Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 63920.07 
• Atom Count: 4430 
• Residue Count: 519 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1OE5

Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase

• DOI: 10.2210/pdb1OE5/pdb
• NDB: NA0260

• Classification: HYDROLASE/DNA
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli


• Deposited: 2003-03-19 Released: 2003-07-11 
• Deposition Author(s): Wibley, J.E.A., Pearl, L.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.229 
• R-Value Work: 0.163 

Literature

Structure and Specificity of the Vertebrate Anti-Mutator Uracil-DNA Glycosylase Smug1

Wibley, J.E.A., Waters, T.R., Haushalter, K., Verdine, G.L., Pearl, L.H.

(2003) Mol.Cell 11: 1647

• PubMed: 12820976 
• Primary Citation of Related Structures:  
  1OE6, 1OE4


• PubMed Abstract: 
  

Cytosine deamination is a major promutagenic process, generating G:U mismatches that can cause transition mutations if not repaired. Uracil is also introduced into DNA via nonmutagenic incorporation of dUTP during replication. In bacteria, uracil is excised by uracil-DNA glycosylases (UDG) related to E. coli UNG, and UNG homologs are found in mammals and viruses. Ung knockout mice display no increase in mutation frequency due to a second UDG activity, SMUG1, which is specialized for antimutational uracil excision in mammalian cells. Remarkably, SMUG1 also excises the oxidation-damage product 5-hydroxymethyluracil (HmU), but like UNG is inactive against thymine (5-methyluracil), a chemical substructure of HmU. We have solved the crystal structure of SMUG1 complexed with DNA and base-excision products. This structure indicates a more invasive interaction with dsDNA than observed with other UDGs and reveals an elegant water displacement/replacement mechanism that allows SMUG1 to exclude thymine from its active site while accepting HmU.

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Organizational Affiliation: 

Cancer Research UK DNA Repair Enzyme Group, Section of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, United Kingdom.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SINGLE-STRAND SELECTIVE MONOFUNCTIONAL URACIL DNA GLYCOSYLASE	A, B	247	Xenopus laevis	Mutation(s): 0  Gene Names: smug1 EC: 3.2.2.-
Find proteins for Q9YGN6 (Xenopus laevis) Go to UniProtKB:  Q9YGN6

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*CP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*G)-3'	E	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
5'-D(*CP*3DRP*GP*GP*AP*CP*TP*3DRP*AP*CP*GP*GP*GP)-3'	F	13	N/A

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EPE	A, B	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HEPES C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DUR	F	2'-DEOXYURIDINE C9 H12 N2 O5 MXHRCPNRJAMMIM-SHYZEUOFSA-N
URA	A	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
IPA	A, B	ISOPROPYL ALCOHOL 2-PROPANOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3DR	F	DNA LINKING	C5 H11 O6 P		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.229 
• R-Value Work: 0.163 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 120.596	α = 90.00
b = 85.653	β = 118.56
c = 78.467	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-03-19 
• Released Date: 2003-07-11 
• Deposition Author(s): Wibley, J.E.A., Pearl, L.H.

Revision History 

• Version 1.0: 2003-07-11
  Type: Initial release
• Version 1.1: 2013-07-17
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance