Structure of PDB 4kyw Chain A

Receptor sequence

>4kywA (length=254) Species: 170187 (Streptococcus pneumoniae TIGR4)

MELHFNLELVETYKSNSQKARILTEDWVYRQSYCPNCGNNPLNHFENNRP
VADFYCNHCSEEFELKSKKGNFSSTINDGAYATMMKRVQADNNPNFFFLT
YTKNFEVNNFLVLPKQFVTPKSIIQRKPLAPTANRAGWIGCNIDLSQVPS
KGRIFLVQDGQVRDPEKVTKEFKQGLFLRKSSLSSRGWTIEILNCIDKIE
GSEFTLEDMYRFESDLKNIFVKNNHIKEKIRQQLQILRDKEIIEFKGRGK
YRKL

3D structure

• PDB: 4kyw Structural basis of the methylation specificity of R.DpnI.
• Chain: A
• Resolution: 2.35 Å

Enzymatic activity

• Enzyme Commision number: 3.1.21.4: type II site-specific deoxyribonuclease.

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	N16 S17 Q18 A20 R21 N48 D53 S67 K69 N77 G79 A80 Y101 R135 W138	N16 S17 Q18 A20 R21 N48 D53 S67 K69 N77 G79 A80 Y101 R135 W138
BS02	dna	A	Y13 K14 S15 Q18 R21 N47 N48 R126 L129 A130 N134	Y13 K14 S15 Q18 R21 N47 N48 R126 L129 A130 N134
BS03	dna	A	W188 K222 N223 N224 H225 E228 K229 Q232	W188 K222 N223 N224 H225 E228 K229 Q232
BS04	dna	A	L206 R231 Q232 Q235 R238 F245 G249 Y251	L206 R231 Q232 Q235 R238 F245 G249 Y251
BS05	ZN	A	C34 C37 C56 C59	C34 C37 C56 C59
BS06	CA	A	D53 E64 L65	D53 E64 L65

Gene Ontology

Molecular Function

• GO:0004519 endonuclease activity
• GO:0009036 type II site-specific deoxyribonuclease activity

Biological Process

• GO:0009307 DNA restriction-modification system

External links

• PDB: RCSB:4kyw, PDBe:4kyw, PDBj:4kyw
• PDBsum: 4kyw
• PubMed: 24966351
• UniProt: P0A459|T2D1_STRPN Type II methyl-directed restriction enzyme DpnI (Gene Name=dpnC)