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(-) Description

Title :  CRYSTAL STRUCTURE OF SIRT1 IN COMPLEX WITH RESVERATROL AND AN AMC-CONTAINING PEPTIDE
 
Authors :  D. Cao, M. Wang, X. Qiu, D. Liu, H. Jiang, N. Yang, R. M. Xu
Date :  03 Jun 15  (Deposition) - 08 Jul 15  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Keywords :  Deacetylase, Human Sirtuin 1, N-Terminal Domain, Catalytic Domain, C- Terminal Domain, Resveratrol, Substrate, Hydrolase-Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Cao, M. Wang, X. Qiu, D. Liu, H. Jiang, N. Yang, R. M. Xu
Structural Basis For Allosteric, Substrate-Dependent Stimulation Of Sirt1 Activity By Resveratrol
Genes Dev. V. 29 1316 2015
PubMed-ID: 26109052  |  Reference-DOI: 10.1101/GAD.265462.115

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-1
    Chains: A, B, C
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28A SMT3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 143-512 AND 641-665
    Gene: SIRT1, SIR2L1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSIRT1,REGULATORY PROTEIN SIR2 HOMOLOG 1,SIR2-LIKE PROTEIN 1,HSIR2
 
Molecule 2 - AMC-CONTAINING PEPTIDE
    Chains: D, E, F
    Engineered: YES
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
2FDL3Mod. Amino AcidN~6~-ACETYL-N-(4-METHYL-2-OXO-2H-CHROMEN-7-YL)-L-LYSINAMIDE
3STL9Ligand/IonRESVERATROL
4ZN3Ligand/IonZINC ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2FDL1Mod. Amino AcidN~6~-ACETYL-N-(4-METHYL-2-OXO-2H-CHROMEN-7-YL)-L-LYSINAMIDE
3STL3Ligand/IonRESVERATROL
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2FDL1Mod. Amino AcidN~6~-ACETYL-N-(4-METHYL-2-OXO-2H-CHROMEN-7-YL)-L-LYSINAMIDE
3STL3Ligand/IonRESVERATROL
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2FDL1Mod. Amino AcidN~6~-ACETYL-N-(4-METHYL-2-OXO-2H-CHROMEN-7-YL)-L-LYSINAMIDE
3STL3Ligand/IonRESVERATROL
4ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:371 , CYS A:374 , CYS A:395 , CYS A:398binding site for residue ZN A 701
02AC2SOFTWARETHR A:209 , PRO A:212 , ASP A:292 , GLN A:294 , ALA A:295 , ASP A:298 , PHE A:414 , LYS A:444 , FDL D:4 , STL D:102binding site for residue STL A 702
03AC3SOFTWARECYS B:371 , CYS B:374 , CYS B:395 , CYS B:398binding site for residue ZN B 701
04AC4SOFTWAREARG B:274 , ASP B:292 , GLN B:294 , ALA B:295 , ASP B:298 , PHE B:414 , LYS B:444 , STL B:703 , FDL E:4binding site for residue STL B 702
05AC5SOFTWAREPRO B:212 , LEU B:215 , GLN B:222 , ASN B:226 , ASP B:298 , PHE B:414 , GLY B:415 , STL B:702 , ARG E:1 , LYS E:3 , FDL E:4binding site for residue STL B 703
06AC6SOFTWARECYS C:371 , ILE C:373 , CYS C:374 , CYS C:395 , ALA C:405binding site for residue ZN C 701
07AC7SOFTWAREPRO C:212 , ASP C:292 , GLN C:294 , ASP C:298 , LYS C:444 , STL C:703 , FDL F:4binding site for residue STL C 702
08AC8SOFTWAREPRO C:212 , LEU C:215 , THR C:219 , GLN C:222 , ILE C:223 , ASN C:226 , PHE C:414 , GLY C:415 , STL C:702 , ARG F:1 , LYS F:3 , FDL F:4binding site for residue STL C 703
09AC9SOFTWARELEU A:206 , PRO A:211 , ILE A:223 , ASN A:226 , GLU A:230 , ARG A:446 , PRO A:447 , LEU A:450 , HIS D:2 , LYS D:3 , FDL D:4binding site for residue STL D 101
10AD1SOFTWARELEU A:215 , GLN A:222 , ASN A:226 , ASP A:298 , GLU A:300 , PHE A:414 , GLY A:415 , STL A:702 , ARG D:1 , LYS D:3 , FDL D:4binding site for residue STL D 102
11AD2SOFTWARELEU B:206 , PRO B:211 , ILE B:223 , ASN B:226 , GLU B:230 , PRO B:447 , HIS E:2 , LYS E:3 , FDL E:4binding site for residue STL E 101
12AD3SOFTWARELEU C:206 , PRO C:211 , ILE C:223 , ASN C:226 , GLU C:230 , ARG C:446 , PRO C:447 , LEU C:450 , HIS F:2 , LYS F:3 , FDL F:4binding site for residue STL F 101
13AD4SOFTWAREASN A:226 , PHE C:148 , ASP C:150 , PRO C:180 , HIS D:2 , LYS D:3 , STL D:102binding site for Di-peptide ACE D 0 and ARG D 1
14AD5SOFTWARELEU A:206 , THR A:209 , ARG A:274 , PHE A:297 , HIS A:363 , VAL A:412 , PHE A:414 , GLY A:415 , GLU A:416 , ASN A:417 , LEU A:418 , ARG A:446 , STL A:702 , ACE D:0 , ARG D:1 , HIS D:2 , STL D:101 , STL D:102binding site for Di-peptide LYS D 3 and FDL D 4
15AD6SOFTWAREPHE A:148 , ASP A:150 , PRO A:180 , ASN B:226 , STL B:703 , HIS E:2 , LYS E:3binding site for Di-peptide ACE E 0 and ARG E 1
16AD7SOFTWARELEU B:206 , HIS B:363 , VAL B:412 , PHE B:414 , GLY B:415 , GLU B:416 , ASN B:417 , LEU B:418 , ARG B:446 , STL B:702 , STL B:703 , ACE E:0 , ARG E:1 , HIS E:2 , STL E:101binding site for Di-peptide LYS E 3 and FDL E 4
17AD8SOFTWAREASP B:150 , PRO B:180 , TYR C:185 , ASN C:226 , STL C:703 , HIS F:2 , LYS F:3binding site for Di-peptide ACE F 0 and ARG F 1
18AD9SOFTWARELEU C:206 , THR C:209 , PHE C:297 , HIS C:363 , VAL C:412 , PHE C:413 , PHE C:414 , GLY C:415 , GLU C:416 , ASN C:417 , LYS C:444 , ARG C:446 , PRO C:447 , STL C:702 , STL C:703 , ACE F:0 , ARG F:1 , HIS F:2 , STL F:101binding site for Di-peptide LYS F 3 and FDL F 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BTR)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Arg A:446 -Pro A:447
2Pro A:646 -Pro A:647
3Arg B:446 -Pro B:447
4Pro B:646 -Pro B:647
5Arg C:446 -Pro C:447
6Pro C:646 -Pro C:647

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BTR)

(-) 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:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee..........eehhhhhhhhhhhhh.hhhhhhhhhh.........hhhhhhhhhhhhhhh...........hhhhhhhhhhhh..eeeee.hhhh............hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh..eeeeee....hhhhhh....eee..eeeeeeee.....eeehhhhhhhhhh.................eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..........eeee.hhhhhhhhhhhhhhhhhhh...............eee...eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5btr A 144 DNLLFGDEIITNGSDWTPRPRIGPYTFVQQHLMIGTDPRTILKDLLPETIPPPELDDMTLWQIVINILSEPPKRKKRKDINTIEDAVKLLQESKKIIVLTGAGVSVSSGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLSSNPVKLSEITEQYLFLPPNRYIFHGAEVY 658
                                   153  ||   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510 ||    648       658
                                      156|                                                                                                                                                                                                                                                                                                                                               512|                 
                                       174                                                                                                                                                                                                                                                                                                                                                641                 


Chain B from PDB  Type:PROTEIN  Length:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........ee..........eehhhhhhhhhhhhh.hhhhhhhhhh.........hhhhhhhhhhhhhhh...........hhhhhhhhhhhh..eeeee.hhhh............hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhh....eee..eeeeeeee.....eeehhhhhhhhhh.................eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..........eeee.hhhhhhhhhhhhhhhhhhh.........eee...eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5btr B 142 SRDNLLFGDEIITNGSDWTPRPRIGPYTFVQQHLMIGTDPRTILKDLLPETIPPPELDDMTLWQIVINILSEPPKRKKRKDINTIEDAVKLLQESKKIIVLTGAGVSVSSGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLSSNITEQYLFLPPNRYIFHGAEVY 658
                                   151    || 178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498    || 642       652      
                                        156|                                                                                                                                                                                                                                                                                                                                      503| ||                 
                                         174                                                                                                                                                                                                                                                                                                                                       510 ||                 
                                                                                                                                                                                                                                                                                                                                                                                     512|                 
                                                                                                                                                                                                                                                                                                                                                                                      641                 


Chain C from PDB  Type:PROTEIN  Length:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee........eehhhhhhhhhhhhh.hhhhhhhhhh.........hhhhhhhhhhhhhhh...........hhhhhhhhhhhh..eeeee..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhh..eeeeee....hhhhhh....eee..eeeeeeee.....eeehhhhhhhhhh........eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..........eeee.hhhhhhhhhhhhhhhhhhhh......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5btr C 144 DNLLFGDEIITNDWTPRPRIGPYTFVQQHLMIGTDPRTILKDLLPETIPPPELDDMTLWQIVINILSEPPKRKKRKDINTIEDAVKLLQESKKIIVLTGYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLSFLPPNRYIFH 653
                                   153 ||    182       192       202       212       222       232       242       252       280       290       300       310       320       330       340       350       360       370       380       390    || 409       419       429       439       449       459       469       479       489       499 ||    651  
                                     155|                                                                                   261|                                                                                                                395|                                                                                             501|         
                                      175                                                                                    280                                                                                                                 405                                                                                              644         


Chain D from PDB  Type:PROTEIN  Length:5
                                     
               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
                 5btr D   0 xRHKx   4
                            |   |
                            0-ACE
                                4-FDL


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               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
                 5btr E   0 xRHKx   4
                            |   |
                            |   |
                            0-ACE
                                4-FDL


Chain F from PDB  Type:PROTEIN  Length:5
                                     
               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
                 5btr F   0 xRHKx   4
                            |   |
                            |   |
                            0-ACE
                                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 5BTR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (161, 161)

Asymmetric Unit(hide GO term definitions)

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        SIR1_HUMAN | Q96EB6: 4i5i 4if6 4ig9 4kxq 4zzh 4zzi 4zzj

(-) Related Entries Specified in the PDB File

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