Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 49.38 kDa 
• Atom Count: 3607 
• Residue Count: 419 
• Unique protein chains: 2

6FGE

Crystal structure of human ZUFSP/ZUP1 in complex with ubiquitin

• DOI: 10.2210/pdb6FGE/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-01-10 Released: 2018-04-04 
• Deposition Author(s): Kwasna, D., Abdul Rehman, S.A., Kulathu, Y.
• Funding Organization(s): Medical Research Council (United Kingdom), European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.209 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Literature

Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability.

Kwasna, D., Abdul Rehman, S.A., Natarajan, J., Matthews, S., Madden, R., De Cesare, V., Weidlich, S., Virdee, S., Ahel, I., Gibbs-Seymour, I., Kulathu, Y.

(2018) Mol Cell 70: 150-164.e6

• PubMed: 29576527 
• DOI: 10.1016/j.molcel.2018.02.023
• Primary Citation of Related Structures:  
  6FGE


• PubMed Abstract: 
  

Deubiquitinating enzymes (DUBs) are important regulators of ubiquitin signaling. Here, we report the discovery of deubiquitinating activity in ZUFSP/C6orf113. High-resolution crystal structures of ZUFSP in complex with ubiquitin reveal several distinctive features of ubiquitin recognition and catalysis. Our analyses reveal that ZUFSP is a novel DUB with no homology to any known DUBs, leading us to classify ZUFSP as the seventh DUB family. Intriguingly, the minimal catalytic domain does not cleave polyubiquitin. We identify two ubiquitin binding domains in ZUFSP: a ZHA (ZUFSP helical arm) that binds to the distal ubiquitin and an atypical UBZ domain in ZUFSP that binds to polyubiquitin. Importantly, both domains are essential for ZUFSP to selectively cleave K63-linked polyubiquitin. We show that ZUFSP localizes to DNA lesions, where it plays an important role in genome stability pathways, functioning to prevent spontaneous DNA damage and also promote cellular survival in response to exogenous DNA damage.

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Organizational Affiliation: 

MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger with UFM1-specific peptidase domain protein	A	348	Homo sapiens	Mutation(s): 0  Gene Names: ZUFSP, C6orf113, ZUP1 EC: 3.4.19.12
Find proteins for Q96AP4 (Homo sapiens) Explore Q96AP4  Go to UniProtKB:  Q96AP4
NIH Common Fund Data Resources
PHAROS:  Q96AP4 GTEx:  ENSG00000153975

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	C	76	Homo sapiens	Mutation(s): 1  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS:  P0CG47

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MLI	A	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	A, C	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NH4	A	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.209 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.484	α = 90
b = 84.484	β = 90
c = 201.867	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-01-10 
• Released Date: 2018-04-04 
Deposition Author(s): Kwasna, D., Abdul Rehman, S.A., Kulathu, Y.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MC_UU_12016/6
European Research Council	United Kingdom	677623

Revision History 

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2018-04-11
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2018-04-18
  Changes: Data collection, Database references