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(-) Description

Title :  STRUCTURE OF NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-1 (OPEN STATE, 2.64 A)
 
Authors :  A. M. Davenport, F. M. Huber, A. Hoelz
Date :  16 Dec 12  (Deposition) - 06 Nov 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Deacetylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Davenport, F. M. Huber, A. Hoelz
Structural And Functional Analysis Of Human Sirt1.
J. Mol. Biol. V. 426 526 2014
PubMed-ID: 24120939  |  Reference-DOI: 10.1016/J.JMB.2013.10.009

(-) Compounds

Molecule 1 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-1
    Chains: A, C, E, G
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 234-510
    Gene: SIR2L1, SIRT1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSIRT1, REGULATORY PROTEIN SIR2 HOMOLOG 1, SIR2-LIKE PROTEIN 1, HSIR2, SIRTT1 75 KDA FRAGMENT, 75SIRT1
 
Molecule 2 - NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-1
    Chains: B, D, F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 641-665
    Gene: SIR2L1, SIRT1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:371 , CYS A:374 , CYS A:395 , CYS A:398BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWARECYS C:371 , CYS C:374 , CYS C:395 , CYS C:398BINDING SITE FOR RESIDUE ZN C 601
3AC3SOFTWARECYS E:371 , CYS E:374 , CYS E:395 , CYS E:398BINDING SITE FOR RESIDUE ZN E 601
4AC4SOFTWARECYS G:371 , CYS G:374 , CYS G:395 , CYS G:398BINDING SITE FOR RESIDUE ZN G 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IG9)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Arg A:276 -Asp A:277
2Arg A:446 -Pro A:447
3Pro B:646 -Pro B:647
4Arg C:276 -Asp C:277
5Arg C:446 -Pro C:447
6Gly D:-2 -Ser D:-1
7Pro D:646 -Pro D:647
8Arg E:446 -Pro E:447
9Pro F:646 -Pro F:647
10Arg G:276 -Asp G:277
11Arg G:446 -Pro G:447
12Pro H:646 -Pro H:647

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IG9)

(-) Exons   (0, 0)

(no "Exon" information available for 4IG9)

(-) 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:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains d4ig9a_ A: automated matches                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh..eeeee.hhhh............hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eee...hhhhhhh.................eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..........eeee.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ig9 A  -1 MRKKRKDINTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLC 501
                            ||     242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492         
                            ||                                                                                                                                                                                                                                                                           
                           -1|                                                                                                                                                                                                                                                                           
                           234                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:21
                                                     
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ...eeee...eee........ Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 4ig9 B  -2 GSQYLFLPPNRYIFHGAEVYS 659
                             ||    648       658 
                            -1|                  
                            641                  


Chain C from PDB  Type:PROTEIN  Length:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains d4ig9c_ C: automated matches                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh..eeeee.hhhhhhhh.........hhhhhhh......hhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....ee....hhhhhhh.................eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhh......eeeee..........eeee.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ig9 C  -1 MRKKRKDINTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLC 501
                            ||     242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492         
                           -1|                                                                                                                                                                                                                                                                           
                           234                                                                                                                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ....eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 4ig9 D  -3 MGSQYLFLPPNRYIFH 653
                              ||   647      
                             -1|            
                             641            


Chain E from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains d4ig9e_ E: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh..eeeee.hhhhhhhh.........hhhhhhh......hhhhh.hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh..eeeeee....hhhhhh....eee..eeeeeeee.....eee...hhhhhhh.................eeeee.......hhhhhhhhhhhh....eeeee.......hhhhhhhh......eeeee..........eeee.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ig9 E  -2 HMRKKRKDINTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLC 501
                             ||    241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501
                            -1|                                                                                                                                                                                                                                                                           
                            234                                                                                                                                                                                                                                                                           


Chain F from PDB  Type:PROTEIN  Length:18
                                                  
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author ......eeee...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 4ig9 F  -5 PHMGSQYLFLPPNRYIFH 653
                                || 645        
                               -1|            
                               641            


Chain G from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains d4ig9g_ G: automated matches                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh..eeeee.hhhh..............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh..eeeeee....hhhhhhh...eee..eeeeeeee.....eee...hhhhhhh.................eeeee..........hhhhhhhhh....eeeee.......hhhhhhhhh.....eeeee..........eeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ig9 G  -1 MRKKRKDINTIEDAVKLLQECKKIIVLTGAGVSVSCGIPDFRSRDGIYARLAVDFPDLPDPQAMFDIEYFRKDPRPFFKFAKEIYPGQFQPSLCHKFIALSDKEGKLLRNYTQNIDTLEQVAGIQRIIQCHGSFATASCLICKYKVDCEAVRGDIFNQVVPRCPRCPADEPLAIMKPEIVFFGENLPEQFHRAMKYDKDEVDLLIVIGSSLKVRPVALIPSSIPHEVPQILINREPLPHLHFDVELLGDCDVIINELCHRLGGEYAKLCC 502
                            ||     242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502
                           -1|                                                                                                                                                                                                                                                                            
                           234                                                                                                                                                                                                                                                                            


Chain H from PDB  Type:PROTEIN  Length:22
                                                      
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author .....eee...eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 4ig9 H  -3 MGSQYLFLPPNRYIFHGAEVYS 659
                              ||   647       657  
                             -1|                  
                             641
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IG9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IG9)

(-) Gene Ontology  (161, 161)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SIR1_HUMAN | Q96EB6: 4i5i 4if6 4kxq 4zzh 4zzi 4zzj 5btr

(-) Related Entries Specified in the PDB File

4i9y 4if5 4if6