Structure of PDB 4dkj Chain A

Receptor sequence

>4dkjA (length=388) Species: 272633 (Malacoplasma penetrans HF-2)

DKIKVIKVFEAFAGIGSQFKALKNIARSKNWEIQHSGMVEWFVDAIVSYV
AIHSKNFNPKIERLDRDILSISNDSKMPISEYGIKKINNTIKASYLNYAK
KHFNNLFDIKKVNKDNFPKNIDIFTYSFPCQDLSVQGLQKGIDKELNTRS
GLLWEIERILEEIKNSFSKEEMPKYLLMENVKNLLSHKNKKNYNTWLKQL
EKFGYKSKTYLLNSKNFDNCQNRERVFCLSIRDDYLEKTGFKFKELEKVK
NPPKKIKDILVDSSNYKYLNLNKYETTTFRETKSNIISRPLKNYTTFNSE
NYVYNINGIGPTLTASGANSRIKIETQQGVRYLTPLECFKYMQFDVNDFK
KVQSTNLISENKMIYIAGNSIPVKILEAIFNTLEFVNN

3D structure

• PDB: 4dkj CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
• Chain: A
• Resolution: 2.15 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C135 E184 R228 R230
• Catalytic site (residue number reindexed from 1): C130 E179 R223 R225
• 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	F133 P134 C135 Q136 S139 V140 Q141 G142 L143 E184 R230 T287 S289 F302 N303 P316 T317 T319 A320 S321 G322 N324 G373	F128 P129 C130 Q131 S134 V135 Q136 G137 L138 E179 R225 T282 S284 F297 N298 P311 T312 T314 A315 S316 G317 N319 G368
BS02	dna	A	Q141 Q144 N188 H192 T300 T301 F302 N303 S304 E305 R326 N366	Q136 Q139 N183 H187 T295 T296 F297 N298 S299 E300 R321 N361
BS03	SAH	A	F17 A18 G19 I20 S22 E45 W46 F112 D113 S132 R154 N374 S375	F12 A13 G14 I15 S17 E40 W41 F107 D108 S127 R149 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:4dkj, PDBe:4dkj, PDBj:4dkj
• PDBsum: 4dkj
• PubMed: 23248272
• UniProt: Q8EVR5