2LXH | pdb_00002lxh

NMR structure of the RING domain in ubiquitin ligase gp78

• PDB DOI: https://doi.org/10.2210/pdb2LXH/pdb
• BMRB: 18677

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-27 Released: 2013-08-28 
• Deposition Author(s): Das, R., Linag, Y., Mariano, J., Li, J., Huang, T., King, A., Weissman, A., Ji, X., Byrd, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine.

Das, R., Liang, Y.H., Mariano, J., Li, J., Huang, T., King, A., Tarasov, S.G., Weissman, A.M., Ji, X., Byrd, R.A.

(2013) EMBO J 32: 2504-2516

• PubMed: 23942235 
• DOI: https://doi.org/10.1038/emboj.2013.174
• Primary Citation Related Structures: 
  2LXH, 2LXP, 4LAD


• PubMed Abstract: 
  

  RING finger proteins constitute the large majority of ubiquitin ligases (E3s) and function by interacting with ubiquitin-conjugating enzymes (E2s) charged with ubiquitin. How low-affinity RING-E2 interactions result in highly processive substrate ubiquitination is largely unknown. The RING E3, gp78, represents an excellent model to study this process. gp78 includes a high-affinity secondary binding region for its cognate E2, Ube2g2, the G2BR. The G2BR allosterically enhances RING:Ube2g2 binding and ubiquitination. Structural analysis of the RING:Ube2g2:G2BR complex reveals that a G2BR-induced conformational effect at the RING:Ube2g2 interface is necessary for enhanced binding of RING to Ube2g2 or Ube2g2 conjugated to Ub. This conformational effect and a key ternary interaction with conjugated ubiquitin are required for ubiquitin transfer. Moreover, RING:Ube2g2 binding induces a second allosteric effect, disrupting Ube2g2:G2BR contacts, decreasing affinity and facilitating E2 exchange. Thus, gp78 is a ubiquitination machine where multiple E2-binding sites coordinately facilitate processive ubiquitination.

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Organizational Affiliation: 
• Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 9.37 kDa 
• Atom Count: 448 
• Modeled Residue Count: 58 
• Deposited Residue Count: 81 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase AMFR	A [auth C]	81	Homo sapiens	Mutation(s): 0  Gene Names: AMFR, RNF45 EC: 6.3.2 (PDB Primary Data), 2.3.2.36 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV5 (Homo sapiens) Explore Q9UKV5  Go to UniProtKB:  Q9UKV5
PHAROS:  Q9UKV5 GTEx:  ENSG00000159461

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth C], C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Das, R., Linag, Y., Mariano, J., Li, J., Huang, T., King, A., Weissman, A., Ji, X., Byrd, R.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-10-02
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references