Structure of PDB 6pbd Chain A

Receptor sequence

>6pbdA (length=350) Species: 155892 (Caulobacter vibrioides)

MKFGPETIIHGDCIEQMNALPEKSVDLIFADPPYNLQLGGDLLRPDNSKV
DAVDDHWDQFESFAAYDKFTREWLKAARRVLKDDGAIWVIGSYHNIFRVG
VAVQDLGFWILNDIVWRKSNPMPNFKGTRFANAHETLIWASKSQNAKRYT
FNYDALKMANDEVQMRSDWTIPLCTGEERIKGADGQKAHPTQKPEALLYR
VILSTTKPGDVILDPFFGVGTTGAAAKRLGRKFIGIEREAEYLEHAKARI
AKVVPIAPEDRAEPRVPFGTIVEAGLLSPGDTLYCSKGTHVAKVRPDGSI
TVGDLSGSIHKIGALVQSAPACNGWTYWHFKTDAGLAPIDVLRAQVRAGM

3D structure

• PDB: 6pbd The cell cycle-regulated DNA adenine methyltransferase CcrM opens a bubble at its DNA recognition site.
• Chain: A
• Resolution: 2.343 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	D31 Y34 L36 Q37 L38 G40 L42 R44 A52 D58 Y93 H94 P121 M122 N124 F125 K126 T128 R129 N132 L173 R179 K187 P190 T191 K193	D31 Y34 L36 Q37 L38 G40 L42 R44 A52 D58 Y93 H94 P121 M122 N124 F125 K126 T128 R129 N132 L173 R179 K187 P190 T191 K193
BS02	dna	A	P45 P123 N124 F125 K126	P45 P123 N124 F125 K126
BS03	SFG	A	D12 C13 D31 W57 H189 T191 F216 V219 T221 E237 R238 Y242	D12 C13 D31 W57 H189 T191 F216 V219 T221 E237 R238 Y242

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0008168 methyltransferase activity
• GO:0008170 N-methyltransferase activity
• GO:0009007 site-specific DNA-methyltransferase (adenine-specific) activity

Biological Process

• GO:0006260 DNA replication
• GO:0032259 methylation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6pbd, PDBe:6pbd, PDBj:6pbd
• PDBsum: 6pbd
• PubMed: 31601797
• UniProt: P0CAW2|CCRM_CAUVC DNA methyltransferase CcrM (Gene Name=ccrMIM)