PDBsum entry 6y4z

Hydrolase

PDB id: 6y4z

Contents

Protein chains

221 a.a.

Ligands

TLA

Waters ×440

PDB id:

6y4z

Name:

Hydrolase

Title:

The crystal structure of human macrod2 in space group p43212

Structure:

Thioredoxin 1,adp-ribose glycohydrolase macrod2. Chain: a, b, c, d. Synonym: trx-1,macro domain-containing protein 2,o-acetyl-adp-ribose deacetylase macrod2,[protein adp-ribosylaspartate] hydrolase macrod2, [protein adp-ribosylglutamate] hydrolase macrod2. Engineered: yes

Source:

Escherichia coli (strain k12), homo sapiens. Human. Organism_taxid: 83333, 9606. Gene: trxa, fipa, tsnc, b3781, jw5856, macrod2, c20orf133. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.202 R-free: 0.228

Authors:

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

Key ref:

S.Wazir et al. (2020). Multiple crystal forms of human MacroD2. Acta Crystallogr F Struct Biol Commun, 76, 477-482. PubMed id: 33006575 DOI: 10.1107/S2053230X20011309

Date:

24-Feb-20 Release date: 30-Sep-20

Protein chains

A1Z1Q3  (MACD2_HUMAN) -  ADP-ribose glycohydrolase MACROD2 from Homo sapiens

Seq: 425 a.a.

Struc: 221 a.a.*

Protein chains

P0AA25  (THIO_ECOLI) -  Thioredoxin 1 from Escherichia coli (strain K12)

Seq: 109 a.a.

Struc: 221 a.a.*

* PDB and UniProt seqs differ at 97 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.3.2.2.- - ?????
• Enzyme class 3: E.C.3.5.1.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1107/S2053230X20011309

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

PubMed id: 33006575

Multiple crystal forms of human MacroD2.

S.Wazir, M.M.Maksimainen, L.Lehtiö.

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 P4₁2₁2, P4₃2₁2 and P4₃, 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.