2BPS

Ubiquitin-like protein YukD of Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb2BPS/pdb

• Classification: UBIQUITIN
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-04-22 Released: 2005-07-04 
• Deposition Author(s): van den Ent, F., Lowe, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.296 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 

Literature

Crystal Structure of Ubiquitin-Like Protein Yukd from Bacillus Subtilis

van den Ent, F., Lowe, J.

(2005) FEBS Lett 579: 3837

• PubMed: 15978580 
• DOI: https://doi.org/10.1016/j.febslet.2005.06.002
• Primary Citation of Related Structures:  
  2BPS


• PubMed Abstract: 
  

  The YukD protein in Bacillus subtilis was identified in a hidden Markov model (HMM) search as being related in sequence to ubiquitin. By solving the crystal structure we show that YukD adopts a fold that is most closely related to ubiquitin, yet has the shortest C-terminal tail of all known ubiquitin-like proteins. The endogenous gene of yukD in B. subtilis was disrupted without an obvious phenotypic effect and an inducible copy encoding a C-Myc and His-tagged version of the protein was introduced at the ectopic locus amyE. Conjugation assays performed both in vitro and in vivo indicate that YukD lacks the capacity for covalent bond formation with other proteins.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 18.48 kDa 
• Atom Count: 1,307 
• Modelled Residue Count: 162 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YUKD PROTEIN	A, B	81	Bacillus subtilis	Mutation(s): 0
UniProt
Find proteins for P71071 (Bacillus subtilis (strain 168)) Explore P71071  Go to UniProtKB:  P71071

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.296 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.328	α = 90
b = 50.328	β = 90
c = 175.106	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-04 
Deposition Author(s): van den Ent, F., Lowe, J.

Revision History  

• Version 1.0: 2005-07-04
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references, Source and taxonomy