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PDBsum entry 1ma3

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protein ligands metals links
Protein binding, transcription PDB id
1ma3
Jmol
Contents
Protein chain
242 a.a. *
Ligands
ARG-HIS-LYS-ALY-
LEU-MET-PHE-LYS-
THR
MES
Metals
_ZN
Waters ×129
* Residue conservation analysis
PDB id:
1ma3
Name: Protein binding, transcription
Title: Structure of a sir2 enzyme bound to an acetylated p53 peptide
Structure: Transcriptional regulatory protein, sir2 family. Chain: a. Synonym: sir2-af2. Engineered: yes. Cellular tumor antigen p53. Chain: b. Fragment: regulatory c-terminal tail (residues 372-389). Synonym: tumor suppressor p53, phosphoprotein, p53, antigen ny-co-13.
Source: Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: sir2-af2. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the sequence of the protein is naturally found in homo sapiens. The protein is an fmoc synthesized peptide.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.209     R-free:   0.254
Authors: J.L.Avalos,I.Celic,S.Muhammad,M.S.Cosgrove,J.D.Boeke, C.Wolberger
Key ref:
J.L.Avalos et al. (2002). Structure of a Sir2 enzyme bound to an acetylated p53 peptide. Mol Cell, 10, 523-535. PubMed id: 12408821 DOI: 10.1016/S1097-2765(02)00628-7
Date:
31-Jul-02     Release date:   16-Oct-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O30124  (NPD2_ARCFU) -  NAD-dependent protein deacylase 2
Seq:
Struc:
253 a.a.
242 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     peptidyl-lysine demalonylation   5 terms 
  Biochemical function     protein-malonyllysine demalonylase activity     8 terms  

 

 
DOI no: 10.1016/S1097-2765(02)00628-7 Mol Cell 10:523-535 (2002)
PubMed id: 12408821  
 
 
Structure of a Sir2 enzyme bound to an acetylated p53 peptide.
J.L.Avalos, I.Celic, S.Muhammad, M.S.Cosgrove, J.D.Boeke, C.Wolberger.
 
  ABSTRACT  
 
Sir2 proteins are NAD(+)-dependent protein deacetylases that play key roles in transcriptional regulation, DNA repair, and life span regulation. The structure of an archaeal Sir2 enzyme, Sir2-Af2, bound to an acetylated p53 peptide reveals that the substrate binds in a cleft in the enzyme, forming an enzyme-substrate beta sheet with two flanking strands in Sir2-Af2. The acetyl-lysine inserts into a conserved hydrophobic tunnel that contains the active site histidine. Comparison with other structures of Sir2 enzymes suggests that the apoenzyme undergoes a conformational change upon substrate binding. Based on the Sir2-Af2 substrate complex structure, mutations were made in the other A. fulgidus sirtuin, Sir2-Af1, that increased its affinity for the p53 peptide.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. The p53 Peptide Binding to Sir2-Af2(A) Schematic drawing of p53-K^Ac382 binding by Sir2-Af2. The substrate peptide is shown in black over a pink background, and the acetyl-lysine is shown in red. β7 and β9 of Sir2-Af2 are shown in cyan and green, respectively. H bonds are shown as dashed lines, and the residues that form the hydrophobic tunnel are represented with yellow semicircles. Single boxes indicate peptide residues in p53-K^Ac382, and double boxes indicate residues in Sir2-Af2. The general region of NAD^+ binding is indicated with a turquoise shadow.(B) Stereo view of the enzyme-substrate β sheet that constitutes the β staple.(C) Stereo view of the FGE loop (cyan), which has a Type II β turn and makes four H bonds with the substrate peptide (white), three of which are with the acetyl-lysine (*). The FGE loop also interacts with the helical module (yellow), the zinc binding module (blue), and the Rossmann fold (green). H bonds are shown in gray and the salt bridge in magenta.(D) The transparent van der Waals surface of the hydrophobic acetyl-lysine binding tunnel. The asterisk labels the carbonyl oxygen of V163 that H bonds with the Nε of the acetyl-lysine. The peptide binding surface is located toward the foreground of the figure, while the NAD^+ binding pocket is located in the distal end of the tunnel.(E) The peptide binding surface of Sir2-Af2 colored according to sequence conservation (same orientation as Figure 1B). Conserved enzyme residues are colored red, similar residues yellow, and variable residues green (as defined in Figure 2). P168, Y197, and M222 are the residues whose counterparts in Sir2-Af1 were mutated as described in the text. The full p53-KAc382 peptide is shown with all side chains labeled.
Figure 4.
Figure 4. Structural Comparison of Sir2-Af2 with Other Sirtuin Structures(A) Superposition of Sir2-Af2 (green) with the Sir2-Af1 open (yellow) and closed (red) conformations and the structure of the human apo-SIRT2 (blue). The p53 peptide bound to Sir2-Af2 is shown in silver. The superposition minimizes the distances between the Rossmann folds of the four structures (lower half of the figure). The inset shows a close-up view of the significant shift in the FGE loop of the apo-SIRT2 protein with respect to its position in the Sir2-Af1-NAD^+ and Sir2-Af2 peptide structures.(B) Structure of Sir2-Af2, with the acetyl-lysine molecule shown in red and the disordered region of the helical module shown with small circles. Residues that form the hydrophobic tunnel (blue) bind the acetyl-lysine and orient it toward the NAD^+ binding pocket. In the absence of cofactor, the NAD^+ binding residues from the flexible loop (yellow) are shifted or disordered. The carbonyl oxygen of V163 is labeled with an asterisk, and the H bond it makes with the Nε of the acetyl-lysine is shown in gray.(C) Structure of Sir2-Af1-NAD^+ complex in the closed conformation, with the NAD^+ molecule shown in green. NAD^+ binding residues from the flexible loop (yellow) pack against the NAD^+ molecule, while the residues that form the hydrophobic tunnel (blue) are in the proper orientation to bind acetyl-lysine. The asterisk labels the carbonyl oxygen of V157 that H bonds the Nε of acetyl-lysine.(D) Structure of apo-SIRT2. NAD^+ binding residues from the flexible loop (yellow) are ordered but shifted from their relative position in Sir2-Af1. In the absence of peptide, the hydrophobic tunnel (blue) is distorted. The asterisk labels the carbonyl oxygen of V233 that H bonds the Nε of acetyl-lysine.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2002, 10, 523-535) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
  20516128 A.C.Joerger, and A.R.Fersht (2010).
The tumor suppressor p53: from structures to drug discovery.
  Cold Spring Harb Perspect Biol, 2, a000919.  
21152297 B.Xue, A.K.Dunker, and V.N.Uversky (2010).
Retro-MoRFs: Identifying Protein Binding Sites by Normal and Reverse Alignment and Intrinsic Disorder Prediction.
  Int J Mol Sci, 11, 3725-3747.  
20100603 B.Xue, R.L.Dunbrack, R.W.Williams, A.K.Dunker, and V.N.Uversky (2010).
PONDR-FIT: a meta-predictor of intrinsically disordered amino acids.
  Biochim Biophys Acta, 1804, 996.  
20975832 C.J.Lynch, Z.H.Shah, S.J.Allison, S.U.Ahmed, J.Ford, L.J.Warnock, H.Li, M.Serrano, and J.Milner (2010).
SIRT1 undergoes alternative splicing in a novel auto-regulatory loop with p53.
  PLoS One, 5, e13502.  
19824050 J.Schemies, U.Uciechowska, W.Sippl, and M.Jung (2010).
NAD(+) -dependent histone deacetylases (sirtuins) as novel therapeutic targets.
  Med Res Rev, 30, 861-889.  
  20885971 J.Soppa (2010).
Protein acetylation in archaea, bacteria, and eukaryotes.
  Archaea, 2010, 0.  
19286366 A.L.Okorokov, and E.V.Orlova (2009).
Structural biology of the p53 tumour suppressor.
  Curr Opin Struct Biol, 19, 197-202.  
19355989 D.Wang (2009).
Computational studies on the histone deacetylases and the design of selective histone deacetylase inhibitors.
  Curr Top Med Chem, 9, 241-256.  
19325869 E.Petsalaki, A.Stark, E.García-Urdiales, and R.B.Russell (2009).
Accurate prediction of peptide binding sites on protein surfaces.
  PLoS Comput Biol, 5, e1000335.  
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
19572575 M.Gutiérrez, E.H.Andrianasolo, W.K.Shin, D.E.Goeger, A.Yokochi, J.Schemies, M.Jung, D.France, S.Cornell-Kennon, E.Lee, and W.H.Gerwick (2009).
Structural and synthetic investigations of tanikolide dimer, a SIRT2 selective inhibitor, and tanikolide seco-acid from the Madagascar marine cyanobacterium Lyngbya majuscula.
  J Org Chem, 74, 5267-5275.  
19473964 M.M.Brent, A.Iwata, J.Carten, K.Zhao, and R.Marmorstein (2009).
Structure and Biochemical Characterization of Protein Acetyltransferase from Sulfolobus solfataricus.
  J Biol Chem, 284, 19412-19419.
PDB code: 3f8k
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
18829457 A.Patel, V.E.Vought, V.Dharmarajan, and M.S.Cosgrove (2008).
A Conserved Arginine-containing Motif Crucial for the Assembly and Enzymatic Activity of the Mixed Lineage Leukemia Protein-1 Core Complex.
  J Biol Chem, 283, 32162-32175.  
18366598 C.J.Oldfield, J.Meng, J.Y.Yang, M.Q.Yang, V.N.Uversky, and A.K.Dunker (2008).
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners.
  BMC Genomics, 9, S1.  
19325715 D.G.Fatkins, and W.Zheng (2008).
Substituting N-thioacetyl-lysine for N-acetyl-lysine in Peptide Substrates as a General Approach to Inhibiting Human NAD-dependent Protein Deacetylases.
  Int J Mol Sci, 9, 1.  
  18329615 H.S.Kwon, M.M.Brent, R.Getachew, P.Jayakumar, L.F.Chen, M.Schnolzer, M.W.McBurney, R.Marmorstein, W.C.Greene, and M.Ott (2008).
Human immunodeficiency virus type 1 Tat protein inhibits the SIRT1 deacetylase and induces T cell hyperactivation.
  Cell Host Microbe, 3, 158-167.  
18203716 K.Li, A.Casta, R.Wang, E.Lozada, W.Fan, S.Kane, Q.Ge, W.Gu, D.Orren, and J.Luo (2008).
Regulation of WRN protein cellular localization and enzymatic activities by SIRT1-mediated deacetylation.
  J Biol Chem, 283, 7590-7598.  
18619997 M.S.Cortese, V.N.Uversky, and A.K.Dunker (2008).
Intrinsic disorder in scaffold proteins: getting more from less.
  Prog Biophys Mol Biol, 98, 85.  
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
17964266 E.J.Kim, J.H.Kho, M.R.Kang, and S.J.Um (2007).
Active regulator of SIRT1 cooperates with SIRT1 and facilitates suppression of p53 activity.
  Mol Cell, 28, 277-290.  
18019526 H.Lin (2007).
Nicotinamide adenine dinucleotide: beyond a redox coenzyme.
  Org Biomol Chem, 5, 2541-2554.  
17242192 J.Mead, R.McCord, L.Youngster, M.Sharma, M.R.Gartenberg, and A.K.Vershon (2007).
Swapping the gene-specific and regional silencing specificities of the Hst1 and Sir2 histone deacetylases.
  Mol Cell Biol, 27, 2466-2475.  
17715127 N.Ahuja, B.Schwer, S.Carobbio, D.Waltregny, B.J.North, V.Castronovo, P.Maechler, and E.Verdin (2007).
Regulation of insulin secretion by SIRT4, a mitochondrial ADP-ribosyltransferase.
  J Biol Chem, 282, 33583-33592.  
17340003 N.Jamonnak, D.G.Fatkins, L.Wei, and W.Zheng (2007).
N(epsilon)-methanesulfonyl-lysine as a non-hydrolyzable functional surrogate for N(epsilon)-acetyl-lysine.
  Org Biomol Chem, 5, 892-896.  
17526736 R.Xiao, Y.Sun, J.H.Ding, S.Lin, D.W.Rose, M.G.Rosenfeld, X.D.Fu, and X.Li (2007).
Splicing regulator SC35 is essential for genomic stability and cell proliferation during mammalian organogenesis.
  Mol Cell Biol, 27, 5393-5402.  
16756498 A.A.Sauve, C.Wolberger, V.L.Schramm, and J.D.Boeke (2006).
The biochemistry of sirtuins.
  Annu Rev Biochem, 75, 435-465.  
16388584 A.L.Garske, and J.M.Denu (2006).
SIRT1 top 40 hits: use of one-bead, one-compound acetyl-peptide libraries and quantum dots to probe deacetylase specificity.
  Biochemistry, 45, 94.  
17053786 A.L.Okorokov, M.B.Sherman, C.Plisson, V.Grinkevich, K.Sigmundsson, G.Selivanova, J.Milner, and E.V.Orlova (2006).
The structure of p53 tumour suppressor protein reveals the basis for its functional plasticity.
  EMBO J, 25, 5191-5200.  
16520376 A.N.Khan, and P.N.Lewis (2006).
Use of substrate analogs and mutagenesis to study substrate binding and catalysis in the Sir2 family of NAD-dependent protein deacetylases.
  J Biol Chem, 281, 11702-11711.  
16717101 D.A.King, B.E.Hall, M.A.Iwamoto, K.Z.Win, J.F.Chang, and T.Ellenberger (2006).
Domain structure and protein interactions of the silent information regulator Sir3 revealed by screening a nested deletion library of protein fragments.
  J Biol Chem, 281, 20107-20119.  
16905097 K.G.Hoff, J.L.Avalos, K.Sens, and C.Wolberger (2006).
Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide.
  Structure, 14, 1231-1240.
PDB codes: 2h4f 2h4h 2h4j 2h59
16923962 M.Fu, M.Liu, A.A.Sauve, X.Jiao, X.Zhang, X.Wu, M.J.Powell, T.Yang, W.Gu, M.L.Avantaggiati, N.Pattabiraman, T.G.Pestell, F.Wang, A.A.Quong, C.Wang, and R.G.Pestell (2006).
Hormonal control of androgen receptor function through SIRT1.
  Mol Cell Biol, 26, 8122-8135.  
17103016 T.Huhtiniemi, C.Wittekindt, T.Laitinen, J.Leppänen, A.Salminen, A.Poso, and M.Lahtela-Kakkonen (2006).
Comparative and pharmacophore model for deacetylase SIRT1.
  J Comput Aided Mol Des, 20, 589-599.  
16131486 A.N.Khan, and P.N.Lewis (2005).
Unstructured conformations are a substrate requirement for the Sir2 family of NAD-dependent protein deacetylases.
  J Biol Chem, 280, 36073-36078.  
15642260 E.A.Sickmier, D.Brekasis, S.Paranawithana, J.B.Bonanno, M.S.Paget, S.K.Burley, and C.L.Kielkopf (2005).
X-ray structure of a Rex-family repressor/NADH complex insights into the mechanism of redox sensing.
  Structure, 13, 43-54.
PDB code: 1xcb
15640142 G.Blander, J.Olejnik, E.Krzymanska-Olejnik, T.McDonagh, M.Haigis, M.B.Yaffe, and L.Guarente (2005).
SIRT1 shows no substrate specificity in vitro.
  J Biol Chem, 280, 9780-9785.  
15780941 J.L.Avalos, K.M.Bever, and C.Wolberger (2005).
Mechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme.
  Mol Cell, 17, 855-868.
PDB codes: 1yc2 1yc5
16122969 J.M.Denu (2005).
The Sir 2 family of protein deacetylases.
  Curr Opin Chem Biol, 9, 431-440.  
15898057 M.Biel, V.Wascholowski, and A.Giannis (2005).
Epigenetics--an epicenter of gene regulation: histones and histone-modifying enzymes.
  Angew Chem Int Ed Engl, 44, 3186-3216.  
15749705 M.T.Borra, B.C.Smith, and J.M.Denu (2005).
Mechanism of human SIRT1 activation by resveratrol.
  J Biol Chem, 280, 17187-17195.  
15611301 R.Sawaya, B.Schwer, and S.Shuman (2005).
Structure-function analysis of the yeast NAD+-dependent tRNA 2'-phosphotransferase Tpt1.
  RNA, 11, 107-113.  
15899897 V.J.Starai, J.G.Gardner, and J.C.Escalante-Semerena (2005).
Residue Leu-641 of Acetyl-CoA synthetase is critical for the acetylation of residue Lys-609 by the Protein acetyltransferase enzyme of Salmonella enterica.
  J Biol Chem, 280, 26200-26205.  
15128440 B.J.North, and E.Verdin (2004).
Sirtuins: Sir2-related NAD-dependent protein deacetylases.
  Genome Biol, 5, 224.  
15189148 G.Blander, and L.Guarente (2004).
The Sir2 family of protein deacetylases.
  Annu Rev Biochem, 73, 417-435.  
15282295 J.C.Tanny, D.S.Kirkpatrick, S.A.Gerber, S.P.Gygi, and D.Moazed (2004).
Budding yeast silencing complexes and regulation of Sir2 activity by protein-protein interactions.
  Mol Cell Biol, 24, 6931-6946.  
15150415 K.Zhao, R.Harshaw, X.Chai, and R.Marmorstein (2004).
Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD(+)-dependent Sir2 histone/protein deacetylases.
  Proc Natl Acad Sci U S A, 101, 8563-8568.
PDB codes: 1szc 1szd
15269219 M.T.Schmidt, B.C.Smith, M.D.Jackson, and J.M.Denu (2004).
Coenzyme specificity of Sir2 protein deacetylases: implications for physiological regulation.
  J Biol Chem, 279, 40122-40129.  
15063846 V.J.Starai, H.Takahashi, J.D.Boeke, and J.C.Escalante-Semerena (2004).
A link between transcription and intermediary metabolism: a role for Sir2 in the control of acetyl-coenzyme A synthetase.
  Curr Opin Microbiol, 7, 115-119.  
12648672 C.L.Brooks, and W.Gu (2003).
Ubiquitination, phosphorylation and acetylation: the molecular basis for p53 regulation.
  Curr Opin Cell Biol, 15, 164-171.  
12517451 J.M.Denu (2003).
Linking chromatin function with metabolic networks: Sir2 family of NAD(+)-dependent deacetylases.
  Trends Biochem Sci, 28, 41-48.  
12694606 J.N.Reeve (2003).
Archaeal chromatin and transcription.
  Mol Microbiol, 48, 587-598.  
12966141 K.J.Bitterman, O.Medvedik, and D.A.Sinclair (2003).
Longevity regulation in Saccharomyces cerevisiae: linking metabolism, genome stability, and heterochromatin.
  Microbiol Mol Biol Rev, 67, 376.  
14502267 K.Zhao, X.Chai, A.Clements, and R.Marmorstein (2003).
Structure and autoregulation of the yeast Hst2 homolog of Sir2.
  Nat Struct Biol, 10, 864-871.
PDB code: 1q14
14604530 K.Zhao, X.Chai, and R.Marmorstein (2003).
Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide.
  Structure, 11, 1403-1411.
PDB codes: 1q17 1q1a
14534292 M.Hirao, J.Posakony, M.Nelson, H.Hruby, M.Jung, J.A.Simon, and A.Bedalov (2003).
Identification of selective inhibitors of NAD+-dependent deacetylases using phenotypic screens in yeast.
  J Biol Chem, 278, 52773-52782.  
12697818 S.C.Dryden, F.A.Nahhas, J.E.Nowak, A.S.Goustin, and M.A.Tainsky (2003).
Role for human SIRT2 NAD-dependent deacetylase activity in control of mitotic exit in the cell cycle.
  Mol Cell Biol, 23, 3173-3185.  
12672491 X.J.Yang, and E.Seto (2003).
Collaborative spirit of histone deacetylases in regulating chromatin structure and gene expression.
  Curr Opin Genet Dev, 13, 143-153.  
12377115 J.C.Tanny, and D.Moazed (2002).
Recognition of acetylated proteins: lessons from an ancient family of enzymes.
  Structure, 10, 1290-1292.  
12429083 R.Marmorstein (2002).
Dehydrogenases, NAD, and transcription--what's the connection?
  Structure, 10, 1465-1466.  
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.