Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.32 kDa 
• Atom Count: 936 
• Modelled Residue Count: 120 
• Deposited Residue Count: 120 
• Unique protein chains: 2

2MRO

Structure of the complex of ubiquitin and the UBA domain from DNA-damage-inducible 1 protein (Ddi1)

• PDB DOI: 10.2210/pdb2MRO/pdb

• Classification: TRANSPORT PROTEIN/SIGNALING PROTEIN
• Organism(s): Homo sapiens, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-14 Released: 2015-02-04 
• Deposition Author(s): Zhang, D., Fushman, D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Literature

DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin.

Nowicka, U., Zhang, D., Walker, O., Krutauz, D., Castaneda, C.A., Chaturvedi, A., Chen, T.Y., Reis, N., Glickman, M.H., Fushman, D.

(2015) Structure 23: 542-557

• PubMed: 25703377 
• DOI: 10.1016/j.str.2015.01.010
• Primary Citation of Related Structures:  
  2MR9, 2MRO, 2MRP, 2MWS


• PubMed Abstract: 
  

Ddi1 belongs to a family of shuttle proteins targeting polyubiquitinated substrates for proteasomal degradation. Unlike the other proteasomal shuttles, Rad23 and Dsk2, Ddi1 remains an enigma: its function is not fully understood and structural properties are poorly characterized. We determined the structure and binding properties of the ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains of Ddi1 from Saccharomyces cerevisiae. We found that while Ddi1UBA forms a characteristic UBA:ubiquitin complex, Ddi1UBL has entirely uncharacteristic binding preferences. Despite having a ubiquitin-like fold, Ddi1UBL does not interact with typical UBL receptors but unexpectedly binds ubiquitin, forming a unique interface mediated by hydrophobic contacts and by salt bridges between oppositely charged residues of Ddi1UBL and ubiquitin. In stark contrast to ubiquitin and other UBLs, the β-sheet surface of Ddi1UBL is negatively charged and therefore is recognized in a completely different way. The dual functionality of Ddi1UBL, capable of binding both ubiquitin and proteasome, suggests an intriguing mechanism for Ddi1 as a proteasomal shuttle.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-inducible protein 1	B	44	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: DDI1, VSM1, YER143W EC: 3.4.23
UniProt
Find proteins for P40087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40087  Go to UniProtKB:  P40087

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 2MRO Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-14 
• Released Date: 2015-02-04 
Deposition Author(s): Zhang, D., Fushman, D.

Revision History  

• Version 1.0: 2015-02-04
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references
• Version 1.2: 2019-11-06
  Changes: Data collection, Database references, Experimental preparation