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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SIRT5 IN COMPLEX WITH FLUOR-DE-LYS PEPTIDE AND RESVERATROL
 
Authors :  M. Gertz, C. Steegborn
Date :  02 Oct 12  (Deposition) - 05 Dec 12  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B,F  (1x)
Keywords :  Nad-Dependent Deacetylase, Sirtuin, Mitochondrial, Activator Complex, Resveratrol, Hydrolase-Hydrolase Activator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Gertz, G. T. Nguyen, F. Fischer, B. Suenkel, C. Schlicker, B. Franzel, J. Tomaschewski, F. Aladini, C. Becker, D. Wolters, C. Steegborn
A Molecular Mechanism For Direct Sirtuin Activation By Resveratrol.
Plos One V. 7 49761 2012
PubMed-ID: 23185430  |  Reference-DOI: 10.1371/JOURNAL.PONE.0049761

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACYLASE SIRTUIN-5, MITOCHONDRIAL
    Chains: A, B
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151/D-TOPO
    Expression System Strain: BL21 (DE3) ROSETTA2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 34-302
    Gene: SIR2L5, SIRT5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: REGULATORY PROTEIN SIR2 HOMOLOG 5, SIR2-LIKE PROTEIN 5
 
Molecule 2 - FLUOR-DE-LYS PEPTIDE
    Chains: F
    Engineered: YES
    Other Details: COUMARIN-MODIFIED TETRA PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABF
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  BF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1FDL1Mod. Amino AcidN~6~-ACETYL-N-(4-METHYL-2-OXO-2H-CHROMEN-7-YL)-L-LYSINAMIDE
2STL1Ligand/IonRESVERATROL
3ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FDL-1Mod. Amino AcidN~6~-ACETYL-N-(4-METHYL-2-OXO-2H-CHROMEN-7-YL)-L-LYSINAMIDE
2STL-1Ligand/IonRESVERATROL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FDL1Mod. Amino AcidN~6~-ACETYL-N-(4-METHYL-2-OXO-2H-CHROMEN-7-YL)-L-LYSINAMIDE
2STL1Ligand/IonRESVERATROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:166 , CYS A:169 , CYS A:207 , CYS A:212BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARECYS B:166 , CYS B:169 , CYS B:207 , CYS B:212BINDING SITE FOR RESIDUE ZN B 401
3AC3SOFTWARELYS B:51 , GLY B:72 , THR B:279 , FDL F:4BINDING SITE FOR RESIDUE STL B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:178 -Pro A:179
2Tyr A:255 -Pro A:256
3Ser B:178 -Pro B:179
4Tyr B:255 -Pro B:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HDA)

(-) 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.eeeeeehhhhhhhh...............hhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhh...eee..eeeeeeee.....eee......hhhhh..............hhhhh...........eeeee.......hhhhhhhhhhhhhh..eeeeee..........hhhhhhhhh..eeeee...........eeee....hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hda A  35 RPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEAL 301
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       


Chain B from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhh...eeeeee.hhhhhh................hhhhh.hhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhhhhh...eeeeee......hhhhh...eee..eeeeeeee.....eee......hhhhh..............................eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhh....eeeee............eee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hda B  33 TARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA 302
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302


Chain F from PDB  Type:PROTEIN  Length:3
                                   
               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
                 4hda F   2 HKk   4
                              |
                              4-FDL
   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 4HDA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)

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  3.5.1.-
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 Related Entries

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        SIR5_HUMAN | Q9NXA8: 2b4y 2nyr 3rig 3riy 4f4u 4f56 4g1c 5bwl

(-) Related Entries Specified in the PDB File

4hd8