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PDBsum entry 2eug
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Hydrolase PDB id
2eug

 

 

 

 

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Contents
Protein chain
225 a.a. *
Ligands
URA
Waters ×277
* Residue conservation analysis
PDB id:
2eug
Name: Hydrolase
Title: Crystal structure of escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited
Structure: Protein (glycosylase). Chain: a. Synonym: udg, ung. Engineered: yes. Mutation: yes. Other_details: the protein is complexed with uracil
Source: Escherichia coli. Organism_taxid: 37762. Strain: b. Gene: ung. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: sigma chemical
Resolution:
1.50Å     R-factor:   0.197    
Authors: G.Xiao,M.Tordova,J.Jagadeesh,A.C.Drohat,J.T.Stivers,G.L.Gilliland
Key ref:
G.Xiao et al. (1999). Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited. Proteins, 35, 13-24. PubMed id: 10090282 DOI: 10.1002/(SICI)1097-0134(19990401)35:1<13::AID-PROT2>3.3.CO;2-U
Date:
13-Oct-98     Release date:   13-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P12295  (UNG_ECOLI) -  Uracil-DNA glycosylase from Escherichia coli (strain K12)
Seq:
Struc: 		229 a.a.
225 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.2.27  - uracil-DNA glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1002/(SICI)1097-0134(19990401)35:1<13::AID-PROT2>3.3.CO;2-U Proteins 35:13-24 (1999)
PubMed id: 10090282  
 
 
Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited.
G.Xiao, M.Tordova, J.Jagadeesh, A.C.Drohat, J.T.Stivers, G.L.Gilliland.
 
  ABSTRACT  
 
The DNA repair enzyme uracil DNA glycosylase (UDG) catalyzes the hydrolysis of premutagenic uracil residues from single-stranded or duplex DNA, producing free uracil and abasic DNA. Here we report the high-resolution crystal structures of free UDG from Escherichia coli strain B (1.60 A), its complex with uracil (1.50 A), and a second active-site complex with glycerol (1.43 A). These represent the first high-resolution structures of a prokaryotic UDG to be reported. The overall structure of the E. coli enzyme is more similar to the human UDG than the herpes virus enzyme. Significant differences between the bacterial and viral structures are seen in the side-chain positions of the putative general-acid (His187) and base (Asp64), similar to differences previously observed between the viral and human enzymes. In general, the active-site loop that contains His187 appears preorganized in comparison with the viral and human enzymes, requiring smaller substrate-induced conformational changes to bring active-site groups into catalytic position. These structural differences may be related to the large differences in the mechanism of uracil recognition used by the E. coli and viral enzymes. The pH dependence of k(cat) for wild-type UDG and the D64N and H187Q mutant enzymes is consistent with general-base catalysis by Asp64, but provides no evidence for a general-acid catalyst. The catalytic mechanism of UDG is critically discussed with respect to these results.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Hypothetical oxycarbenium-ion transition-state for glycosidic bond hydrolysis in DNA. 		Figure 8.
Figure 8. Pyrrolidine-based transition-state analog for DNA glycosylases.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (1999, 35, 13-24) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
19909758 D.O.Zharkov, G.V.Mechetin, and G.A.Nevinsky (2010).
Uracil-DNA glycosylase: Structural, thermodynamic and kinetic aspects of lesion search and recognition.
  Mutat Res, 685, 11-20.  
19933279 H.A.Cole, J.M.Tabor-Godwin, and J.J.Hayes (2010).
Uracil DNA glycosylase activity on nucleosomal DNA depends on rotational orientation of targets.
  J Biol Chem, 285, 2876-2885.  
18453691 P.S.Kaushal, R.K.Talawar, P.D.Krishna, U.Varshney, and M.Vijayan (2008).
Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources.
  Acta Crystallogr D Biol Crystallogr, 64, 551-560.
PDB code: 2zhx
18669665 R.H.Porecha, and J.T.Stivers (2008).
Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils.
  Proc Natl Acad Sci U S A, 105, 10791-10796.  
17108049 C.C.Lu, H.T.Huang, J.T.Wang, G.Slupphaug, T.K.Li, M.C.Wu, Y.C.Chen, C.P.Lee, and M.R.Chen (2007).
Characterization of the uracil-DNA glycosylase activity of Epstein-Barr virus BKRF3 and its role in lytic viral DNA replication.
  J Virol, 81, 1195-1208.  
17704764 J.B.Parker, M.A.Bianchet, D.J.Krosky, J.I.Friedman, L.M.Amzel, and J.T.Stivers (2007).
Enzymatic capture of an extrahelical thymine in the search for uracil in DNA.
  Nature, 449, 433-437.
PDB codes: 2oxm 2oyt
17605817 N.Schormann, A.Grigorian, A.Samal, R.Krishnan, L.DeLucas, and D.Chattopadhyay (2007).
Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly.
  BMC Struct Biol, 7, 45.
PDB codes: 2owq 2owr
17284454 S.R.Bellamy, K.Krusong, and G.S.Baldwin (2007).
A rapid reaction analysis of uracil DNA glycosylase indicates an active mechanism of base flipping.
  Nucleic Acids Res, 35, 1478-1487.  
16306042 K.Krusong, E.P.Carpenter, S.R.Bellamy, R.Savva, and G.S.Baldwin (2006).
A comparative study of uracil-DNA glycosylases from human and herpes simplex virus type 1.
  J Biol Chem, 281, 4983-4992.
PDB codes: 2c53 2c56
16041069 I.Leiros, E.Moe, A.O.Smalås, and S.McSweeney (2005).
Structure of the uracil-DNA N-glycosylase (UNG) from Deinococcus radiodurans.
  Acta Crystallogr D Biol Crystallogr, 61, 1049-1056.
PDB code: 2boo
14990576 H.J.Lee, H.M.Lim, and S.Adhya (2004).
An unsubstituted C2 hydrogen of adenine is critical and sufficient at the -11 position of a promoter to signal base pair deformation.
  J Biol Chem, 279, 16899-16902.  
12876336 I.Leiros, E.Moe, O.Lanes, A.O.Smalås, and N.P.Willassen (2003).
The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features.
  Acta Crystallogr D Biol Crystallogr, 59, 1357-1365.
PDB code: 1okb
14654697 N.Acharya, R.K.Talawar, K.Saikrishnan, M.Vijayan, and U.Varshney (2003).
Substitutions at tyrosine 66 of Escherichia coli uracil DNA glycosylase lead to characterization of an efficient enzyme that is recalcitrant to product inhibition.
  Nucleic Acids Res, 31, 7216-7226.  
11907039 I.Wong, A.J.Lundquist, A.S.Bernards, and D.W.Mosbaugh (2002).
Presteady-state analysis of a single catalytic turnover by Escherichia coli uracil-DNA glycosylase reveals a "pinch-pull-push" mechanism.
  J Biol Chem, 277, 19424-19432.  
12136137 K.Saikrishnan, M.Bidya Sagar, R.Ravishankar, S.Roy, K.Purnapatre, P.Handa, U.Varshney, and M.Vijayan (2002).
Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG.
  Acta Crystallogr D Biol Crystallogr, 58, 1269-1276.
PDB codes: 1lqg 1lqj 1lqm 1lqn
11859082 Y.L.Jiang, A.C.Drohat, Y.Ichikawa, and J.T.Stivers (2002).
Probing the limits of electrostatic catalysis by uracil DNA glycosylase using transition state mimicry and mutagenesis.
  J Biol Chem, 277, 15385-15392.  
12220189 Y.L.Jiang, and J.T.Stivers (2002).
Mutational analysis of the base-flipping mechanism of uracil DNA glycosylase.
  Biochemistry, 41, 11236-11247.  
11555290 S.K.Mokkapati, A.R.Fernández de Henestrosa, and A.S.Bhagwat (2001).
Escherichia coli DNA glycosylase Mug: a growth-regulated enzyme required for mutation avoidance in stationary-phase cells.
  Mol Microbiol, 41, 1101-1111.  
11551943 Y.L.Jiang, K.Kwon, and J.T.Stivers (2001).
Turning On uracil-DNA glycosylase using a pyrene nucleotide switch.
  J Biol Chem, 276, 42347-42354.  
11009598 A.C.Drohat, and J.T.Stivers (2000).
Escherichia coli uracil DNA glycosylase: NMR characterization of the short hydrogen bond from His187 to uracil O2.
  Biochemistry, 39, 11865-11875.  
11052677 J.Dong, A.C.Drohat, J.T.Stivers, K.W.Pankiewicz, and P.R.Carey (2000).
Raman spectroscopy of uracil DNA glycosylase-DNA complexes: insights into DNA damage recognition and catalysis.
  Biochemistry, 39, 13241-13250.  
10818343 J.E.Ladner, P.Reddy, A.Davis, M.Tordova, A.J.Howard, and G.L.Gilliland (2000).
The 1.30 A resolution structure of the Bacillus subtilis chorismate mutase catalytic homotrimer.
  Acta Crystallogr D Biol Crystallogr, 56, 673-683.
PDB code: 1dbf
11087352 R.M.Werner, and J.T.Stivers (2000).
Kinetic isotope effect studies of the reaction catalyzed by uracil DNA glycosylase: evidence for an oxocarbenium ion-uracil anion intermediate.
  Biochemistry, 39, 14054-14064.  
11027138 R.M.Werner, Y.L.Jiang, R.G.Gordley, G.J.Jagadeesh, J.E.Ladner, G.Xiao, M.Tordova, G.L.Gilliland, and J.T.Stivers (2000).
Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase.
  Biochemistry, 39, 12585-12594.
PDB code: 1flz
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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