PDBsum entry 4js5

Hydrolase/DNA

PDB id: 4js5

Contents

Protein chains

464 a.a.

DNA/RNA

Ligands

SO4 ×2

PDB id:

4js5

Name:

Hydrolase/DNA

Title:

Crystal structure of e. Coli exonuclease i in complex with a dt13 oligonucleotide

Structure:

Dt13 oligonucleotide. Chain: c, d. Engineered: yes. Exodeoxyribonuclease i. Chain: a, b. Synonym: exonuclease i, DNA deoxyribophosphodiesterase, drpase. Engineered: yes

Source:

Synthetic: yes. Other_details: chemical synthesis. Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: sbcb, cpea, xona, b2011, jw1993. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

3.50Å R-factor: 0.308 R-free: 0.346

Authors:

C.E.Bell

Key ref:

S.K.Korada et al. (2013). Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion. Nucleic Acids Res, 41, 5887-5897. PubMed id: 23609540 DOI: 10.1093/nar/gkt278

Date:

22-Mar-13 Release date: 08-May-13

Protein chains

P04995  (EX1_ECOLI) -  Exodeoxyribonuclease I from Escherichia coli (strain K12)

Seq: 475 a.a.

Struc: 464 a.a.

DNA/RNA chains

T-T-T-T-T-T-T-T-T-T-T 11 bases

T-T-T-T-T-T-T-T-T-T 10 bases

Enzyme reactions

• Enzyme class: E.C.3.1.11.1 - exodeoxyribonuclease I.
• Reaction: Degradation of single-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing nucleoside 5'-phosphates.

DOI no: 10.1093/nar/gkt278

Nucleic Acids Res 41:5887-5897 (2013)

PubMed id: 23609540

Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion.

S.K.Korada, T.D.Johns, C.E.Smith, N.D.Jones, K.A.McCabe, C.E.Bell.

ABSTRACT

Escherichia coli Exonuclease I (ExoI) digests single-stranded DNA (ssDNA) in the 3'-5' direction in a highly processive manner. The crystal structure of ExoI, determined previously in the absence of DNA, revealed a C-shaped molecule with three domains that form a central positively charged groove. The active site is at the bottom of the groove, while an extended loop, proposed to encircle the DNA, crosses over the groove. Here, we present crystal structures of ExoI in complex with four different ssDNA substrates. The structures all have the ssDNA bound in essentially the predicted manner, with the 3'-end in the active site and the downstream end under the crossover loop. The central nucleotides of the DNA form a prominent bulge that contacts the SH3-like domain, while the nucleotides at the downstream end of the DNA form extensive interactions with an 'anchor' site. Seven of the complexes are similar to one another, but one has the ssDNA bound in a distinct conformation. The highest-resolution structure, determined at 1.95 Å, reveals an Mg(2+) ion bound to the scissile phosphate in a position corresponding to Mg(B) in related two-metal nucleases. The structures provide new insights into the mechanism of processive digestion that will be discussed.