spacer
spacer

PDBsum entry 1yfh

Go to PDB code: 
protein dna_rna metals Protein-protein interface(s) links
Transferase/DNA PDB id
1yfh
Jmol
Contents
Protein chains
165 a.a. *
149 a.a. *
DNA/RNA
Metals
_ZN ×3
Waters ×6
* Residue conservation analysis
PDB id:
1yfh
Name: Transferase/DNA
Title: Wt human o6-alkylguanine-DNA alkyltransferase bound to DNA containing an alkylated cytosine
Structure: 5'-d( Gp Tp Gp Gp Ap Tp Gp (Xcy) p Gp Tp Gp Tp Ap Gp Gp T)-3'. Chain: d, f. Engineered: yes. 5'- d( Cp Cp Tp Ap Cp Ap Cp Ap Cp Ap Tp Cp Cp Ap Cp A)-3'. Chain: e, g. Engineered: yes. Methylated-DNA--protein-cysteine
Source: Synthetic: yes. Other_details: oligonucleotide synthesized by automated phosphoramidite technique containing unatural base. Phosphoramidite technique. Homo sapiens. Human. Organism_taxid: 9606. Gene: mgmt. Expressed in: escherichia coli bl21.
Biol. unit: Trimer (from PQS)
Resolution:
3.01Å     R-factor:   0.246     R-free:   0.286
Authors: E.M.Duguid,P.A.Rice,C.He
Key ref:
E.M.Duguid et al. (2005). The structure of the human AGT protein bound to DNA and its implications for damage detection. J Mol Biol, 350, 657-666. PubMed id: 15964013 DOI: 10.1016/j.jmb.2005.05.028
Date:
31-Dec-04     Release date:   13-Dec-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P16455  (MGMT_HUMAN) -  Methylated-DNA--protein-cysteine methyltransferase
Seq:
Struc:
207 a.a.
165 a.a.
Protein chain
Pfam   ArchSchema ?
P16455  (MGMT_HUMAN) -  Methylated-DNA--protein-cysteine methyltransferase
Seq:
Struc:
207 a.a.
149 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.2.1.1.63  - Methylated-DNA--[protein]-cysteine S-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA (containing 6-O-methylguanine) + protein L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine
DNA (containing 6-O-methylguanine)
+ protein L-cysteine
= DNA (without 6-O-methylguanine)
+ protein S-methyl-L-cysteine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2005.05.028 J Mol Biol 350:657-666 (2005)
PubMed id: 15964013  
 
 
The structure of the human AGT protein bound to DNA and its implications for damage detection.
E.M.Duguid, P.A.Rice, C.He.
 
  ABSTRACT  
 
O6-Alklyguanine-DNA alkyltransferase (AGT) is an important DNA repair protein that protects cells from mutagenesis and toxicity arising from alkylating agents. We present an X-ray crystal structure of the wild-type human protein (hAGT) bound to double-stranded DNA with a chemically modified cytosine base. The protein binds at two different sites: one at the modified base, and the other across a sticky-ended DNA junction. The protein molecule that binds the modified cytosine base flips the base and recognizes it in its active site. The one that binds ends of neighboring DNA molecules partially flips an overhanging thymine base. This base is not inserted into the active-site pocket of the protein. These two different hAGT/DNA interactions observed in the structure suggest that hAGT may not detect DNA lesions by searching for the adduct itself, but rather for weakened and/or distorted base-pairs caused by base damage in the duplex DNA. We propose that hAGT imposes a strain on the DNA duplex and searches for DNA regions where the native structure is destabilized. The structure provides implications for pyrimidine recognition, improved inhibitor design, and a possible protein/protein interaction patch on hAGT.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Comparison of the overall protein/DNA interactions between (a) hAGT-A and (b) hAGT-B.
Figure 5.
Figure 5. Protein/DNA interactions observed in two hAGT monomers. (a) Recognition of C^# by hAGT-A. Tyr114 forms a strong hydrogen bond (2.5 Å) with the O2 atom of the base. Cys145 is in an in-line position to attack the carbon atom linked to the N4 atom of C^#. (b) The overhang base thymine is partially inserted into hAGT-B (compare the relative position of the base with C^# in hAGT-A). Tyr114 is within hydrogen bonding distance to T. (c) The protein makes three major contacts to the DNA (hAGT-A is shown here). The second helix (H6) of the HTH is buried in the DNA minor groove.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 350, 657-666) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20714665 F.P.McManus, Q.Fang, J.D.Booth, A.M.Noronha, A.E.Pegg, and C.J.Wilds (2010).
Synthesis and characterization of an O(6)-2'-deoxyguanosine-alkyl-O(6)-2'-deoxyguanosine interstrand cross-link in a 5'-GNC motif and repair by human O(6)-alkylguanine-DNA alkyltransferase.
  Org Biomol Chem, 8, 4414-4426.  
20502938 J.L.Tubbs, and J.A.Tainer (2010).
Alkyltransferase-like proteins: molecular switches between DNA repair pathways.
  Cell Mol Life Sci, 67, 3749-3762.  
20026607 Q.Fang, S.Kanugula, J.L.Tubbs, J.A.Tainer, and A.E.Pegg (2010).
Repair of O4-alkylthymine by O6-alkylguanine-DNA alkyltransferases.
  J Biol Chem, 285, 8185-8195.  
19472322 A.G.Kalapila, N.A.Loktionova, and A.E.Pegg (2009).
Effect of O6-alkylguanine-DNA alkyltransferase on genotoxicity of epihalohydrins.
  Environ Mol Mutagen, 50, 502-514.  
19358853 C.A.Adams, M.Melikishvili, D.W.Rodgers, J.J.Rasimas, A.E.Pegg, and M.G.Fried (2009).
Topologies of complexes containing O6-alkylguanine-DNA alkyltransferase and DNA.
  J Mol Biol, 389, 248-263.  
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.  
19516334 J.L.Tubbs, V.Latypov, S.Kanugula, A.Butt, M.Melikishvili, R.Kraehenbuehl, O.Fleck, A.Marriott, A.J.Watson, B.Verbeek, G.McGown, M.Thorncroft, M.F.Santibanez-Koref, C.Millington, A.S.Arvai, M.D.Kroeger, L.A.Peterson, D.M.Williams, M.G.Fried, G.P.Margison, A.E.Pegg, and J.A.Tainer (2009).
Flipping of alkylated DNA damage bridges base and nucleotide excision repair.
  Nature, 459, 808-813.
PDB codes: 3gva 3gx4 3gyh
19531487 R.Guza, L.Ma, Q.Fang, A.E.Pegg, and N.Tretyakova (2009).
Cytosine methylation effects on the repair of O6-methylguanines within CG dinucleotides.
  J Biol Chem, 284, 22601-22610.  
19254550 Y.Lin, T.Zhao, X.Jian, Z.Farooqui, X.Qu, C.He, A.R.Dinner, and N.F.Scherer (2009).
Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA.
  Biophys J, 96, 1911-1917.  
19635647 Y.Zhu, J.Hu, Y.Hu, and W.Liu (2009).
Targeting DNA repair pathways: a novel approach to reduce cancer therapeutic resistance.
  Cancer Treat Rev, 35, 590-596.  
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.  
19061338 M.Melikishvili, J.J.Rasimas, A.E.Pegg, and M.G.Fried (2008).
Interactions of human O(6)-alkylguanine-DNA alkyltransferase (AGT) with short double-stranded DNAs.
  Biochemistry, 47, 13754-13763.  
18803403 Q.Fang, A.M.Noronha, S.P.Murphy, C.J.Wilds, J.L.Tubbs, J.A.Tainer, G.Chowdhury, F.P.Guengerich, and A.E.Pegg (2008).
Repair of O6-G-alkyl-O6-G interstrand cross-links by human O6-alkylguanine-DNA alkyltransferase.
  Biochemistry, 47, 10892-10903.  
17482892 A.E.Pegg, Q.Fang, and N.A.Loktionova (2007).
Human variants of O6-alkylguanine-DNA alkyltransferase.
  DNA Repair (Amst), 6, 1071-1078.  
17138560 J.J.Rasimas, S.R.Kar, A.E.Pegg, and M.G.Fried (2007).
Interactions of human O6-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs.
  J Biol Chem, 282, 3357-3366.  
17485252 J.L.Tubbs, A.E.Pegg, and J.A.Tainer (2007).
DNA binding, nucleotide flipping, and the helix-turn-helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy.
  DNA Repair (Amst), 6, 1100-1115.  
16826543 A.Roberts, J.G.Pelton, and D.E.Wemmer (2006).
Structural studies of MJ1529, an O6-methylguanine-DNA methyltransferase.
  Magn Reson Chem, 44, S71-S82.
PDB code: 2g7h
16697054 J.Ding, Z.H.Miao, L.H.Meng, and M.Y.Geng (2006).
Emerging cancer therapeutic opportunities target DNA-repair systems.
  Trends Pharmacol Sci, 27, 338-344.  
16464003 Y.Mishina, E.M.Duguid, and C.He (2006).
Direct reversal of DNA alkylation damage.
  Chem Rev, 106, 215-232.  
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.