Structure of PDB 8cy4 Chain C

Receptor sequence

>8cy4C (length=540) Species: 1496 (Clostridioides difficile)

GIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILY
DLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSL
TNKIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKKYKKFLLEKYS
EVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLSGKDLREYIKS
NVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDVFKIKNEDICI
NKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFYNKIQEKCKYS
LEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWIKSKNINKYIV
DKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRECKSGIRKWYEL
QWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYSFFIKEEYLDK
FSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMKIRIFRDNNYE
EIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI

3D structure

• PDB: 8cy4 Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
• Chain: C
• Resolution: 2.34 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	C	Y30 N165 Y168 K173 K193 Y221 S227 F253 I256 G257 Q346 R432 W439 R441 K456 Y476 K511 M513 Y521 P522 N523	Y3 N128 Y131 K136 K156 Y184 S190 F216 I219 G220 Q309 R395 W402 R404 K419 Y439 K474 M476 Y484 P485 N486
BS02	dna	C	H171 K172 K179 D192 K193 I349 G351 D353 K378 K380 R425 Q438 W439 Y455 K456	H134 K135 K142 D155 K156 I312 G314 D316 K341 K343 R388 Q401 W402 Y418 K419
BS03	QA6	C	D114 I115 D149 S150 P167 Y178 F200	D87 I88 D112 S113 P130 Y141 F163

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:8cy4, PDBe:8cy4, PDBj:8cy4
• PDBsum: 8cy4
• PubMed: 36581322
• UniProt: Q183J3