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(-) Description

Title :  HUMAN SIRT2 IN COMPLEX WITH 2-O-MYRISTOYL-ADP-RIBOSE
 
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 :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sirtuin, Sirt, Nad-Dependent Deacetylase, 2-O-Myristoyl-Adp-Ribose, Acyl-Adp-Ribose, Complex, Deacylase, Intermediate, Hydrolase (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, C, D
    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

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1OMR4Ligand/Ion[(2S,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL-PHOSPHORYL]OXYMETHYL]-2,4-BIS(OXIDANYL)OXOLAN-3-YL] TETRADECANOATE
2ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:195 , CYS A:200 , CYS A:221 , CYS A:224binding site for residue ZN A 501
2AC2SOFTWAREGLY A:84 , ALA A:85 , GLY A:86 , THR A:89 , ASP A:95 , PHE A:96 , ARG A:97 , TYR A:104 , PHE A:119 , PHE A:143 , GLN A:167 , ILE A:169 , 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 , HOH A:601 , HOH A:614 , HOH A:625 , SER D:238binding site for residue OMR A 502
3AC3SOFTWARECYS B:195 , CYS B:200 , CYS B:221 , CYS B:224binding site for residue ZN B 501
4AC4SOFTWAREGLY B:84 , ALA B:85 , GLY B:86 , THR B:89 , ASP B:95 , PHE B:96 , ARG B:97 , TYR B:104 , PHE B:119 , LEU B:138 , 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 , HOH B:603 , HOH B:614 , HOH B:624 , HOH B:627binding site for residue OMR B 502
5AC5SOFTWARECYS C:195 , CYS C:200 , CYS C:221 , CYS C:224binding site for residue ZN C 501
6AC6SOFTWAREGLY C:84 , ALA C:85 , GLY C:86 , THR C:89 , ASP C:95 , PHE C:96 , ARG C:97 , TYR C:104 , PHE C:119 , GLN C:167 , HIS C:187 , PHE C:190 , PHE C:235 , GLY C:261 , THR C:262 , SER C:263 , VAL C:266 , ASN C:286 , LYS C:287 , GLU C:288 , GLY C:322 , GLU C:323 , CYS C:324 , HOH C:604 , HOH C:605 , HOH C:611 , HOH C:636binding site for residue OMR C 502
7AC7SOFTWARECYS D:195 , CYS D:200 , CYS D:221 , CYS D:224binding site for residue ZN D 501
8AC8SOFTWAREGLY D:84 , ALA D:85 , GLY D:86 , THR D:89 , ASP D:95 , ARG D:97 , PHE D:119 , LEU D:138 , HIS D:187 , PHE D:190 , GLY D:261 , THR D:262 , SER D:263 , VAL D:266 , ASN D:286 , LYS D:287 , GLU D:288 , GLY D:322 , GLU D:323 , CYS D:324binding site for residue OMR D 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y6Q)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gln A:267 -Pro A:268
2Gln B:267 -Pro B:268
3Gln C:267 -Pro C:268
4Gln D:267 -Pro D:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y6Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y6Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y6Q)

(-) 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:287
                                                                                                                                                                                                                                                                                                                               
               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........hhhhhhh......eeeee.................eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6q A  56 ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285     ||308       318       328       338       348       
                                                                                                                                                                                                                                                                     291|                                                  
                                                                                                                                                                                                                                                                      305                                                  


Chain B from PDB  Type:PROTEIN  Length:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.....eeeee.hhhhh............hhhhhhhhhh..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
                 4y6q B  56 ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ 355
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285     ||308       318       328       338       348       
                                                                                                                                                                                                                                                                     291|                                                  
                                                                                                                                                                                                                                                                      305                                                  


Chain C from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               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.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6q C  56 ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDA 354
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285     ||308       318       328       338       348      
                                                                                                                                                                                                                                                                     291|                                                 
                                                                                                                                                                                                                                                                      305                                                 


Chain D from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.....eeeee.hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.......eehhhhhhhhhhh............eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee.................eeeee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6q D  56 ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDA 354
                                    65        75        85        95     ||119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289 ||    312       322       332       342       352  
                                                                       101|                                                                                                                                                                            291|                                                 
                                                                        116                                                                                                                                                                             305
   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 4Y6Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y6Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y6Q)

(-) Gene Ontology  (117, 117)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gln A:267 - Pro A:268   [ RasMol ]  
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    Gln D:267 - Pro D:268   [ RasMol ]  
 

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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 4y6o 5d7o 5d7p 5d7q 5dy4 5dy5 5fyq 5g4c 5mar 5mat

(-) Related Entries Specified in the PDB File

4y6l THE SAME PROTEINS.
4y6o