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)

Macromolecule Content

• Total Structure Weight: 48.51 kDa 
• Atom Count: 3565 
• Residue Count: 410 
• Unique protein chains: 2

6EI1

Crystal structure of the covalent complex between deubiquitinase ZUFSP (ZUP1) and Ubiquitin-PA

• DOI: 10.2210/pdb6EI1/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-16 Released: 2018-03-07 
• Deposition Author(s): Pichlo, C., Baumann, U., Hofmann, K., Hermanns, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.203 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Literature

A family of unconventional deubiquitinases with modular chain specificity determinants.

Hermanns, T., Pichlo, C., Woiwode, I., Klopffleisch, K., Witting, K.F., Ovaa, H., Baumann, U., Hofmann, K.

(2018) Nat Commun 9: 799-799

• PubMed: 29476094 
• DOI: 10.1038/s41467-018-03148-5
• Primary Citation of Related Structures:  
  6EI1


• PubMed Abstract: 
  

Deubiquitinating enzymes (DUBs) regulate ubiquitin signaling by trimming ubiquitin chains or removing ubiquitin from modified substrates. Similar activities exist for ubiquitin-related modifiers, although the enzymes involved are usually not related. Here, we report human ZUFSP (also known as ZUP1 and C6orf113) and fission yeast Mug105 as founding members of a DUB family different from the six known DUB classes. The crystal structure of human ZUFSP in covalent complex with propargylated ubiquitin shows that the DUB family shares a fold with UFM1- and Atg8-specific proteases, but uses a different active site more similar to canonical DUB enzymes. ZUFSP family members differ widely in linkage specificity through differential use of modular ubiquitin-binding domains (UBDs). While the minimalistic Mug105 prefers K48 chains, ZUFSP uses multiple UBDs for its K63-specific endo-DUB activity. K63 specificity, localization, and protein interaction network suggest a role for ZUFSP in DNA damage response.

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Organizational Affiliation: 

Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674, Cologne, Germany. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger with UFM1-specific peptidase domain protein	A	347	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	B	75	Homo sapiens	Mutation(s): 0  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	A	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
AYE	A	prop-2-en-1-amine C3 H7 N VVJKKWFAADXIJK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.203 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.23	α = 90
b = 84.23	β = 90
c = 201.78	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-09-16 
• Released Date: 2018-03-07 
Deposition Author(s): Pichlo, C., Baumann, U., Hofmann, K., Hermanns, T.

Revision History 

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-03-14
  Changes: Structure summary
• Version 1.2: 2019-10-16
  Changes: Data collection