6Y4Y

The crystal structure of human MACROD2 in space group P41212

• PDB DOI: https://doi.org/10.2210/pdb6Y4Y/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-24 Released: 2020-09-30 
• Deposition Author(s): Wazir, S., Maksimainen, M.M., Lehtio, L.
• Funding Organization(s): Academy of Finland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.227 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

Multiple crystal forms of human MacroD2.

Wazir, S., Maksimainen, M.M., Lehtio, L.

(2020) Acta Crystallogr F Struct Biol Commun 76: 477-482

• PubMed: 33006575 
• DOI: https://doi.org/10.1107/S2053230X20011309
• Primary Citation of Related Structures:  
  6Y4Y, 6Y4Z, 6Y73


• PubMed Abstract: 
  

  MacroD2 is one of the three human macrodomain proteins characterized by their protein-linked mono-ADP-ribosyl-hydrolyzing activity. MacroD2 is a single-domain protein that contains a deep ADP-ribose-binding groove. In this study, new crystallization conditions for MacroD2 were found and three crystal structures of human MacroD2 in the apo state were solved in space groups P4 ₁ 2 ₁ 2, P4 ₃ 2 ₁ 2 and P4 ₃ , and refined at 1.75, 1.90 and 1.70 Å resolution, respectively. Structural comparison of the apo crystal structures with the previously reported crystal structure of MacroD2 in complex with ADP-ribose revealed conformational changes in the side chains of Val101, Ile189 and Phe224 induced by the binding of ADP-ribose in the active site. These conformational variations may potentially facilitate design efforts of a MacroD2 inhibitor.

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Organizational Affiliation: 

Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5400, Oulu 90014, Finland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 163.78 kDa 
• Atom Count: 7,402 
• Modelled Residue Count: 864 
• Deposited Residue Count: 1,464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin 1,ADP-ribose glycohydrolase MACROD2	A, B, C, D	366	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: trxA, fipA, tsnC, b3781, JW5856, MACROD2, C20orf133 EC: 3.5.1 (PDB Primary Data), 3.2.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25  Go to UniProtKB:  P0AA25
Find proteins for A1Z1Q3 (Homo sapiens) Explore A1Z1Q3  Go to UniProtKB:  A1Z1Q3
PHAROS:  A1Z1Q3 GTEx:  ENSG00000172264
UniProt Groups	P0AA25A1Z1Q3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	E [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.227 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.65	α = 90
b = 95.65	β = 90
c = 258.72	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Wazir, S., Maksimainen, M.M., Lehtio, L.

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Funding Organization	Location	Grant Number
Academy of Finland	Finland	287063
Academy of Finland	Finland	294085

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2020-10-14
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description