Structure of PDB 7rfm Chain A

Receptor sequence

>7rfmA (length=550) Species: 272563 (Clostridioides difficile 630)

KKASGIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVY
DILYDLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISIL
KDSLTNKKVDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKK
YKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLS
GKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDV
FKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFY
NKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWI
KSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRREC
KSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYS
FFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMK
IRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI

3D structure

• PDB: 7rfm Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA.
• Chain: A
• Resolution: 2.68 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.72: site-specific DNA-methyltransferase (adenine-specific).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	H171 K172 K179 D192 K193 N255 I349 C352 D353 K378 K380 R425 Q438 W439 Y455	H144 K145 K152 D165 K166 N228 I322 C325 D326 K351 K353 R398 Q411 W412 Y428
BS02	dna	A	Y30 N165 Y168 K173 K193 Y221 S227 F253 G257 F345 Q346 W439 R441 K456 Y476 K511 M513 Y521 N523	Y7 N138 Y141 K146 K166 Y194 S200 F226 G230 F318 Q319 W412 R414 K429 Y449 K484 M486 Y494 N496
BS03	0QK	A	K25 Y30 S62 G64 C65 D114 I115 A119 D149 S150 N165 P167	K2 Y7 S39 G41 C42 D91 I92 A96 D122 S123 N138 P140

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0008168 methyltransferase activity
• GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity

Biological Process

• GO:0006304 DNA modification
• GO:0032259 methylation

External links

• PDB: RCSB:7rfm, PDBe:7rfm, PDBj:7rfm
• PDBsum: 7rfm
• PubMed: 34523387
• UniProt: Q183J3