Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.99 kDa 
• Atom Count: 1357 
• Residue Count: 149 
• Unique protein chains: 1

2ESP

Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala

• DOI: 10.2210/pdb2ESP/pdb

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


• Deposited: 2005-10-26 Released: 2005-12-06 
• Deposition Author(s): Ozkan, E., Yu, H., Deisenhofer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Literature

Mechanistic insight into the allosteric activation of a ubiquitin-conjugating enzyme by RING-type ubiquitin ligases

Ozkan, E., Yu, H., Deisenhofer, J.

(2005) Proc Natl Acad Sci U S A 102: 18890-18895

• PubMed: 16365295 
• DOI: 10.1073/pnas.0509418102
• Primary Citation of Related Structures:  
  2ESQ, 2ESP, 2ESO, 2ESK


• PubMed Abstract: 
  

Ubiquitin-conjugating enzymes (E2s) collaborate with the ubiquitin-activating enzyme (E1) and ubiquitin ligases (E3s) to attach ubiquitin to target proteins. RING-containing E3s simultaneously bind to E2s and substrates, bringing them into close proximity and thus facilitating ubiquitination. We show herein that, although the E3-binding site on the human E2 UbcH5b is distant from its active site, two RING-type minimal E3 modules lacking substrate-binding functions greatly stimulate the rate of ubiquitin release from the UbcH5b-ubiquitin thioester. Using statistical coupling analysis and mutagenesis, we identify and characterize clusters of coevolving and functionally linked residues within UbcH5b that span its E3-binding and active sites. Several UbcH5b mutants are defective in their stimulation by E3s despite their abilities to bind to these E3s, to form ubiquitin thioesters, and to release ubiquitin at a basal rate. One such mutation, I37A, is distant from both the active site and the E3-binding site of UbcH5b. Our studies reveal structural determinants for communication between distal functional sites of E2s and suggest that RING-type E3s activate E2s allosterically.

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Organizational Affiliation: 

Department of Biochemistry and Pharmacology and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D2	A	149	Homo sapiens	Mutation(s): 1  Gene Names: UBE2D2, UBC4, UBCH5B, PUBC1, UBC5B, UBCH4 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
Find proteins for P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
NIH Common Fund Data Resources
PHAROS  P62837 GTEx  ENSG00000131508

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.233 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.877	α = 90
b = 49.224	β = 90
c = 62.128	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-26 
• Released Date: 2005-12-06 
Deposition Author(s): Ozkan, E., Yu, H., Deisenhofer, J.

Revision History 

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description