1OE5 | pdb_00001oe5

Xenopus SMUG1, an anti-mutator uracil-DNA Glycosylase

• PDB DOI: https://doi.org/10.2210/pdb1OE5/pdb
• NAKB: 1OE5

• Classification: HYDROLASE/DNA
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.30 Å
• R-Value Free: 
  0.229 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1016/s1097-2765(03)00235-1
• Primary Citation Related Structures: 
  1OE4, 1OE5, 1OE6


• 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.

Biological Assembly 1  

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: 63.92 kDa 
• Atom Count: 4,657 
• Modeled Residue Count: 514 
• Deposited Residue Count: 519 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

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

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

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	H [auth A], J [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
DUR	K [auth F]	2'-DEOXYURIDINE C9 H12 N2 O5 MXHRCPNRJAMMIM-SHYZEUOFSA-N
URA	E [auth A]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA	G [auth A], I [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.229 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.596	α = 90
b = 85.653	β = 118.56
c = 78.467	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description