PDBsum entry 4zcf

Hydrolase-DNA complex

PDB id: 4zcf

Contents

Protein chains

616 a.a.

612 a.a.

627 a.a.

DNA/RNA

Ligands

AMP

Metals

_MN ×2

_CA

Waters ×95

PDB id:

4zcf

Name:

Hydrolase-DNA complex

Title:

Structural basis of asymmetric DNA methylation and atp-triggered long- range diffusion by ecop15i

Structure:

Restriction endonuclease ecop15i, modification subunit. Chain: a, b. Engineered: yes. Restriction endonuclease ecop15i, restriction subunit. Chain: c. Engineered: yes. DNA 20-mer atacagcagtagactatgat. Chain: d. Engineered: yes.

Source:

Escherichia coli. Organism_taxid: 562. Gene: ecop15imod. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ecop15ires. Synthetic: yes. Organism_taxid: 562

Resolution:

2.60Å R-factor: 0.221 R-free: 0.263

Authors:

Y.K.Gupta,S.H.Chan,S.Y.Xu,A.K.Aggarwal

Key ref:

Y.K.Gupta et al. (2015). Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I. Nat Commun, 6, 7363. PubMed id: 26067164 DOI: 10.1038/ncomms8363

Date:

15-Apr-15 Release date: 29-Jul-15

Protein chain

P12364  (T3MO_ECOLX) -  Type III restriction-modification enzyme EcoP15I Mod subunit from Escherichia coli

Seq: 644 a.a.

Struc: 616 a.a.

Protein chain

P12364  (T3MO_ECOLX) -  Type III restriction-modification enzyme EcoP15I Mod subunit from Escherichia coli

Seq: 644 a.a.

Struc: 612 a.a.

Protein chain

Q5ZND2  (T3RE_ECOLX) -  Type III restriction-modification enzyme EcoP15I Res subunit from Escherichia coli

Seq: 970 a.a.

Struc: 627 a.a.

DNA/RNA chains

A-T-A-C-A-G-C-A-G-T-A-G-A-C-T-A-T-G-A-T 20 bases

A-A-T-C-A-T-A-G-T-C-T-A-C-T-G-C-T-G-T-A 20 bases

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.1.1.72 - site-specific DNA-methyltransferase (adenine-specific).
• Reaction: a 2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = an N₆-methyl- 2'-deoxyadenosine in DNA + S-adenosyl-L-homocysteine + H⁺

2'-deoxyadenosine in DNA + S-adenosyl-L-methionine = N(6)-methyl- 2'-deoxyadenosine in DNA + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = AMP) matches with 58.06% similarity)

• Enzyme class 2: Chain C: E.C.3.1.21.5 - type Iii site-specific deoxyribonuclease.
• Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.

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.

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

Added reference

DOI no: 10.1038/ncomms8363

Nat Commun 6:7363 (2015)

PubMed id: 26067164

Structural basis of asymmetric DNA methylation and ATP-triggered long-range diffusion by EcoP15I.

Y.K.Gupta, S.H.Chan, S.Y.Xu, A.K.Aggarwal.

ABSTRACT

Type III R-M enzymes were identified >40 years ago and yet there is no structural information on these multisubunit enzymes. Here we report the structure of a Type III R-M system, consisting of the entire EcoP15I complex (Mod2Res1) bound to DNA. The structure suggests how ATP hydrolysis is coupled to long-range diffusion of a helicase on DNA, and how a dimeric methyltransferase functions to methylate only one of the two DNA strands. We show that the EcoP15I motor domains are specifically adapted to bind double-stranded DNA and to facilitate DNA sliding via a novel 'Pin' domain. We also uncover unexpected 'division of labour', where one Mod subunit recognizes DNA, while the other Mod subunit methylates the target adenine-a mechanism that may extend to adenine N6 RNA methylation in mammalian cells. Together the structure sheds new light on the mechanisms of both helicases and methyltransferases in DNA and RNA metabolism.