Structure of PDB 1skm Chain A

Receptor sequence

>1skmA (length=327) Species: 726 (Haemophilus haemolyticus)

MIEIKDKQLTGLRFIDLFAGLGGFRLALESCGAECVYSNEWDKYAQEVYE
MNFGEKPEGDITQVNEKTIPDHDILCAGFPCQAFSISGKQKGFEDSRGTL
FFDIARIVREKKPKVVFMENVKNFASHDNGNTLEVVKNTMNELDYSFHAK
VLNALDYGIPQKRERIYMICFRNDLNIQNFQFPKPFELNTFVKDLLLPDS
EVEHLVIDRKDLVMTNQEIEQTTPKTVRLGIVGKGGQGERIYSTRGIAIT
LSAYGGGIFAKTGGYLVNGKTRKLHPRECARVMGYPDSYKVHPSTSQAYK
QFGNSVVINVLQYIAYNIGSSLNFKPY

3D structure

• PDB: 1skm Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase
• Chain: A
• Resolution: 2.2 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): C81 E119 R163 R165
• Catalytic site (residue number reindexed from 1): C81 E119 R163 R165
• 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	D42 K43 I86 Q90 S126 K234 G236 Q237 G256 G257 S294 Q297	D42 K43 I86 Q90 S126 K234 G236 Q237 G256 G257 S294 Q297
BS02	dna	A	S85 I86 S87 G88 K89 R97 K162 T226 R228 Q237 R240 Y242 T250 S252 Y254 G255	S85 I86 S87 G88 K89 R97 K162 T226 R228 Q237 R240 Y242 T250 S252 Y254 G255
BS03	SAH	A	F18 A19 L21 G23 E40 W41 D60 I61 G78 N304 S305	F18 A19 L21 G23 E40 W41 D60 I61 G78 N304 S305

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• 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:1skm, PDBe:1skm, PDBj:1skm
• PDBsum: 1skm
• PubMed: 15273274
• UniProt: P05102|MTH1_HAEPH Type II methyltransferase M.HhaI (Gene Name=hhaIM)