Structure of PDB 8cy2 Chain A

Receptor sequence

>8cy2A (length=544) Species: 1496 (Clostridioides difficile)

GIYYTPKIIVDYIVKKTLKNHDIIKNPYPRILDISCGCGNFLLEVYDILY
DLFEENIYELKKKYDENYWTVDNIHRHILNYCIYGADIDEKAISILKDSL
TNKKESDIKINLFCCDSLKKKWRYKFDYIVGNPPYIGHKKLEKKYKKFLL
EKYSEVYKDKADLYFCFYKKIIDILKQGGIGSVITPRYFLESLSGKDLRE
YIKSNVNVQEIVDFLGANIFKNIGVSSCILTFDKKKTKETYIDVFKIKNE
DICINKFETLEELLKSSKFEHFNINQRLLSDEWILVNKDDETFYNKIQEK
CKYSLEDIAISFQGIITGCDKAFILSKDDVKLNLVDDKFLKCWIKSKNIN
KYIVDKSEYRLIYSNDIDNENTNKRILDEIIGLYKTKLENRRECKSGIRK
WYELQWGREKLFFERKKIMYPYKSNENRFAIDYDNNFSSADVYSFFIKEE
YLDKFSYEYLVGILNSSVYDKYFKITAKKMSKNIYDYYPNKVMKIRIFRD
NNYEEIENLSKQIISILLNKSIDKGKVEKLQIKMDNLIMDSLGI

3D structure

• PDB: 8cy2 Systematic Design of Adenosine Analogs as Inhibitors of a Clostridioides difficile- Specific DNA Adenine Methyltransferase Required for Normal Sporulation and Persistence.
• Chain: A
• Resolution: 2.81 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	Y30 N165 Y168 H171 K173 K193 Y221 S227 F253 G257 Q346 W439 R441 K456 Y476 K511 M513 Y521 P522 N523	Y3 N132 Y135 H138 K140 K160 Y188 S194 F220 G224 Q313 W406 R408 K423 Y443 K478 M480 Y488 P489 N490
BS02	dna	A	H171 K172 K179 D192 K193 I349 C352 D353 K378 K380 R425 Q438 W439 Y455 A473 K515	H138 K139 K146 D159 K160 I316 C319 D320 K345 K347 R392 Q405 W406 Y422 A440 K482
BS03	QA2	A	D114 I115 D149 S150 P167 L174 Y178	D87 I88 D116 S117 P134 L141 Y145

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:8cy2, PDBe:8cy2, PDBj:8cy2
• PDBsum: 8cy2
• PubMed: 36581322
• UniProt: Q183J3