2JRJ | pdb_00002jrj

Solution structure of the human Pirh2 RING-H2 domain. Northeast Structural Genomics Consortium Target HT2B

• PDB DOI: https://doi.org/10.2210/pdb2JRJ/pdb

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


• Deposited: 2007-06-27 Released: 2007-07-10 
• Deposition Author(s): Sheng, Y., Lemak, A., Laister, R.C., Wu, B., Arrowsmith, C.H., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

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

Literature

Molecular basis of Pirh2-mediated p53 ubiquitylation.

Sheng, Y., Laister, R.C., Lemak, A., Wu, B., Tai, E., Duan, S., Lukin, J., Sunnerhagen, M., Srisailam, S., Karra, M., Benchimol, S., Arrowsmith, C.H.

(2008) Nat Struct Mol Biol 15: 1334-1342

• PubMed: 19043414 
• DOI: https://doi.org/10.1038/nsmb.1521
• Primary Citation Related Structures: 
  2JRJ, 2K2C, 2K2D


• PubMed Abstract: 
  

  Pirh2 (p53-induced RING-H2 domain protein; also known as Rchy1) is an E3 ubiquitin ligase involved in a negative-feedback loop with p53. Using NMR spectroscopy, we show that Pirh2 is a unique cysteine-rich protein comprising three modular domains. The protein binds nine zinc ions using a variety of zinc coordination schemes, including a RING domain and a left-handed beta-spiral in which three zinc ions align three consecutive small beta-sheets in an interleaved fashion. We show that Pirh2-p53 interaction is dependent on the C-terminal zinc binding module of Pirh2, which binds to the tetramerization domain of p53. As a result, Pirh2 preferentially ubiquitylates the tetrameric form of p53 in vitro and in vivo, suggesting that Pirh2 regulates protein turnover of the transcriptionally active form of p53.

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Organizational Affiliation: 
• Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Ontario M5G1L7, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.13 kDa 
• Atom Count: 416 
• Modeled Residue Count: 52 
• Deposited Residue Count: 52 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ring finger and CHY zinc finger domain containing protein 1	A	52	Homo sapiens	Mutation(s): 0  Gene Names: RCHY1 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PM5 (Homo sapiens) Explore Q96PM5  Go to UniProtKB:  Q96PM5
PHAROS:  Q96PM5 GTEx:  ENSG00000163743

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	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: 2007-07-10 
Deposition Author(s): Sheng, Y., Lemak, A., Laister, R.C., Wu, B., Arrowsmith, C.H., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2007-07-10
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-09
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-12-20
  Changes: Data collection, Other