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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SIRT1 CATALYTIC DOMAIN BOUND TO NAD AND AN EX527 ANALOG
 
Authors :  X. Zhao, D. Allison, B. Condon, F. Zhang, T. Gheyi, A. Zhang, S. Ashok, M. I. Macewan, Y. Qian, J. A. Jamison, J. G. Luz
Date :  28 Nov 12  (Deposition) - 23 Jan 13  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Rossmann Fold, Histone Deacetylase, Epigenetics, Cancer, Sirtuin, Acetylated Lysine Of Histone, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Zhao, D. Allison, B. Condon, F. Zhang, T. Gheyi, A. Zhang, S. Ashok, M. Russell, I. Macewan, Y. Qian, J. A. Jamison, J. G. Luz
The 2. 5 Angstrom Crystal Structure Of The Sirt1 Catalytic Domain Bound To Nicotinamide Adenine Dinucleotide (Nad+) An An Indole (Ex527 Analogue) Reveals A Novel Mechanism Of Histone Deacetylase Inhibition.
J. Med. Chem. V. 56 963 2013
PubMed-ID: 23311358  |  Reference-DOI: 10.1021/JM301431Y

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-1
    ChainsA, B
    EC Number3.5.1.-
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System VectorPFASTBAC
    Expression System Vector TypeBACULOVIRUS
    FragmentDEACETYLASE SIRTUIN-TYPE CATALYTIC DOMAIN RESIDUES 241-516
    GeneSIRT1, SIR2L1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHSIRT1, REGULATORY PROTEIN SIR2 HOMOLOG 1, SIR2-LIKE PROTEIN 1, HSIR2, SIRTT1 75 KDA FRAGMENT, 75SIRT1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
14I52Ligand/Ion(6S)-2-CHLORO-5,6,7,8,9,10-HEXAHYDROCYCLOHEPTA[B]INDOLE-6-CARBOXAMIDE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
14I51Ligand/Ion(6S)-2-CHLORO-5,6,7,8,9,10-HEXAHYDROCYCLOHEPTA[B]INDOLE-6-CARBOXAMIDE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
14I51Ligand/Ion(6S)-2-CHLORO-5,6,7,8,9,10-HEXAHYDROCYCLOHEPTA[B]INDOLE-6-CARBOXAMIDE
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
14I52Ligand/Ion(6S)-2-CHLORO-5,6,7,8,9,10-HEXAHYDROCYCLOHEPTA[B]INDOLE-6-CARBOXAMIDE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:270 , PRO A:271 , PHE A:273 , PHE A:297 , GLN A:345 , ASN A:346 , ILE A:347 , ASP A:348 , ILE A:411 , VAL A:412 , PHE A:413 , NAD A:602 , HOH A:702BINDING SITE FOR RESIDUE 4I5 A 601
2AC2SOFTWAREGLY A:261 , ALA A:262 , GLY A:263 , VAL A:266 , ASP A:272 , PHE A:273 , ARG A:274 , TYR A:280 , GLN A:294 , PHE A:297 , GLN A:345 , HIS A:363 , VAL A:412 , PHE A:414 , GLY A:440 , SER A:441 , SER A:442 , VAL A:445 , ASN A:465 , ARG A:466 , GLU A:467 , GLY A:480 , ASP A:481 , CYS A:482 , LEU A:507 , 4I5 A:601 , HOH A:712 , HOH A:717 , HOH A:752BINDING SITE FOR RESIDUE NAD A 602
3AC3SOFTWARECYS A:371 , CYS A:374 , CYS A:395 , CYS A:398BINDING SITE FOR RESIDUE ZN A 603
4AC4SOFTWAREILE B:270 , PRO B:271 , PHE B:273 , PHE B:297 , GLN B:345 , ASN B:346 , ILE B:347 , ASP B:348 , ILE B:411 , VAL B:412 , PHE B:413 , NAD B:602 , HOH B:704BINDING SITE FOR RESIDUE 4I5 B 601
5AC5SOFTWAREGLY B:261 , ALA B:262 , GLY B:263 , VAL B:266 , ASP B:272 , PHE B:273 , ARG B:274 , TYR B:280 , GLN B:294 , PHE B:297 , GLN B:345 , HIS B:363 , VAL B:412 , PHE B:414 , GLY B:440 , SER B:441 , SER B:442 , VAL B:445 , ASN B:465 , ARG B:466 , GLU B:467 , GLY B:480 , ASP B:481 , CYS B:482 , LEU B:507 , 4I5 B:601 , HOH B:713 , HOH B:718 , HOH B:727 , HOH B:752BINDING SITE FOR RESIDUE NAD B 602
6AC6SOFTWARECYS B:371 , CYS B:374 , CYS B:395 , CYS B:398BINDING SITE FOR RESIDUE ZN B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I5I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Arg A:446 -Pro A:447
2Arg B:446 -Pro B:447

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I5I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I5I)

(-) Exons   (0, 0)

(no "Exon" information available for 4I5I)

(-) 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:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeee.hhhhh...........hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eeehhhhhhhhhh.................eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..........eeee.hhhhhhhhhhhhhh.hhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i5i A 241 NTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLCCNPVKLSEITE 512
                                   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  

Chain B from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeeee.hhhhh...........hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eeehhhhhhhhhh.................eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..........eeee.hhhhhhhhhhhhhh.hhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i5i B 241 NTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLCCNPVKLSEITE 512
                                   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  

   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 4I5I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I5I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I5I)

(-) Gene Ontology  (161, 161)

Asymmetric Unit(hide GO term definitions)

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        SIR1_HUMAN | Q96EB64if6 4ig9 4kxq 4zzh 4zzi 4zzj 5btr

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