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PDBsum entry 2f5q

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protein dna_rna metals links
Hydrolase/DNA PDB id
2f5q
Jmol
Contents
Protein chain
273 a.a. *
DNA/RNA
Metals
_ZN
Waters ×35
* Residue conservation analysis
PDB id:
2f5q
Name: Hydrolase/DNA
Title: Catalytically inactive (e3q) mutm crosslinked to oxog:c containing DNA cc2
Structure: 5'- d( Ap Gp G Tp Ap Gp Ap Cp Cp Tp Gp Gp Ap Cp Gp C)-3'. Chain: b. Engineered: yes. 5'-d( Tp Gp Cp G Tp Cp Cp Ap (8Og) p Gp Tp Cp Tp Ap Cp C)-3'. Chain: c. Engineered: yes. Formamidopyrimidine-DNA glycosidase.
Source: Synthetic: yes. Other_details: synthetic DNA. Other_details: synthetic DNA containing a backbone modification. Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
2.35Å     R-factor:   0.213     R-free:   0.249
Authors: A.Banerjee,W.L.Santos,G.L.Verdine
Key ref:
A.Banerjee et al. (2006). Structure of a DNA glycosylase searching for lesions. Science, 311, 1153-1157. PubMed id: 16497933 DOI: 10.1126/science.1120288
Date:
26-Nov-05     Release date:   07-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P84131  (P84131_GEOSE) -  Formamidopyrimidine-DNA glycosylase
Seq:
Struc:
274 a.a.
273 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     12 terms  

 

 
DOI no: 10.1126/science.1120288 Science 311:1153-1157 (2006)
PubMed id: 16497933  
 
 
Structure of a DNA glycosylase searching for lesions.
A.Banerjee, W.L.Santos, G.L.Verdine.
 
  ABSTRACT  
 
DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA helix while searching for damage.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Schematic representation of MutM-DNA complexes. (A) The MutM LRC used as the basis for the design of the cross-linking system. (B to D) Interrogation complexes showing the positioning of MutM over the DNA duplex, with the target base pair in aqua. The side chain of the helix-probe residue Phe^114 is indicated. The numbering system for the base pairs and backbone phosphates is as indicated. The curved green line denotes the thiol-bearing tether engaged in a cross-link to Cys166. Each blue box indicates the site of tether attachment to DNA, the position of the target base pair, and the separation between them, here referred to as the register. Dashed blue lines indicate the lack of order in the oxoG recognition loop. (E and F) Overall view of complexes CC1 (E) and IC1 (F). CC1 is a lesion recognition complex (LRC) formed by disulfide cross-linking between MutM and oxoG-containing DNA. IC1 is the corresponding interrogation complex having MutM cross-linked to non-lesion-containing DNA. Blue box denotes the target base pair, which is disrupted in (E) and intact but buckled in (F).
Figure 4.
Fig. 4. Direct and water-mediated interactions between MutM and the DNA backbone in the control LRC CC2 (A) and interrogation complexes IC1 (B) and IC2 (C). Dashed lines indicate hydrogen bonding interactions among backbone phosphates in DNA, ordered waters (red spheres), and residues in MutM. The side chains of amino acid residues are shown in green with the numbers colored according to which moiety on the amino acid is involved in the contact: green, side chain; blue, backbone amide NH; red, backbone amide carbonyl; gray, no contact in that particular complex.
 
  The above figures are reprinted by permission from the AAAs: Science (2006, 311, 1153-1157) copyright 2006.  
  Figures were selected by an automated process.  

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
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
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.  
20927102 E.H.Rubinson, A.S.Gowda, T.E.Spratt, B.Gold, and B.F.Eichman (2010).
An unprecedented nucleic acid capture mechanism for excision of DNA damage.
  Nature, 468, 406-411.
PDB codes: 3jx7 3jxy 3jxz 3jy1
20540060 M.Winnacker, V.Welzmiller, R.Strasser, and T.Carell (2010).
Development of a DNA photoaffinity probe for the analysis of 8-OxodG-binding proteins in a human proteome.
  Chembiochem, 11, 1345-1349.  
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
19145606 C.G.Yang, K.Garcia, and C.He (2009).
Damage detection and base flipping in direct DNA alkylation repair.
  Chembiochem, 10, 417-423.  
19852088 C.Yi, C.G.Yang, and C.He (2009).
A non-heme iron-mediated chemical demethylation in DNA and RNA.
  Acc Chem Res, 42, 519-529.  
19522502 G.M.Clore, and J.Iwahara (2009).
Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.
  Chem Rev, 109, 4108-4139.  
18978813 K.A.Malecka, W.C.Ho, and R.Marmorstein (2009).
Crystal structure of a p53 core tetramer bound to DNA.
  Oncogene, 28, 325-333.
PDB codes: 3exj 3exl
19961158 K.Nam, G.L.Verdine, and M.Karplus (2009).
Analysis of an anomalous mutant of MutM DNA glycosylase leads to new insights into the catalytic mechanism.
  J Am Chem Soc, 131, 18208-18209.  
18802931 K.S.Sandhu (2009).
Intrinsic disorder explains diverse nuclear roles of chromatin remodeling proteins.
  J Mol Recognit, 22, 1-8.  
19012292 M.Winnacker, S.Breeger, R.Strasser, and T.Carell (2009).
Novel diazirine-containing DNA photoaffinity probes for the investigation of DNA-protein-interactions.
  Chembiochem, 10, 109-118.  
19898474 P.C.Blainey, G.Luo, S.C.Kou, W.F.Mangel, G.L.Verdine, B.Bagchi, and X.S.Xie (2009).
Nonspecifically bound proteins spin while diffusing along DNA.
  Nat Struct Mol Biol, 16, 1224-1229.  
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.  
20183575 X.Hou, G.Wang, B.L.Gaffney, and R.A.Jones (2009).
Synthesis of guanosine and deoxyguanosine phosphoramidites with cross-linkable thioalkyl tethers for direct incorporation into RNA and DNA.
  Nucleosides Nucleotides Nucleic Acids, 28, 1076-1094.  
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
18682218 B.R.Bowman, S.Lee, S.Wang, and G.L.Verdine (2008).
Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA.
  Structure, 16, 1166-1174.
PDB codes: 3cvs 3cvt 3cw7 3cwa 3cws 3cwt 3cwu
18172202 C.A.Minetti, D.P.Remeta, and K.J.Breslauer (2008).
A continuous hyperchromicity assay to characterize the kinetics and thermodynamics of DNA lesion recognition and base excision.
  Proc Natl Acad Sci U S A, 105, 70-75.  
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
18682223 G.Komazin-Meredith, R.J.Petrella, W.L.Santos, D.J.Filman, J.M.Hogle, G.L.Verdine, M.Karplus, and D.M.Coen (2008).
The human cytomegalovirus UL44 C clamp wraps around DNA.
  Structure, 16, 1214-1225.  
18178550 G.Komazin-Meredith, W.L.Santos, D.J.Filman, J.M.Hogle, G.L.Verdine, and D.M.Coen (2008).
The positively charged surface of herpes simplex virus UL42 mediates DNA binding.
  J Biol Chem, 283, 6154-6161.  
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.  
18072751 J.C.Delaney, and J.M.Essigmann (2008).
Biological properties of single chemical-DNA adducts: a twenty year perspective.
  Chem Res Toxicol, 21, 232-252.  
18557781 V.S.Sidorenko, G.V.Mechetin, G.A.Nevinsky, and D.O.Zharkov (2008).
Ionic strength and magnesium affect the specificity of Escherichia coli and human 8-oxoguanine-DNA glycosylases.
  FEBS J, 275, 3747-3760.  
17410210 A.H.Metz, T.Hollis, and B.F.Eichman (2007).
DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
  EMBO J, 26, 2411-2420.
PDB codes: 2ofi 2ofk
17617640 G.Tamulaitis, M.Zaremba, R.H.Szczepanowski, M.Bochtler, and V.Siksnys (2007).
Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.
  Nucleic Acids Res, 35, 4792-4799.  
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
17637338 J.E.Corn, and J.M.Berger (2007).
FASTDXL: a generalized screen to trap disulfide-stabilized complexes for use in structural studies.
  Structure, 15, 773-780.  
17531815 J.J.Warren, T.J.Pohlhaus, A.Changela, R.R.Iyer, P.L.Modrich, and L.S.Beese (2007).
Structure of the human MutSalpha DNA lesion recognition complex.
  Mol Cell, 26, 579-592.
PDB codes: 2o8b 2o8c 2o8d 2o8e 2o8f
17432829 L.Jia, V.Shafirovich, N.E.Geacintov, and S.Broyde (2007).
Lesion specificity in the base excision repair enzyme hNeil1: modeling and dynamics studies.
  Biochemistry, 46, 5305-5314.  
17655276 N.Krishnamurthy, J.G.Muller, C.J.Burrows, and S.S.David (2007).
Unusual structural features of hydantoin lesions translate into efficient recognition by Escherichia coli Fpg.
  Biochemistry, 46, 9355-9365.  
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.  
17581577 S.S.David, V.L.O'Shea, and S.Kundu (2007).
Base-excision repair of oxidative DNA damage.
  Nature, 447, 941-950.  
17194756 V.C.Pierre, J.T.Kaiser, and J.K.Barton (2007).
Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator.
  Proc Natl Acad Sci U S A, 104, 429-434.
PDB code: 2o1i
17015827 A.Banerjee, and G.L.Verdine (2006).
A nucleobase lesion remodels the interaction of its normal neighbor in a DNA glycosylase complex.
  Proc Natl Acad Sci U S A, 103, 15020-15025.
PDB code: 2i5w
17017766 C.Cao, Y.L.Jiang, D.J.Krosky, and J.T.Stivers (2006).
The catalytic power of uracil DNA glycosylase in the opening of thymine base pairs.
  J Am Chem Soc, 128, 13034-13035.  
16888824 H.A.Wagenknecht (2006).
The search for single DNA damage among millions of base pairs: DNA glycosylases trapped at work.
  Angew Chem Int Ed Engl, 45, 5583-5585.  
17008406 J.Iwahara, M.Zweckstetter, and G.M.Clore (2006).
NMR structural and kinetic characterization of a homeodomain diffusing and hopping on nonspecific DNA.
  Proc Natl Acad Sci U S A, 103, 15062-15067.  
16585517 P.C.Blainey, A.M.van Oijen, A.Banerjee, G.L.Verdine, and X.S.Xie (2006).
A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA.
  Proc Natl Acad Sci U S A, 103, 5752-5757.  
17115714 R.K.Walker, A.K.McCullough, and R.S.Lloyd (2006).
Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase.
  Biochemistry, 45, 14192-14200.  
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.