Structure of PDB 7rfm Chain B Binding Site BS01

Receptor Information

>7rfm Chain B (length=555) Species: 272563 (Clostridioides difficile 630)

TKKASGIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEV
YDILYDLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISI
LKDSLTNKKVVNDLDESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHK
KLEKKYKKFLLEKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYF
LESLSGKDLREYIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKE
TYIDVFKIKNEDICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKD
DETFYNKIQEKCKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKF
LKCWIKSKNINKYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLE
NRRECKSGIRKWYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSS
ADVYSFFIKEEYLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYP
NKVMKIRIFRDNNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIM
DSLGI

Ligand information

>7rfm Chain F (length=14)

ttcaaaaagtccca

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7rfm Repurposing epigenetic inhibitors to target the Clostridioides difficile- specific DNA adenine methyltransferase and sporulation regulator CamA.
• Resolution: 2.68 Å
• Binding residue (original residue number in PDB): Y30 N165 P166 Y168 K173 Y221 S227 I256 G257 F345 Q346 R432 W439 R441 K456 Y476 K511 M513 S514 Y521 P522 N523
• Binding residue (residue number reindexed from 1): Y8 N143 P144 Y146 K151 Y199 S205 I234 G235 F323 Q324 R410 W417 R419 K434 Y454 K489 M491 S492 Y499 P500 N501

Enzymatic activity

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

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