3I2D | pdb_00003i2d

Crystal Structure of S. Cerevisiae SUMO E3 Ligase SIZ1

• PDB DOI: https://doi.org/10.2210/pdb3I2D/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-29 Released: 2009-09-15 
• Deposition Author(s): Lima, C.D., Yunus, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.259 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.213 (DCC) 

Literature

Structure of the Siz/PIAS SUMO E3 ligase Siz1 and determinants required for SUMO modification of PCNA.

Yunus, A.A., Lima, C.D.

(2009) Mol Cell 35: 669-682

• PubMed: 19748360 
• DOI: https://doi.org/10.1016/j.molcel.2009.07.013
• Primary Citation Related Structures: 
  3I2D


• PubMed Abstract: 
  

  Siz1 is a founding member of the Siz/PIAS RING family of SUMO E3 ligases. The X-ray structure of an active Siz1 ligase revealed an elongated tripartite architecture comprised of an N-terminal PINIT domain, a central zinc-containing RING-like SP-RING domain, and a C-terminal domain we term the SP-CTD. Structure-based mutational analysis and biochemical studies show that the SP-RING and SP-CTD are required for activation of the E2 approximately SUMO thioester, while the PINIT domain is essential for redirecting SUMO conjugation to the proliferating cell nuclear antigen (PCNA) at lysine 164, a nonconsensus lysine residue that is not modified by the SUMO E2 in the absence of Siz1. Mutational analysis of Siz1 and PCNA revealed surfaces on both proteins that are required for efficient SUMO modification of PCNA in vitro and in vivo.

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Organizational Affiliation: 
• Sloan-Kettering Institute, New York, NY 10065, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.76 kDa 
• Atom Count: 2,302 
• Modeled Residue Count: 280 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 SUMO-protein ligase SIZ1	A	371	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SIZ1, ULL1, YDR409W EC: 6 (PDB Primary Data), 2.3.2 (UniProt)
UniProt
Find proteins for Q04195 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04195  Go to UniProtKB:  Q04195

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.259 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.213 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.487	α = 90
b = 88.98	β = 90
c = 105.598	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Lima, C.D., Yunus, A.A.

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-21
  Changes: Database references
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations