PDBsum entry 5tda

Ligase

PDB id: 5tda

Contents

Protein chain

71 a.a.

Ligands

ARG-LEU-TRP-SER

Metals

_ZN ×3

Waters ×107

PDB id:

5tda

Name:

Ligase

Title:

Crystal structure of the ubr-box domain from ubr2 in complex with rlws n-degron

Structure:

E3 ubiquitin-protein ligase ubr2. Chain: a. Synonym: n-recognin-2,ubiquitin-protein ligase e3-alpha-2,ubiquitin- protein ligase e3-alpha-ii. Engineered: yes. Arg-leu-trp-ser peptide. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ubr2, c6orf133, kiaa0349. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

0.79Å R-factor: 0.121 R-free: 0.128

Authors:

J.Munoz-Escobar,G.Kozlov,K.Gehring

Key ref:

J.Muñoz-Escobar et al. (2017). Bound Waters Mediate Binding of Diverse Substrates to a Ubiquitin Ligase. Structure, 25, 719. PubMed id: 28392261 DOI: 10.1016/j.str.2017.03.004

Date:

19-Sep-16 Release date: 22-Mar-17

Protein chain

Q8IWV8  (UBR2_HUMAN) -  E3 ubiquitin-protein ligase UBR2 from Homo sapiens

Seq: 1755 a.a.

Struc: 71 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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: 10.1016/j.str.2017.03.004

Structure 25:719 (2017)

PubMed id: 28392261

Bound Waters Mediate Binding of Diverse Substrates to a Ubiquitin Ligase.

J.Muñoz-Escobar, E.Matta-Camacho, C.Cho, G.Kozlov, K.Gehring.

ABSTRACT

The N-end rule pathway controls the half-life of proteins based on their N-terminal residue. Positively charged type 1 N-degrons are recognized by a negatively charged pocket on the Zn finger named the UBR box. Here, we show that the UBR box is rigid, but bound water molecules in the pocket provide the structural plasticity required to bind different positively charged amino acids. Ultra-high-resolution crystal structures of arginine, histidine, and methylated arginine reveal that water molecules mediate the binding of N-degron peptides. Using a high-throughput binding assay and isothermal titration calorimetry, we demonstrate that the UBR box is able to bind methylated arginine and lysine peptides with high affinity and measure the preference for hydrophobic residues in the second position in the N-degron peptide. Finally, we show that the V122L mutation present in Johanson-Blizzard syndrome patients changes the specificity for the second position due to occlusion of the secondary pocket.