4FC2 | pdb_00004fc2

Crystal structure of mouse poly(ADP-ribose) glycohydrolase (PARG) catalytic domain

PDB DOI: https://doi.org/10.2210/pdb4FC2/pdb

Classification: HYDROLASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-05-23 Released: 2012-06-06
Deposition Author(s): Wang, Z., Cheng, Z., Xu, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.214 (Depositor), 0.223 (DCC)
R-Value Work:
0.174 (Depositor), 0.182 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystallographic and biochemical analysis of the mouse poly(ADP-ribose) glycohydrolase.

Wang, Z., Gagne, J.P., Poirier, G.G., Xu, W.

(2014) PLoS One 9: e86010-e86010

PubMed: 24465839 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0086010
Primary Citation Related Structures:
4FC2, 4N9Y, 4N9Z, 4NA0, 4NA4, 4NA5, 4NA6

PubMed Abstract:
Protein poly(ADP-ribosyl)ation (PARylation) regulates a number of important cellular processes. Poly(ADP-ribose) glycohydrolase (PARG) is the primary enzyme responsible for hydrolyzing the poly(ADP-ribose) (PAR) polymer in vivo. Here we report crystal structures of the mouse PARG (mPARG) catalytic domain, its complexes with ADP-ribose (ADPr) and a PARG inhibitor ADP-HPD, as well as four PARG catalytic residues mutants. With these structures and biochemical analysis of 20 mPARG mutants, we provide a structural basis for understanding how the PAR polymer is recognized and hydrolyzed by mPARG. The structures and activity complementation experiment also suggest how the N-terminal flexible peptide preceding the PARG catalytic domain may regulate the enzymatic activity of PARG. This study contributes to our understanding of PARG catalytic and regulatory mechanisms as well as the rational design of PARG inhibitors.

Organizational Affiliation

Department of Biological Structure, University of Washington, Seattle, Washington, United States of America.

Macromolecule Content

Total Structure Weight: 244.74 kDa
Atom Count: 18,082
Modeled Residue Count: 2,031
Deposited Residue Count: 2,084
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ADP-ribose) glycohydrolase	A, B, C, D	521	Mus musculus	Mutation(s): 0 Gene Names: Parg EC: 3.2.1.143
UniProt & NIH Common Fund Data Resources
Find proteins for O88622 (Mus musculus) Explore O88622 Go to UniProtKB: O88622
IMPC: MGI:1347094
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O88622
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth D] SDF format, chain X [auth C] SDF format, chain Q [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain X [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain X [auth C] mmCIF format, chain Q [auth B]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] E [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], FA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth C], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.214 (Depositor), 0.223 (DCC)
R-Value Work: 0.174 (Depositor), 0.182 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.141	α = 81.64
b = 90.401	β = 88.41
c = 104.696	γ = 89.36

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-06-06

Deposition Author(s):

Wang, Z.

Cheng, Z.

Xu, W.

Revision History (Full details and data files)

Version 1.0: 2012-06-06
Type: Initial release
Version 1.1: 2014-01-29
Changes: Database references
Version 1.2: 2018-10-10
Changes: Data collection, Database references, Structure summary
Version 1.3: 2018-10-17
Changes: Data collection, Database references, Structure summary
Version 1.4: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary