PDBsum entry 6sjf

Hydrolase

PDB id: 6sjf

Contents

Protein chains

1129 a.a.

1121 a.a.

597 a.a.

DNA/RNA

PDB id:

6sjf

Name:

Hydrolase

Title:

Cryo-em structure of the recbcd chi unrecognised complex

Structure:

Recbcd enzyme subunit recb. Chain: b. Synonym: exodeoxyribonuclease v 135 kda polypeptide, exodeoxyribonuclease v beta chain,exonuclease v subunit recb,exov subunit recb,helicase/nuclease recbcd subunit recb. Engineered: yes. Mutation: yes. Recbcd enzyme subunit recc. Chain: c.

Source:

Escherichia coli. Organism_taxid: 562. Gene: recb, ior, rora, b2820, jw2788. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: recc, b2822, jw2790. Gene: recd, hope, b2819, jw2787. Synthetic: yes. Synthetic construct.

Authors:

K.Cheng,M.Wilkinson,D.B.Wigley

Key ref:

K.Cheng et al. (2020). A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair. Nat Struct Mol Biol, 27, 71-77. PubMed id: 31907455 DOI: 10.1038/s41594-019-0355-2

Date:

13-Aug-19 Release date: 01-Jan-20

Protein chain

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

Seq: 1180 a.a.

Struc: 1129 a.a.*

Protein chain

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

Seq: 1122 a.a.

Struc: 1121 a.a.

Protein chain

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

Seq: 608 a.a.

Struc: 597 a.a.

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

DNA/RNA chain

T-T-T-T-T-T-T-T-T-T-T-T-G-A-G-C-G-A-C-T-G-C-A-C-T-A-C-A-A-C-G-T-T-G-T-A-G-T-G- 54 bases

Enzyme reactions

• Enzyme class 2: Chains B, C: 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: Chain B: E.C.5.6.2.4 - Dna 3'-5' helicase.
• Enzyme class 4: Chain D: 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.

DOI no: 10.1038/s41594-019-0355-2

Nat Struct Mol Biol 27:71-77 (2020)

PubMed id: 31907455

A conformational switch in response to Chi converts RecBCD from phage destruction to DNA repair.

K.Cheng, M.Wilkinson, Y.Chaban, D.B.Wigley.

ABSTRACT

The RecBCD complex plays key roles in phage DNA degradation, CRISPR array acquisition (adaptation) and host DNA repair. The switch between these roles is regulated by a DNA sequence called Chi. We report cryo-EM structures of the Escherichia coli RecBCD complex bound to several different DNA forks containing a Chi sequence, including one in which Chi is recognized and others in which it is not. The Chi-recognized structure shows conformational changes in regions of the protein that contact Chi and reveals a tortuous path taken by the DNA. Sequence specificity arises from interactions with both the RecC subunit and the sequence itself. These structures provide molecular details for how Chi is recognized and insights into the changes that occur in response to Chi binding that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition to constructive host DNA repair.