PDBsum entry 8cxx

DNA binding protein/DNA

PDB id: 8cxx

Contents

Protein chains

546 a.a.

DNA/RNA

Ligands

EDO ×13

T9I ×3

Metals

__K ×7

Waters ×523

PDB id:

8cxx

Name:

DNA binding protein/DNA

Title:

Cama adenine methyltransferase complexed to cognate substrate DNA and compound 6

Structure:

Site-specific DNA-methyltransferase (adenine-specific). Chain: a, b, c. Synonym: cama methyltransferase. Engineered: yes. DNA strand 1. Chain: d, f, h. Engineered: yes. DNA strand 2. Chain: e, g, i.

Source:

Clostridioides difficile 630. Organism_taxid: 272563. Strain: 630. Gene: cd630_27580. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: rosetta. Synthetic: yes. Clostridioides difficile.

Resolution:

2.34Å R-factor: 0.181 R-free: 0.208

Authors:

J.R.Horton,J.Zhou,X.Cheng

Key ref:

J.Zhou et al. Systematic design of adenosine analogs as inhibitors clostridioides difficile- Specific DNA adenine methyltransferase required for normal sporulation and persistence.. J med chem, . PubMed id: 36581322

Date:

22-May-22 Release date: 11-Jan-23

Protein chains

Q183J3  (Q183J3_PEPD6) -  site-specific DNA-methyltransferase (adenine-specific) from Clostridioides difficile (strain 630)

Seq: 577 a.a.

Struc: 546 a.a.

DNA/RNA chains

T-T-C-A-A-A-A-A-G-T-C-C-C-A 14 bases

A-T-G-G-G-A-C-T-T-T-T-T-G-A 14 bases

T-T-C-A-A-A-A-A-G-T-C-C-C-A 14 bases

A-T-G-G-G-A-C-T-T-T-T-T-G-A 14 bases

T-T-C-A-A-A-A-A-G-T-C-C-C-A 14 bases

A-T-G-G-G-A-C-T-T-T-T-T-G-A 14 bases

Enzyme reactions

• Enzyme class: 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 = T9I) matches with 50.00% similarity)

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