3ZGV | pdb_00003zgv

Structure of human SIRT2 in complex with ADP-ribose

PDB DOI: https://doi.org/10.2210/pdb3ZGV/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-12-19 Released: 2013-03-13
Deposition Author(s): Moniot, S., Steegborn, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.188 (Depositor), 0.184 (DCC)
R-Value Work:
0.149 (Depositor), 0.149 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure Analysis of Human Sirt2 and its Adp-Ribose Complex

Moniot, S., Schutkowski, M., Steegborn, C.

(2013) J Struct Biol 182: 136

PubMed: 23454361 Search on PubMed
DOI: https://doi.org/10.1016/j.jsb.2013.02.012
Primary Citation Related Structures:
3ZGO, 3ZGV

PubMed Abstract:
Sirtuins are NAD(+)-dependent protein deacetylases that regulate metabolism and aging-related processes. Sirt2 is the only cytoplasmic isoform among the seven mamalian Sirtuins (Sirt1-7) and structural information concerning this isoform is limited. We crystallized Sirt2 in complex with a product analog, ADP-ribose, and solved this first crystal structure of a Sirt2 ligand complex at 2.3Å resolution. Additionally, we re-refined the structure of the Sirt2 apoform and analyzed the conformational changes associated with ligand binding to derive insights into the dynamics of the enzyme. Our analyses also provide information on Sirt2 peptide substrate binding and structural states of a Sirt2-specific protein region, and our insights and the novel Sirt2 crystal form provide helpful tools for the development of Sirt2 specific inhibitors.

Organizational Affiliation

Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany.

Macromolecule Content

Total Structure Weight: 75.2 kDa
Atom Count: 5,115
Modeled Residue Count: 596
Deposited Residue Count: 650
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2	A, B	325	Homo sapiens	Mutation(s): 0 EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXJ6 (Homo sapiens) Explore Q8IXJ6 Go to UniProtKB: Q8IXJ6
PHAROS: Q8IXJ6 GTEx: ENSG00000068903
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IXJ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AR6 Query on AR6 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C₁₅ H₂₃ N₅ O₁₄ P₂ SRNWOUGRCWSEMX-ZQSHOCFMSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A] F [auth A] G [auth A] H [auth A] J [auth B] D [auth A], F [auth A], G [auth A], H [auth A], J [auth B], L [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.188 (Depositor), 0.184 (DCC)
R-Value Work: 0.149 (Depositor), 0.149 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.86	α = 90
b = 77.98	β = 90
c = 114.33	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-03-13

Deposition Author(s):

Moniot, S.

Steegborn, C.

Revision History (Full details and data files)

Version 1.0: 2013-03-13
Type: Initial release
Version 1.1: 2013-04-03
Changes: Database references
Version 1.2: 2013-05-08
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary