PDBsum entry 1d9d

Transferase/DNA, RNA

PDB id: 1d9d

Contents

Protein chain

601 a.a. *

DNA/RNA

Ligands

SO4 ×4

Metals

_ZN ×4

_MG

Waters ×265

* Residue conservation analysis

PDB id:

1d9d

Name:

Transferase/DNA, RNA

Title:

Crystall structure of the complex of DNA polymerase i klenow fragment with short DNA fragment carrying 2'-0-aminopropyl-RNA modifications 5'-d(tcg)-ap(auc)-3'

Structure:

5'-d( Tp Cp Gp)-r(ap (U31)p (C31))-3'. Chain: b. Engineered: yes. Other_details: 3'-terminal adenosine, uracil, and cytosine nucleotides have 3-aminopropyl bound to o2 . DNA polymerase i. Chain: a. Fragment: klenow fragment. Synonym: pol i, DNA directed DNA polymerase.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.18Å R-factor: 0.215 R-free: 0.238

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:

27-Oct-99 Release date: 02-Dec-99

Protein chain

P00582  (DPO1_ECOLI) -  DNA polymerase I from Escherichia coli (strain K12)

Seq: 928 a.a.

Struc: 601 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chain

A-U31-C31 3 bases

Enzyme reactions

• Enzyme class: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added 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.