1WLJ

human ISG20

• PDB DOI: https://doi.org/10.2210/pdb1WLJ/pdb

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


• Deposited: 2004-06-28 Released: 2004-12-21 
• Deposition Author(s): Horio, T., Murai, M., Inoue, T., Hamasaki, T., Tanaka, T., Ohgi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.227 
• R-Value Work: 0.207 

Literature

Crystal structure of human ISG20, an interferon-induced antiviral ribonuclease

Horio, T., Murai, M., Inoue, T., Hamasaki, T., Tanaka, T., Ohgi, T.

(2004) FEBS Lett 577: 111-116

• PubMed: 15527770 
• DOI: https://doi.org/10.1016/j.febslet.2004.09.074
• Primary Citation of Related Structures:  
  1WLJ


• PubMed Abstract: 
  

  ISG20 is an interferon-induced antiviral exoribonuclease that acts on single-stranded RNA and also has minor activity towards single-stranded DNA. It belongs to the DEDDh group of RNases of the DEDD exonuclease superfamily. We have solved the crystal structure of human ISG20 complexed with two Mn2+ ions and uridine 5'-monophosphate (UMP) at 1.9 A resolution. Its structure, including that of the active site, is very similar to those of the corresponding domains of two DEDDh-group DNases, the epsilon subunit of Escherichia coli DNA polymerase III and E. coli exonuclease I, strongly suggesting that its catalytic mechanism is identical to that of the two DNases. However, ISG20 also has distinctive residues, Met14 and Arg53, to accommodate hydrogen bonds with the 2'-OH group of the UMP ribose, and these residues may be responsible for the preference of ISG20 for RNA substrates.

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Organizational Affiliation: 

Research Laboratories, Nippon Shinyaku Co. Ltd, 3-14-1 Sakura, Tsukuba, Ibaraki 305-0003, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 22.02 kDa 
• Atom Count: 1,420 
• Modelled Residue Count: 168 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
interferon stimulated gene 20kDa	A	189	Homo sapiens	Mutation(s): 0  EC: 3.1 (PDB Primary Data), 3.1.13.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96AZ6 (Homo sapiens) Explore Q96AZ6  Go to UniProtKB:  Q96AZ6
PHAROS:  Q96AZ6 GTEx:  ENSG00000172183

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	F [auth A]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	B [auth A], C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.227 
• R-Value Work: 0.207 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.42	α = 90
b = 63.42	β = 90
c = 97.91	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
CNX	refinement
HKL-2000	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-21 
Deposition Author(s): Horio, T., Murai, M., Inoue, T., Hamasaki, T., Tanaka, T., Ohgi, T.

Revision History  

• Version 1.0: 2004-12-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations