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(-) Description

Title :  SIRT2 IN COMPLEX WITH A 13-MER TRIFLUOROACETYLATED RAN PEPTIDE
 
Authors :  P. Knyphausen, S. De Boor, L. Scislowski, A. Extra, L. Baldus, M. Schac U. Baumann, I. Neundorf, M. Lammers
Date :  09 Mar 16  (Deposition) - 25 May 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Hydrolase, Sirtuin, Kdac, Lysine-Deacetylase, Lysine-Acetylation, Genetic-Code Expansion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Knyphausen, S. De Boor, N. Kuhlmann, L. Scislowski, A. Extra, L. Baldus, M. Schacherl, U. Baumann, I. Neundorf, M. Lammers
Insights Into Lysine-Deacetylation Of Natively Folded Substrate Proteins By Sirtuins.
J. Biol. Chem. V. 291 14677 2016
PubMed-ID: 27226597  |  Reference-DOI: 10.1074/JBC.M116.726307

(-) 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
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: 50-356
    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 - RAN AA 31-43
    Chains: C, D
    Fragment: PART OF SWITCH I, RESIDUES 31-43
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: TRIFLUOROACETYLATED AT K37
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1FAK2Mod. Amino AcidN~6~-(TRIFLUOROACETYL)-L-LYSINE
2SO42Ligand/IonSULFATE ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FAK1Mod. Amino AcidN~6~-(TRIFLUOROACETYL)-L-LYSINE
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FAK1Mod. Amino AcidN~6~-(TRIFLUOROACETYL)-L-LYSINE
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:84 , ALA B:85 , ASP B:95 , ARG B:97 , GLY B:261 , THR B:262 , SER B:263 , GLN B:265BINDING SITE FOR RESIDUE SO4 B1357
2AC2SOFTWAREARG A:97 , GLN A:167 , THR A:262 , SER A:263 , LEU A:264BINDING SITE FOR RESIDUE SO4 A1357
3AC3SOFTWARECYS B:195 , CYS B:200 , VAL B:217 , HOH B:2041BINDING SITE FOR RESIDUE ZN B1358
4AC4SOFTWARECYS A:195 , CYS A:221 , CYS A:224BINDING SITE FOR RESIDUE ZN A1358

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:195 -A:221

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Lys A:109 -Tyr A:110
2Tyr A:139 -Pro A:140
3Ser A:207 -Trp A:208
4Gln A:267 -Pro A:268
5Ala B:135 -Lys B:136
6Tyr B:139 -Pro B:140
7Pro B:140 -Gly B:141
8Cys B:195 -Val B:196
9Ala B:198 -Ser B:199
10Leu B:206 -Ser B:207
11Gln B:267 -Pro B:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FYQ)

(-) 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:282
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.....eeeee.hhhh......................hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeeee.....hhhhhhhhhhh............eeeee.......hhhhhhhhhhhhhhh.eeeee.......hhhhhhhh......eeeee...................eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5fyq A   56 ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS  356
                                    65        75        85        95   ||  109       119       129       139       149       159       169       179       189       199|      213       223       233       243       253       263       273       283       293|      314       324       334       344       354  
                                                                      99|                                                                                            199|                                                                                      293|                                                   
                                                                      104                                                                                             204                                                                                       305                                                   


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.....eeeee.hhhhhhhh........hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh..eeeeee....hhhhhh..hhh.eee..eeeeeee........................eeee........hhhhhhhhhhhhhh.eeeee.......hhhhhhhhh.....eeeee..................eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fyq B   56 ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS  356
                                    65        75        85        95   ||  118       128       138       148       158       168       178       188       198       208       228       238       248       258       268       278       288   ||  310       320       330       340       350      
                                                                      99|                                                                                                     217|                                                             292|                                                   
                                                                      113                                                                                                      228                                                              305                                                   


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
                5fyq C 1005 EFEkKYV 1011
                               |   
                            1008-FAK


Chain D from PDB  Type:PROTEIN  Length:8
                                         
               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
                5fyq D 1004 GEFEkKYV 1011
                                |   
                                |   
                             1008-FAK
   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 5FYQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (173, 183)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAN_HUMAN | P62826: 1i2m 1ibr 1k5d 1k5g 1qbk 1rrp 2mmc 2mmg 2n1b 3ch5 3ea5 3gj0 3gj3 3gj4 3gj5 3gj6 3gj7 3gj8 3gjx 3nby 3nbz 3nc0 3nc1 3zjy 4c0q 4gmx 4gpt 4hat 4hau 4hav 4haw 4hax 4hay 4haz 4hb0 4hb2 4hb3 4hb4 4ol0 4wvf 5ciq 5cit 5ciw 5cj2 5cll 5clq 5dh9 5dha 5dhf 5di9 5dif 5dis 5dlq 5jlj 5uwh 5uwi 5uwj 5uwo 5uwp 5uwq 5uwr 5uws 5uwt 5uwu 5uww
        SIR2_HUMAN | Q8IXJ6: 1j8f 3zgo 3zgv 4l3o 4r8m 4rmg 4rmh 4rmi 4rmj 4x3o 4x3p 4y6l 4y6o 4y6q 5d7o 5d7p 5d7q 5dy4 5dy5 5g4c 5mar 5mat

(-) Related Entries Specified in the PDB File

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