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PDBsum entry 1d8y

Go to PDB code: 
protein dna_rna ligands metals links
Transferase/DNA PDB id
1d8y
Jmol
Contents
Protein chain
601 a.a. *
DNA/RNA
Ligands
SO4 ×3
Metals
_ZN
Waters ×335
* Residue conservation analysis
PDB id:
1d8y
Name: Transferase/DNA
Title: Crystal structure of the complex of DNA polymerase i klenow fragment with DNA
Structure: D(t)19 oligomer. Chain: b. Engineered: yes. DNA polymerase i. Chain: a. Fragment: klenow fragment. Synonym: pol i, DNA directed DNA polymerase. Engineered: yes. Mutation: yes
Source: Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.08Å     R-factor:   0.217     R-free:   0.233
Authors: M.Teplova,S.T.Wallace,V.Tereshko,G.Minasov,A.M.Simons, P.D.Cook,M.Manoharan,M.Egli
Key ref:
M.Teplova et al. (1999). Structural origins of the exonuclease resistance of a zwitterionic RNA. Proc Natl Acad Sci U S A, 96, 14240-14245. PubMed id: 10588690 DOI: 10.1073/pnas.96.25.14240
Date:
26-Oct-99     Release date:   02-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00582  (DPO1_ECOLI) -  DNA polymerase I
Seq:
Struc:
 
Seq:
Struc:
928 a.a.
601 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.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleobase-containing compound metabolic process   3 terms 
  Biochemical function     nucleic acid binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.96.25.14240 Proc Natl Acad Sci U S A 96:14240-14245 (1999)
PubMed id: 10588690  
 
 
Structural origins of the exonuclease resistance of a zwitterionic RNA.
M.Teplova, S.T.Wallace, V.Tereshko, G.Minasov, A.M.Symons, P.D.Cook, M.Manoharan, M.Egli.
 
  ABSTRACT  
 
Nuclease resistance and RNA affinity are key criteria in the search for optimal antisense nucleic acid modifications, but the origins of the various levels of resistance to nuclease degradation conferred by chemical modification of DNA and RNA are currently not understood. The 2'-O-aminopropyl (AP)-RNA modification displays the highest nuclease resistance among all phosphodiester-based analogues and its RNA binding affinity surpasses that of phosphorothioate DNA by 1 degrees C per modified residue. We found that oligodeoxynucleotides containing AP-RNA residues at their 3' ends competitively inhibit the degradation of single-stranded DNA by the Escherichia coli Klenow fragment (KF) 3'-5' exonuclease and snake venom phosphodiesterase. To shed light on the origins of nuclease resistance brought about by the AP modification, we determined the crystal structure of an A-form DNA duplex with AP-RNA modifications at 1.6-A resolution. In addition, the crystal structures of complexes between short DNA fragments carrying AP-RNA modifications and wild-type KF were determined at resolutions between 2.2 and 3.0 A and compared with the structure of the complex between oligo(dT) and the D355A/E357A KF mutant. The structural models suggest that interference of the positively charged 2'-O-substituent with the metal ion binding site B of the exonuclease allows AP-RNA to effectively slow down degradation.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Chemical structures of DNA, PS-DNA, AP-RNA, and 2'-O-butyl RNA.
Figure 7.
Fig. 7. The two orientations and resulting interactions of d(T)-AP(U)-d(T)-3' at the wt-KF exonuclease active site. Only one of the orientations is compatible with a direct phosphate-metal ion interaction (A). However, the Zn2+ ... 0 distance is longer (2.49 Å) compared with the hexamer complex (1.81 Å, Fig. 6A). See Fig. 6 for color scheme and further explanations.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20087997 M.Egli, and P.S.Pallan (2010).
Crystallographic studies of chemically modified nucleic acids: a backward glance.
  Chem Biodivers, 7, 60-89.  
17979170 J.Winkler, M.Gilbert, A.Kocourková, M.Stessl, and C.R.Noe (2008).
2'-O-Lysylaminohexyl oligonucleotides: modifications for antisense and siRNA.
  ChemMedChem, 3, 102-110.  
18253536 P.S.Pallan, D.Ittig, A.Héroux, Z.Wawrzak, C.J.Leumann, and M.Egli (2008).
Crystal structure of tricyclo-DNA: an unusual compensatory change of two adjacent backbone torsion angles.
  Chem Commun (Camb), (), 883-885.
PDB code: 2rf3
17341465 E.C.Juan, J.Kondo, T.Kurihara, T.Ito, Y.Ueno, A.Matsuda, and A.Takénaka (2007).
Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules.
  Nucleic Acids Res, 35, 1969-1977.
PDB codes: 2dp7 2dpb 2dpc 2dqo 2dqp 2dqq
17288535 M.Egli, and P.S.Pallan (2007).
Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides.
  Annu Rev Biophys Biomol Struct, 36, 281-305.  
16027443 P.Haeberli, I.Berger, P.S.Pallan, and M.Egli (2005).
Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine.
  Nucleic Acids Res, 33, 3965-3975.
PDB code: 2a0p
17191797 T.S.Zatsepin, Y.M.Ivanova, and T.S.Oretskaya (2004).
Synthesis of (2'S)- and (2'R)-2'-deoxy-2'-[(2-methoxyethoxy)amino] pyrimidine nucleosides and oligonucleotides.
  Chem Biodivers, 1, 1537-1545.  
12655016 S.Park, M.Seetharaman, A.Ogdie, D.Ferguson, and N.Tretyakova (2003).
3'-Exonuclease resistance of DNA oligodeoxynucleotides containing O6-[4-oxo-4-(3-pyridyl)butyl]guanine.
  Nucleic Acids Res, 31, 1984-1994.  
12641455 Z.A.Doddridge, R.D.Bertram, C.J.Hayes, and P.Soultanas (2003).
Effects of vinylphosphonate internucleotide linkages on the cleavage specificity of exonuclease III and on the activity of DNA polymerase I.
  Biochemistry, 42, 3239-3246.  
12074364 M.Manoharan (2002).
Oligonucleotide conjugates as potential antisense drugs with improved uptake, biodistribution, targeted delivery, and mechanism of action.
  Antisense Nucleic Acid Drug Dev, 12, 103-128.  
12458793 Y.G.Ren, J.Martínez, L.A.Kirsebom, and A.Virtanen (2002).
Inhibition of Klenow DNA polymerase and poly(A)-specific ribonuclease by aminoglycosides.
  RNA, 8, 1393-1400.  
11222771 V.Tereshko, C.J.Wilds, G.Minasov, T.P.Prakash, M.A.Maier, A.Howard, Z.Wawrzak, M.Manoharan, and M.Egli (2001).
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments.
  Nucleic Acids Res, 29, 1208-1215.
PDB codes: 1i0f 1i0g 1i0j 1i0k 1i0m 1i0n 1i0o 1i0p 1i0q 1i0t
10736151 G.Minasov, M.Teplova, P.Nielsen, J.Wengel, and M.Egli (2000).
Structural basis of cleavage by RNase H of hybrids of arabinonucleic acids and RNA.
  Biochemistry, 39, 3525-3532.
PDB code: 1ei4
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.