Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.94 kDa 
• Atom Count: 2123 
• Residue Count: 251 
• Unique protein chains: 2

1MA3

Structure of a Sir2 enzyme bound to an acetylated p53 peptide

• DOI: 10.2210/pdb1MA3/pdb

• Classification: PROTEIN BINDING, TRANSCRIPTION
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-07-31 Released: 2002-10-16 
• Deposition Author(s): Avalos, J.L., Celic, I., Muhammad, S., Cosgrove, M.S., Boeke, J.D., Wolberger, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.254 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Structure of a Sir2 enzyme bound to an acetylated p53 peptide

Avalos, J.L., Celic, I., Muhammad, S., Cosgrove, M.S., Boeke, J.D., Wolberger, C.

(2002) Mol Cell 10: 523-535

• PubMed: 12408821 
• DOI: 10.1016/s1097-2765(02)00628-7
• Primary Citation of Related Structures:  
  1MA3


• PubMed 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.

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Organizational Affiliation: 

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein, Sir2 family	A	253	Archaeoglobus fulgidus	Mutation(s): 0  Gene Names: SIR2-Af2 EC: 2.3.1.286
Find proteins for O30124 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)) Explore O30124  Go to UniProtKB:  O30124

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	B	18	N/A	Mutation(s): 1
Find proteins for P04637 (Homo sapiens) Explore P04637  Go to UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS  P04637 GTEx  ENSG00000141510

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.254 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.892	α = 90
b = 35.591	β = 90
c = 184.683	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-07-31 
• Released Date: 2002-10-16 
Deposition Author(s): Avalos, J.L., Celic, I., Muhammad, S., Cosgrove, M.S., Boeke, J.D., Wolberger, C.

Revision History 

• Version 1.0: 2002-10-16
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance