PDBsum entry 4zld

RNA binding protein/RNA

PDB id: 4zld

Contents

Protein chain

151 a.a.

DNA/RNA

Ligands

GOL ×4

Waters ×186

PDB id:

4zld

Name:

RNA binding protein/RNA

Title:

Crystal structure of human roquin-2 roq domain in complex with roquin cde RNA

Structure:

Roquin-2. Chain: a. Fragment: unp residues 171-325. Synonym: membrane-associated nucleic acid-binding protein,ring finger and ccch-type zinc finger domain-containing protein 2,ring finger protein 164. Engineered: yes. RNA (5'- r( Up Ap Ap Cp Up Up Cp Up Gp Up Gp Ap Ap Gp Up Up G)-3').

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rc3h2, mnab, rnf164. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606

Resolution:

1.60Å R-factor: 0.156 R-free: 0.176

Authors:

S.Sakurai,U.Ohto,T.Shimizu

Key ref:

S.Sakurai et al. (2015). Structure of human Roquin-2 and its complex with constitutive-decay element RNA. Acta Crystallogr F Struct Biol Commun, 71, 1048-1054. PubMed id: 26249698 DOI: 10.1107/S2053230X15011887

Date:

01-May-15 Release date: 19-Aug-15

Protein chain

Q9HBD1  (RC3H2_HUMAN) -  Roquin-2 from Homo sapiens

Seq: 1191 a.a.

Struc: 151 a.a.

DNA/RNA chain

U-A-A-C-U-U-C-U-G-U-G-A-A-G-U-U-G 17 bases

Enzyme reactions

• Enzyme class: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

DOI no: 10.1107/S2053230X15011887

Acta Crystallogr F Struct Biol Commun 71:1048-1054 (2015)

PubMed id: 26249698

Structure of human Roquin-2 and its complex with constitutive-decay element RNA.

S.Sakurai, U.Ohto, T.Shimizu.

ABSTRACT

Roquin mediates mRNA degradation by recognizing the constitutive-decay element (CDE) in the 3' untranslated region of the target gene followed by recruitment of the deadenylation machinery. Deficiency or dysfunction of Roquin has been associated with autoimmunity and inflammation. To establish the structural basis for the recognition of CDE RNA by Roquin, the crystal structure of the ROQ domain of human Roquin-2 was determined in ligand-free and CDE-derived RNA-bound forms. The ROQ domain of Roquin-2 folded into a winged-helix structure in which the wing region showed structural flexibility and acted as a lid for RNA binding. The CDE RNA, forming a stem-loop structure, bound to the positively charged surface of the ROQ domain and was mainly recognized via direct interactions with the phosphate backbone in the 5' half of the stem-loop and its triloop and via indirect water-mediated interactions. Structural comparison with Roquin-1 revealed conserved features of the RNA-binding mode. Therefore, it is suggested that the Roquin proteins function redundantly in mRNA degradation.