PDBsum entry 2ogb

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Ligase PDB id
Protein chains
123 a.a. *
GOL ×2
Waters ×122
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Crystal structure of thE C-terminal domain of mouse nrdp1
Structure: Ring finger protein 41. Chain: a, b. Fragment: nrdp1 c-terminal domain. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: rnf41. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.95Å     R-factor:   0.213     R-free:   0.234
Authors: S.Bouyain,D.J.Leahy
Key ref:
S.Bouyain and D.J.Leahy (2007). Structure-based mutagenesis of the substrate-recognition domain of Nrdp1/FLRF identifies the binding site for the receptor tyrosine kinase ErbB3. Protein Sci, 16, 654-661. PubMed id: 17384230 DOI: 10.1110/ps.062700307
05-Jan-07     Release date:   16-Jan-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q8BH75  (RNF41_MOUSE) -  E3 ubiquitin-protein ligase NRDP1
317 a.a.
123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein ubiquitination   1 term 
  Biochemical function     protein tag     2 terms  


DOI no: 10.1110/ps.062700307 Protein Sci 16:654-661 (2007)
PubMed id: 17384230  
Structure-based mutagenesis of the substrate-recognition domain of Nrdp1/FLRF identifies the binding site for the receptor tyrosine kinase ErbB3.
S.Bouyain, D.J.Leahy.
The E3 ubiquitin ligase neuregulin receptor degrading protein 1 (Nrdp1) mediates the ligand-independent degradation of the epidermal growth factor receptor family member ErbB3/HER3. By regulating cellular levels of ErbB3, Nrdp1 influences ErbB3-mediated signaling, which is essential for normal vertebrate development. Nrdp1 belongs to the tripartite or RBCC (RING, B-box, coiled-coil) family of ubiquitin ligases in which the RING domain is responsible for ubiquitin ligation and a variable C-terminal region mediates substrate recognition. We report here the 1.95 A crystal structure of the C-terminal domain of Nrdp1 and show that this domain is sufficient to mediate ErbB3 binding. Furthermore, we have used site-directed mutagenesis to map regions of the Nrdp1 surface that are important for interacting with ErbB3 and mediating its degradation in transfected cells. The ErbB3-binding site localizes to a region of Nrdp1 that is conserved from invertebrates to vertebrates, in contrast to ErbB3, which is only found in vertebrates. This observation suggests that Nrdp1 uses a common binding site to recognize its targets in different species.
  Selected figure(s)  
Figure 1.
Figure 1. Crystal structure of Nrdp1C. (A) Ribbon diagrams of Nrdp1C.
Figure 5.
Figure 5. Comparison of the USP8- and ErbB3-binding sites on Nrdp1C.
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2007, 16, 654-661) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20868762 K.L.Carraway (2010).
E3 ubiquitin ligases in ErbB receptor quantity control.
  Semin Cell Dev Biol, 21, 936-943.  
18986647 S.Kim, S.Zhang, K.H.Choi, R.Reister, C.Do, A.F.Baykiz, and H.K.Gershenfeld (2009).
An E3 ubiquitin ligase, Really Interesting New Gene (RING) Finger 41, is a candidate gene for anxiety-like behavior and beta-carboline-induced seizures.
  Biol Psychiatry, 65, 425-431.  
18425425 A.W.Hamburger (2008).
The role of ErbB3 and its binding partners in breast cancer progression and resistance to hormone and tyrosine kinase directed therapies.
  J Mammary Gland Biol Neoplasia, 13, 225-233.  
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