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PDBsum entry 2oxm

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protein dna_rna links
Hydrolase/DNA PDB id
2oxm
Jmol
Contents
Protein chain
223 a.a. *
DNA/RNA
Waters ×107
* Residue conservation analysis
PDB id:
2oxm
Name: Hydrolase/DNA
Title: Crystal structure of a ung2/modified DNA complex that represent a stabilized short-lived extrahelical state in ezymatic DNA base flipping
Structure: Uracil-DNA glycosylase. Chain: a. Engineered: yes. DNA (5'-d( Tp Gp Tp Tp Ap Tp Cp Tp T)-3'). Chain: b. Synonym: udg. Engineered: yes. DNA (5'-d( Ap Ap Ap Gp Ap Tp (4Mf)p Ap Cp A)-3'). Chain: c.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ung, dgu, ung1, ung15. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetically made. Other_details: synthetically made
Resolution:
2.50Å     R-factor:   0.257     R-free:   0.328
Authors: M.A.Bianchet,D.J.Krosky,Stivers J.T.,L.M.Amzel
Key ref:
J.B.Parker et al. (2007). Enzymatic capture of an extrahelical thymine in the search for uracil in DNA. Nature, 449, 433-437. PubMed id: 17704764 DOI: 10.1038/nature06131
Date:
20-Feb-07     Release date:   30-Oct-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P13051  (UNG_HUMAN) -  Uracil-DNA glycosylase
Seq:
Struc:
313 a.a.
223 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.2.27  - Uracil-DNA glycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   2 terms 
  Biochemical function     hydrolase activity, hydrolyzing N-glycosyl compounds     2 terms  

 

 
DOI no: 10.1038/nature06131 Nature 449:433-437 (2007)
PubMed id: 17704764  
 
 
Enzymatic capture of an extrahelical thymine in the search for uracil in DNA.
J.B.Parker, M.A.Bianchet, D.J.Krosky, J.I.Friedman, L.M.Amzel, J.T.Stivers.
 
  ABSTRACT  
 
The enzyme uracil DNA glycosylase (UNG) excises unwanted uracil bases in the genome using an extrahelical base recognition mechanism. Efficient removal of uracil is essential for prevention of C-to-T transition mutations arising from cytosine deamination, cytotoxic U*A pairs arising from incorporation of dUTP in DNA, and for increasing immunoglobulin gene diversity during the acquired immune response. A central event in all of these UNG-mediated processes is the singling out of rare U*A or U*G base pairs in a background of approximately 10(9) T*A or C*G base pairs in the human genome. Here we establish for the human and Escherichia coli enzymes that discrimination of thymine and uracil is initiated by thermally induced opening of T*A and U*A base pairs and not by active participation of the enzyme. Thus, base-pair dynamics has a critical role in the genome-wide search for uracil, and may be involved in initial damage recognition by other DNA repair glycosylases.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Extrahelical uracil recognition by UNG and reaction coordinate tuning. Uracil emerges from the DNA base stack (reactant or R state) by spontaneous U circle A base-pair breathing, where it is then trapped by UNG as an unstable early intermediate state (EI) on the base-flipping reaction coordinate. EI is very unstable (high energy), compared to the low-energy intrahelical bound state for a T circle A or U circle A base pair or the fully-flipped (FF) state^8, ^9. Substitution of adenine with its nonpolar analogue, 4-methylindole (M), energetically destabilizes the intrahelical R' state. Substitution of uracil with 5-methyluracil (5-MeU or thymine, T) greatly destabilizes the FF' state because the bulkier T fits poorly into the uracil active site, but T can access the EI' state^8, ^9. The energetic effects of reaction coordinate tuning on base flipping are shown by the vertical arrows. Destabilization of the R and FF states allows population of the otherwise unstable EI intermediate, allowing its structural characterization by X-ray crystallography. The free energy levels that are depicted in this figure are exaggerated for clarity of exposition.
Figure 3.
Figure 3: Conformational changes in the sugar and base along the flipping reaction coordinate.
Figure 3 : Conformational changes in the sugar and base along the flipping reaction coordinate. Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com-
In the first step of the reaction to form EI, the sugar plane rotates about an apparent angle of 30°, and the base rotates 180° around the glycosidic bond and moves about 4.4 Å relative to the B-DNA reactant state (R, blue). In the second step (EI arrow FF), the sugar plane and base rotate a further 120° and 90°, respectively. Note that the structure of the FF state was obtained using the C-glycoside analogue of deoxyuridine, pseudodeoxyuridine. Changes in the DNA backbone torsional angles that accompany these transformations are listed in the figure.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 449, 433-437) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22659876 C.Yi, B.Chen, B.Qi, W.Zhang, G.Jia, L.Zhang, C.J.Li, A.R.Dinner, C.G.Yang, and C.He (2012).
Duplex interrogation by a direct DNA repair protein in search of base damage.
  Nat Struct Mol Biol, 19, 671-676.
PDB codes: 3rzg 3rzh 3rzj 3rzk 3rzl 3rzm 3s57 3s5a
20876689 E.Fadda, and R.Pomès (2011).
On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics.
  Nucleic Acids Res, 39, 767-780.  
21036872 M.I.Ponferrada-Marín, J.T.Parrilla-Doblas, T.Roldán-Arjona, and R.R.Ariza (2011).
A discontinuous DNA glycosylase domain in a family of enzymes that excise 5-methylcytosine.
  Nucleic Acids Res, 39, 1473-1484.  
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.  
20118965 G.M.Li (2010).
Novel molecular insights into the mechanism of GO removal by MutM.
  Cell Res, 20, 116-118.  
20151717 M.N.Kinde-Carson, C.Ferguson, N.A.Oyler, G.S.Harbison, and G.A.Meints (2010).
Solid state 2H NMR analysis of furanose ring dynamics in DNA containing uracil.
  J Phys Chem B, 114, 3285-3293.  
20097063 R.P.Rambo, and J.A.Tainer (2010).
Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering.
  Curr Opin Struct Biol, 20, 128-137.  
19889642 Y.Qi, M.C.Spong, K.Nam, M.Karplus, and G.L.Verdine (2010).
Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.
  J Biol Chem, 285, 1468-1478.
PDB codes: 3jr4 3jr5
19720997 A.K.Boal, J.C.Genereux, P.A.Sontz, J.A.Gralnick, D.K.Newman, and J.K.Barton (2009).
Redox signaling between DNA repair proteins for efficient lesion detection.
  Proc Natl Acad Sci U S A, 106, 15237-15242.  
19880517 A.Maiti, M.T.Morgan, and A.C.Drohat (2009).
Role of two strictly conserved residues in nucleotide flipping and N-glycosylic bond cleavage by human thymine DNA glycosylase.
  J Biol Chem, 284, 36680-36688.  
19145606 C.G.Yang, K.Garcia, and C.He (2009).
Damage detection and base flipping in direct DNA alkylation repair.
  Chembiochem, 10, 417-423.  
19805252 C.J.Burrows, and A.M.Fleming (2009).
Finding needles in DNA stacks.
  Proc Natl Acad Sci U S A, 106, 16010-16011.  
  19077538 H.Hashimoto, J.R.Horton, X.Zhang, and X.Cheng (2009).
UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
  Epigenetics, 4, 8.
PDB codes: 3f8i 3f8j 3fde
19339520 J.I.Friedman, A.Majumdar, and J.T.Stivers (2009).
Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage.
  Nucleic Acids Res, 37, 3493-3500.  
19772348 K.L.Brown, A.K.Basu, and M.P.Stone (2009).
The cis-(5R,6S)-thymine glycol lesion occupies the wobble position when mismatched with deoxyguanosine in DNA.
  Biochemistry, 48, 9722-9733.
PDB codes: 2kh7 2kh8
18976666 L.A.Schroeder, T.J.Gries, R.M.Saecker, M.T.Record, M.E.Harris, and P.L.DeHaseth (2009).
Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA.
  J Mol Biol, 385, 339-349.  
19681599 L.Jia, K.Kropachev, S.Ding, B.Van Houten, N.E.Geacintov, and S.Broyde (2009).
Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB.
  Biochemistry, 48, 8948-8957.  
19200715 S.Schneider, S.Schorr, and T.Carell (2009).
Crystal structure analysis of DNA lesion repair and tolerance mechanisms.
  Curr Opin Struct Biol, 19, 87-95.  
20010681 Y.Qi, M.C.Spong, K.Nam, A.Banerjee, S.Jiralerspong, M.Karplus, and G.L.Verdine (2009).
Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.
  Nature, 462, 762-766.
PDB codes: 3go8 3gp1 3gpp 3gpu 3gpx 3gpy 3gq3 3gq4 3gq5
18432238 C.G.Yang, C.Yi, E.M.Duguid, C.T.Sullivan, X.Jian, P.A.Rice, and C.He (2008).
Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
  Nature, 452, 961-965.
PDB codes: 3bi3 3bie 3bkz 3btx 3bty 3btz 3bu0 3buc
18820295 G.Tamulaitis, M.Zaremba, R.H.Szczepanowski, M.Bochtler, and V.Siksnys (2008).
How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets.
  Nucleic Acids Res, 36, 6101-6108.  
19053196 H.Ding, A.Majumdar, J.R.Tolman, and M.M.Greenberg (2008).
Multinuclear NMR and kinetic analysis of DNA interstrand cross-link formation.
  J Am Chem Soc, 130, 17981-17987.  
18772888 H.Hashimoto, J.R.Horton, X.Zhang, M.Bostick, S.E.Jacobsen, and X.Cheng (2008).
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
  Nature, 455, 826-829.
PDB codes: 2zo0 2zo1 2zo2
18854319 I.Tessmer, Y.Yang, J.Zhai, C.Du, P.Hsieh, M.M.Hingorani, and D.A.Erie (2008).
Mechanism of MutS searching for DNA mismatches and signaling repair.
  J Biol Chem, 283, 36646-36654.  
18652484 J.B.Parker, and J.T.Stivers (2008).
Uracil DNA glycosylase: revisiting substrate-assisted catalysis by DNA phosphate anions.
  Biochemistry, 47, 8614-8622.  
18353991 J.Hu, A.Ma, and A.R.Dinner (2008).
A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT.
  Proc Natl Acad Sci U S A, 105, 4615-4620.  
18362349 K.D.Goodwin, M.A.Lewis, E.C.Long, and M.M.Georgiadis (2008).
Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding.
  Proc Natl Acad Sci U S A, 105, 5052-5056.
PDB codes: 2r2r 2r2s 2r2t 2r2u
18166975 M.L.Hegde, T.K.Hazra, and S.Mitra (2008).
Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells.
  Cell Res, 18, 27-47.  
18208817 P.Liu, J.A.Theruvathu, A.Darwanto, V.V.Lao, T.Pascal, W.Goddard, and L.C.Sowers (2008).
Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylase.
  J Biol Chem, 283, 8829-8836.  
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.  
18453630 R.Pfoh, H.Laatsch, and G.M.Sheldrick (2008).
Crystal structure of trioxacarcin A covalently bound to DNA.
  Nucleic Acids Res, 36, 3508-3514.
PDB code: 3c2j
18157156 W.Yang (2008).
Structure and mechanism for DNA lesion recognition.
  Cell Res, 18, 184-197.  
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 codes are shown on the right.