Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52544.15 
• Atom Count: 3439 
• Residue Count: 454 
• Unique protein chains: 1

3ZRH

Crystal structure of the Lys29, Lys33-linkage-specific TRABID OTU deubiquitinase domain reveals an Ankyrin-repeat ubiquitin binding domain (AnkUBD)

• DOI: 10.2210/pdb3ZRH/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2011-06-16 Released: 2011-12-14 
• Deposition Author(s): Licchesi, J.D.F., Akutsu, M., Komander, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.248 
• R-Value Work: 0.200 

Literature

An Ankyrin-Repeat Ubiquitin-Binding Domain Determines Trabid'S Specificity for Atypical Ubiquitin Chains.

Licchesi, J.D.F., Mieszczanek, J., Mevissen, T.E.T., Rutherford, T.J., Akutsu, M., Virdee, S., Oualid, F.E., Chin, J.W., Ovaa, H., Bienz, M., Komander, D.

(2011) Nat.Struct.Mol.Biol. 19: 62

• PubMed: 22157957 
• DOI: 10.1038/nsmb.2169


• PubMed Abstract: 
  

Eight different types of ubiquitin linkages are present in eukaryotic cells that regulate diverse biological processes. Proteins that mediate specific assembly and disassembly of atypical Lys6, Lys27, Lys29 and Lys33 linkages are mainly unknown. We here reveal how the human ovarian tumor (OTU) domain deubiquitinase (DUB) TRABID specifically hydrolyzes both Lys29- and Lys33-linked diubiquitin. A crystal structure of the extended catalytic domain reveals an unpredicted ankyrin repeat domain that precedes an A20-like catalytic core. NMR analysis identifies the ankyrin domain as a new ubiquitin-binding fold, which we have termed AnkUBD, and DUB assays in vitro and in vivo show that this domain is crucial for TRABID efficiency and linkage specificity. Our data are consistent with AnkUBD functioning as an enzymatic S1' ubiquitin-binding site, which orients a ubiquitin chain so that Lys29 and Lys33 linkages are cleaved preferentially.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
UBIQUITIN THIOESTERASE ZRANB1	A	454	Homo sapiens	Mutation(s): 0  Gene Names: ZRANB1 (TRABID) EC: 3.4.19.12
Find proteins for Q9UGI0 (Homo sapiens) Go to Gene View: ZRANB1 Go to UniProtKB:  Q9UGI0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.248 
• R-Value Work: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 60.400	α = 90.00
b = 72.150	β = 90.00
c = 133.010	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
SHARP	phasing
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-06-16 
• Released Date: 2011-12-14 
• Deposition Author(s): Licchesi, J.D.F., Akutsu, M., Komander, D.

Revision History 

• Version 1.0: 2011-12-14
  Type: Initial release
• Version 1.1: 2012-01-25
  Type: Other