1MA3 | pdb_00001ma3

Structure of a Sir2 enzyme bound to an acetylated p53 peptide

PDB DOI: https://doi.org/10.2210/pdb1MA3/pdb

Classification: PROTEIN BINDING, TRANSCRIPTION
Organism(s): Archaeoglobus fulgidus, Homo sapiens
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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.254 (Depositor), 0.249 (DCC)
R-Value Work:
0.209 (Depositor), 0.205 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/s1097-2765(02)00628-7
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 30.94 kDa
Atom Count: 2,123
Modeled Residue Count: 251
Deposited Residue Count: 271
Unique protein chains: 2

Macromolecules

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| 3D Structure

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
UniProt
Find proteins for O30124 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O30124 Go to UniProtKB: O30124
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O30124
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	B	18	N/A	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637 Go to UniProtKB: P04637
PHAROS: P04637 GTEx: ENSG00000141510
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04637
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on 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 (Depositor), 0.249 (DCC)
R-Value Work: 0.209 (Depositor), 0.205 (DCC)
R-Value Observed: 0.211 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2002-10-16

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary