:237 , VAL A:266 , GLN A:267 , ARG C:8 , THR C:11 , GLY C:12 , HOH C:103 , HOH C:105binding site for Di-peptide MYK C 9 and SER C 10
5AC5SOFTWAREPHE B:96 , PHE B:143 , HIS B:187 , VAL B:233 , PHE B:235 , GLY B:236 , GLU B:237 , GLN B:267 , THR D:6 , ALA D:7 , SER D:10 , HOH D:103binding site for Di-peptide ARG D 8 and MYK D 9
6AC6SOFTWAREPHE B:96 , PHE B:143 , HIS B:187 , VAL B:233 , PHE B:235 , GLY B:236 , GLU B:237 , VAL B:266 , GLN B:267 , ARG D:8 , THR D:11 , GLY D:12 , HOH D:103binding site for Di-peptide MYK D 9 and SER D 10

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y6L)

(-) 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 4Y6L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y6L)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y6L)

(-) 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.....hhhhhh..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
                 4y6l A  56 ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    65        75        85        95 ||    113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283      |308       318       328       338       348       
                                                                    97|                                                                                                                                                                                     290|                                                 
                                                                    106                                                                                                                                                                                      306                                                 


Chain B from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               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.......hhhhhhhhh.....eeeee................eeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6l B  55 KERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    64        74        84        94  ||   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288  ||   312       322       332       342       352   
                                                                     97|                                                                                                                                                                                291|                                                 
                                                                     112                                                                                                                                                                                 306                                                 


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
                 4y6l C   6 TARxSTG  12
                               |   
                               9-MYK


Chain D 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
                 4y6l D   6 TARxSTG  12
                               |   
                               9-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 4Y6L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y6L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y6L)

(-) Gene Ontology  (140, 145)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H31_HUMAN | P68431: 1cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
        SIR2_HUMAN | Q8IXJ6: 1j8f 3zgo 3zgv 4l3o 4r8m 4rmg 4rmh 4rmi 4rmj 4x3o 4x3p 4y6o 4y6q 5d7o 5d7p 5d7q 5dy4 5dy5 5fyq 5g4c 5mar 5mat

(-) Related Entries Specified in the PDB File

4y6o 4y6q