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PDBsum entry 2h4f

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Hydrolase PDB id
2h4f
Jmol
Contents
Protein chain
240 a.a. *
Ligands
SER-ARG-HIS-LYS-
ALY-LEU-MET-PHE
NAD
Metals
_ZN
Waters ×70
* Residue conservation analysis
PDB id:
2h4f
Name: Hydrolase
Title: Sir2-p53 peptide-NAD+
Structure: NAD-dependent deacetylase. Chain: a. Synonym: regulatory protein sir2 homolog. Engineered: yes. Cellular tumor antigen p53. Chain: d. Synonym: tumor suppressor p53, phosphoprotein p53, antigen ny-co-13. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: npda. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: f-moc synthetic construct
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.194     R-free:   0.228
Authors: K.G.Hoff,J.L.Avalos,K.Sens,C.Wolberger
Key ref:
K.G.Hoff et al. (2006). Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide. Structure, 14, 1231-1240. PubMed id: 16905097 DOI: 10.1016/j.str.2006.06.006
Date:
24-May-06     Release date:   05-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9WYW0  (NPD_THEMA) -  NAD-dependent protein deacetylase
Seq:
Struc:
246 a.a.
240 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     protein deacetylation   1 term 
  Biochemical function     protein-malonyllysine demalonylase activity     8 terms  

 

 
DOI no: 10.1016/j.str.2006.06.006 Structure 14:1231-1240 (2006)
PubMed id: 16905097  
 
 
Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide.
K.G.Hoff, J.L.Avalos, K.Sens, C.Wolberger.
 
  ABSTRACT  
 
Sirtuin proteins comprise a unique class of NAD+-dependent protein deacetylases. Although several structures of sirtuins have been determined, the mechanism by which NAD+ cleavage occurs has remained unclear. We report the structures of ternary complexes containing NAD+ and acetylated peptide bound to the bacterial sirtuin Sir2Tm and to a catalytic mutant (Sir2Tm(H116Y)). NAD+ in these structures binds in a conformation different from that seen in previous structures, exposing the alpha face of the nicotinamide ribose to the carbonyl oxygen of the acetyl lysine substrate. The NAD+ conformation is identical in both structures, suggesting that proper coenzyme orientation is not dependent on contacts with the catalytic histidine. We also present the structure of Sir2Tm(H116A) bound to deacteylated peptide and 3'-O-acetyl ADP ribose. Taken together, these structures suggest a mechanism for nicotinamide cleavage in which an invariant phenylalanine plays a central role in promoting formation of the O-alkylamidate reaction intermediate and preventing nicotinamide exchange.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of the Ternary Complex of Sir2Tm Bound to Acetylated Peptide and NAD^+
(A) Overall structure of Sir2Tm bound to an acetylated peptide corresponding to residues 372–389 of the p53 protein (yellow) and β-NAD^+ (gray). The Sir2Tm Rossmann fold domain, the α-helical subdomain and Zn binding subdomain, and the Zn atom are colored teal, blue, and gold, respectively.
(B) Electron density for the sirtuin substrates. The 2F[o] − F[c] electron density map contoured at 1σ is shown surrounding the acetylated p53 peptide (yellow) and β-NAD^+ bound to the active site of Sir2Tm.
(C) Stereodiagram of NAD^+ (white) in the active site of Sir2Tm (teal) bound to acetylated peptide (yellow). Active site residues that make contact with NAD^+ are shown as lines, the acetyl lysine substrate and NAD^+ are shown as sticks, and water contacts are shown as dashed, gray sticks.
(D) Schematic representation of Sir2Tm contacts with NAD^+ and acetyl lysine. Sir2Tm residues are shown as ovals containing the amino acid designation and number; invariant residues shaded in blue, waters are shown as red circles, and the acetyl lysine side chain is designated as Ac-K and shaded yellow. Hydrogen bonds between NAD^+ and backbone amides and carbonyls are shown as blue and red dashes, respectively. Hydrogen bonds to amino acid side chains are represented as green dashes, and van der Waals interactions are indicated by yellow semicircles.
Figure 2.
Figure 2. Comparison of NAD^+ and NAD^+-Analog Bound Sirtuin Structures
Structural alignment of Sir2Tm-acetylated p53 peptide-NAD^+ (blue), Hst2Sc-acetylated histone H4 peptide-carba-NAD^+ (green), and Sir2Af2-NAD^+ (pink) based on atoms in the adenine ring, adenine ribose, nicotinamide, and the catalytic histidine. Acetyl lysine and active site residues for the corresponding structures are indicated.
 
  The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 1231-1240) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20842312 B.M.Hirsch, and W.Zheng (2011).
Sirtuin mechanism and inhibition: explored with N(ε)-acetyl-lysine analogs.
  Mol Biosyst, 7, 16-28.  
21243715 K.E.Dittenhafer-Reed, J.L.Feldman, and J.M.Denu (2011).
Catalysis and mechanistic insights into sirtuin activation.
  Chembiochem, 12, 281-289.  
21080423 P.Bheda, J.T.Wang, J.C.Escalante-Semerena, and C.Wolberger (2011).
Structure of Sir2Tm bound to a propionylated peptide.
  Protein Sci, 20, 131-139.
PDB code: 3pdh
21184005 Y.Cen, J.N.Falco, P.Xu, D.Y.Youn, and A.A.Sauve (2011).
Mechanism-based affinity capture of sirtuins.
  Org Biomol Chem, 9, 987-993.  
  20345662 H.A.Crosby, E.K.Heiniger, C.S.Harwood, and J.C.Escalante-Semerena (2010).
Reversible N epsilon-lysine acetylation regulates the activity of acyl-CoA synthetases involved in anaerobic benzoate catabolism in Rhodopseudomonas palustris.
  Mol Microbiol, 76, 874-888.  
19634988 M.A.Wouters, S.W.Fan, and N.L.Haworth (2010).
Disulfides as redox switches: from molecular mechanisms to functional significance.
  Antioxid Redox Signal, 12, 53-91.  
19217394 A.R.Kinjo, and H.Nakamura (2009).
Comprehensive structural classification of ligand-binding motifs in proteins.
  Structure, 17, 234-246.  
18603028 B.C.Smith, and J.M.Denu (2009).
Chemical mechanisms of histone lysine and arginine modifications.
  Biochim Biophys Acta, 1789, 45-57.  
19895577 K.Fahie, P.Hu, S.Swatkoski, R.J.Cotter, Y.Zhang, and C.Wolberger (2009).
Side chain specificity of ADP-ribosylation by a sirtuin.
  FEBS J, 276, 7159-7176.  
19535340 L.Jin, W.Wei, Y.Jiang, H.Peng, J.Cai, C.Mao, H.Dai, W.Choy, J.E.Bemis, M.R.Jirousek, J.C.Milne, C.H.Westphal, and R.B.Perni (2009).
Crystal structures of human SIRT3 displaying substrate-induced conformational changes.
  J Biol Chem, 284, 24394-24405.
PDB codes: 3glr 3gls 3glt 3glu
19801667 W.F.Hawse, and C.Wolberger (2009).
Structure-based mechanism of ADP-ribosylation by sirtuins.
  J Biol Chem, 284, 33654-33661.
PDB code: 3jr3
19479736 Y.Li, K.Chen, Q.Yao, J.Li, Y.Wang, H.Liu, C.Zhang, and G.Huang (2009).
The effect of calorie restriction on growth and development in silkworm, Bombyx mori.
  Arch Insect Biochem Physiol, 71, 159-172.  
18940661 B.C.Smith, W.C.Hallows, and J.M.Denu (2008).
Mechanisms and molecular probes of sirtuins.
  Chem Biol, 15, 1002-1013.  
18729382 J.B.French, Y.Cen, and A.A.Sauve (2008).
Plasmodium falciparum Sir2 is an NAD+-dependent deacetylase and an acetyllysine-dependent and acetyllysine-independent NAD+ glycohydrolase.
  Biochemistry, 47, 10227-10239.  
18800048 P.A.Cole (2008).
Chemical probes for histone-modifying enzymes.
  Nat Chem Biol, 4, 590-597.  
19049465 P.Hu, S.Wang, and Y.Zhang (2008).
Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations.
  J Am Chem Soc, 130, 16721-16728.  
18786399 W.F.Hawse, K.G.Hoff, D.G.Fatkins, A.Daines, O.V.Zubkova, V.L.Schramm, W.Zheng, and C.Wolberger (2008).
Structural insights into intermediate steps in the Sir2 deacetylation reaction.
  Structure, 16, 1368-1377.
PDB codes: 3d4b 3d81
17355872 A.Schuetz, J.Min, T.Antoshenko, C.L.Wang, A.Allali-Hassani, A.Dong, P.Loppnau, M.Vedadi, A.Bochkarev, R.Sternglanz, and A.N.Plotnikov (2007).
Structural basis of inhibition of the human NAD+-dependent deacetylase SIRT5 by suramin.
  Structure, 15, 377-389.
PDB code: 2nyr
18019526 H.Lin (2007).
Nicotinamide adenine dinucleotide: beyond a redox coenzyme.
  Org Biomol Chem, 5, 2541-2554.  
17684016 J.Garrity, J.G.Gardner, W.Hawse, C.Wolberger, and J.C.Escalante-Semerena (2007).
N-lysine propionylation controls the activity of propionyl-CoA synthetase.
  J Biol Chem, 282, 30239-30245.  
17694092 S.C.Hodawadekar, and R.Marmorstein (2007).
Chemistry of acetyl transfer by histone modifying enzymes: structure, mechanism and implications for effector design.
  Oncogene, 26, 5528-5540.  
16905094 B.C.Smith, and J.M.Denu (2006).
Sirtuins caught in the act.
  Structure, 14, 1207-1208.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.