PDBsum entry 3k70

Hydrolase/DNA

PDB id: 3k70

Contents

Protein chains

1155 a.a. *

1121 a.a. *

547 a.a. *

DNA/RNA

Metals

_CA ×2

* Residue conservation analysis

PDB id:

3k70

Name:

Hydrolase/DNA

Title:

Crystal structure of the complete initiation complex of recbcd

Structure:

Exodeoxyribonuclease v beta chain. Chain: b, e. Synonym: exodeoxyribonuclease v 135 kda polypeptide. Engineered: yes. Exodeoxyribonuclease v gamma chain. Chain: c, f. Synonym: exodeoxyribonuclease v 125 kda polypeptide. Engineered: yes. Exodeoxyribonuclease v alpha chain.

Source:

Escherichia coli k-12. Organism_taxid: 83333. Strain: k12. Gene: b2820, jw2788, recb, rora. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: b2822, jw2790, recc. Gene: b2819, jw2787, recd. Synthetic: yes.

Resolution:

3.59Å R-factor: 0.248 R-free: 0.296

Authors:

K.Saikrishnan,D.B.Wigley

Key ref:

K.Saikrishnan et al. (2008). DNA binding to RecD: role of the 1B domain in SF1B helicase activity. Embo J, 27, 2222-2229. PubMed id: 18668125

Date:

11-Oct-09 Release date: 10-Nov-09

Protein chains

P08394  (RECB_ECOLI) -  RecBCD enzyme subunit RecB from Escherichia coli (strain K12)

Seq: 1180 a.a.

Struc: 1155 a.a.

Protein chains

P07648  (RECC_ECOLI) -  RecBCD enzyme subunit RecC from Escherichia coli (strain K12)

Seq: 1122 a.a.

Struc: 1121 a.a.

Protein chains

P04993  (RECD_ECOLI) -  RecBCD enzyme subunit RecD from Escherichia coli (strain K12)

Seq: 608 a.a.

Struc: 547 a.a.

DNA/RNA chains

5IU-5IU-5IU-5IU-5IU-A-5IU-C-5IU-A-A-T-G-C-G-A-G-C-A-C-T-G-C-T-A-T-A-G-C-A-G-T- 46 bases

5IU-5IU-5IU-5IU-5IU-A-5IU-C-5IU-A-A-T-G-C-G-A-G-C-A-C-T-G-C-T-A-T-A-G-C-A-G-T- 46 bases

Enzyme reactions

• Enzyme class 2: Chains B, C, E, F: E.C.3.1.11.5 - exodeoxyribonuclease V.
• Reaction: Exonucleolytic cleavage (in the presence of ATP) in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides.
• Enzyme class 3: Chains B, E: E.C.5.6.2.4 - Dna 3'-5' helicase.
• Enzyme class 4: Chains D, G: E.C.5.6.2.3 - Dna 5'-3' helicase.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Embo J 27:2222-2229 (2008)

PubMed id: 18668125

DNA binding to RecD: role of the 1B domain in SF1B helicase activity.

K.Saikrishnan, S.P.Griffiths, N.Cook, R.Court, D.B.Wigley.

ABSTRACT

The molecular mechanism of superfamily 1Balpha helicases remains unclear. We present here the crystal structure of the RecD2 helicase from Deinococcus radiodurans at 2.2-A resolution. The structure reveals the folds of the 1B and 2B domains of RecD that were poorly ordered in the structure of the Escherichia coli RecBCD enzyme complex reported previously. The 2B domain adopts an SH3 fold which, although common in eukaryotes, is extremely rare in bacterial systems. In addition, the D. radiodurans RecD2 structure has aided us in deciphering lower resolution (3.6 A) electron density maps for the E. coli RecBCD enzyme in complex with a long DNA substrate that interacts with the RecD subunit. Taken together, these structures indicated an important role for the 1B domain of RecD, a beta-hairpin that extends from the surface of the 1A domain and interacts with the DNA substrate. On the basis of these structural data, we designed a mutant RecD2 helicase that lacks this pin. The 'pin-less' mutant protein is a fully active ssDNA-dependent ATPase but totally lacks helicase activity.