2RSD | pdb_00002rsd

Solution structure of the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice

• PDB DOI: https://doi.org/10.2210/pdb2RSD/pdb
• BMRB: 11469

• Classification: LIGASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-12 Released: 2012-08-15 
• Deposition Author(s): Shindo, H., Tsuchiya, W., Suzuki, R., Yamazaki, T.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

PHD finger of the SUMO ligase Siz/PIAS family in rice reveals specific binding for methylated histone H3 at lysine 4 and arginine 2

Shindo, H., Suzuki, R., Tsuchiya, W., Taichi, M., Nishiuchi, Y., Yamazaki, T.

(2012) FEBS Lett 586: 1783-1789

• PubMed: 22626555 
• DOI: https://doi.org/10.1016/j.febslet.2012.04.063
• Primary Citation Related Structures: 
  2RSD


• PubMed Abstract: 
  

  We determined the three-dimensional structure of the PHD finger of the rice Siz/PIAS-type SUMO ligase, OsSiz1, by NMR spectroscopy and investigated binding ability for a variety of methylated histone H3 tails, showing that OsSiz1-PHD primarily recognizes dimethylated Arg2 of the histone H3 and that methylations at Arg2 and Lys4 reveal synergy effect on binding to OsSiz1-PHD. The K4 cage of OsSiz1-PHD for trimethylated Lys4 of H3K4me3 was similar to that of the BPTF-PHD finger, while the R2 pocket for Arg2 was different. It is intriguing that the PHD module of Siz/PIAS plays an important role, with collaboration with the DNA binding domain SAP, in gene regulation through SUMOylation of a variety of effectors associated with the methylated arginine-riched chromatin domains.

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Organizational Affiliation: 
• Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.8 kDa 
• Atom Count: 531 
• Modeled Residue Count: 68 
• Deposited Residue Count: 68 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 SUMO-protein ligase SIZ1	A	68	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: SIZ1, Os05g0125000, LOC_Os05g03430, OSJNBb0079L11.3 EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
UniProt
Find proteins for Q6L4L4 (Oryza sativa subsp. japonica) Explore Q6L4L4  Go to UniProtKB:  Q6L4L4

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 least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Shindo, H., Tsuchiya, W., Suzuki, R., Yamazaki, T.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references