Structure of PDB 8c56 Chain A

Receptor sequence

>8c56A (length=388) Species: 272633 (Malacoplasma penetrans HF-2)

DKIKVIKVFEAFAGIGSQFKALKNIARSKNWEIQHSGMVEWFVDAIVSYV
AIHSKNFNPKIERLDRDILSISNDSKMPISEYGIKKINNTIKASYLNYAK
KHFNNLFDIKKVNKDNFPKNIDIFTYSFPCQDLSVQGLQKGIDKELNTRS
GLLWEIERILEEIKNSFSKEEMPKYLLMENVKNLLSHKNKKNYNTWLKQL
EKFGYKSKTYLLNSKNFDNCQNRERVFCLSIRDDYLEKTGFKFKELEKVK
NPPKKIKDILVDSSNYKYLNLNKYETTTFRETKSNIISRPLKNYTTFNSE
NYVYNINGIGPTLTASGANSRIKIETQQGVRYLTPLECFKYMQFDVNDFK
KVQSTNLISENKMIYIAGNSIPVKILEAIFNTLEFVNN

3D structure

• PDB: 8c56 CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
• Chain: A
• Resolution: 2.4 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.37: DNA (cytosine-5-)-methyltransferase.

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	C135 Q136 S139 V140 Q141 G142 L143 E184 R228 R230 T287 S289 F302 N303 P316 T317 T319 A320 S321 G322 G373 N374	C130 Q131 S134 V135 Q136 G137 L138 E179 R223 R225 T282 S284 F297 N298 P311 T312 T314 A315 S316 G317 G368 N369
BS02	dna	A	Q141 Q144 H192 K193 T300 T301 F302 N303 S304 R326 N366	Q136 Q139 H187 K188 T295 T296 F297 N298 S299 R321 N361
BS03	SAH	A	F17 A18 G19 I20 S22 E45 W46 D113 I114 S132 L157 N374 S375	F12 A13 G14 I15 S17 E40 W41 D108 I109 S127 L152 N369 S370

Gene Ontology

Molecular Function

• GO:0003886 DNA (cytosine-5-)-methyltransferase activity
• GO:0008168 methyltransferase activity

Biological Process

• GO:0009307 DNA restriction-modification system
• GO:0032259 methylation

External links

• PDB: RCSB:8c56, PDBe:8c56, PDBj:8c56
• PDBsum: 8c56
• PubMed: 38966999
• UniProt: Q8EVR5