Structure of PDB 3khh Chain A

Receptor sequence

>3khhA (length=341) Species: 273057 (Saccharolobus solfataricus P2)

GIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

3D structure

• PDB: 3khh Mechanism of error-free and semitargeted mutagenic bypass of an aromatic amine lesion by Y-family polymerase Dpo4.
• Chain: A
• Resolution: 2.7 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

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	P184 G185 G187 I189 T190 V296 S297 R298 R300 T301 K339	P184 G185 G187 I189 T190 V296 S297 R298 R300 T301 K339
BS02	dna	A	F33 S34 G35 G218 E219 A220 R240 R242 K243 S244 I245 G246 R247 I248 T250 R332	F33 S34 G35 G218 E219 A220 R240 R242 K243 S244 I245 G246 R247 I248 T250 R332
BS03	DGT	A	D7 Y10 Y12 D105 E106	D7 Y10 Y12 D105 E106
BS04	CA	A	D105 E106	D105 E106
BS05	CA	A	D7 F8 D105	D7 F8 D105
BS06	CA	A	A181 I186	A181 I186
BS07	AF	A	I248 V287 R336	I248 V287 R336

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006281 DNA repair
• GO:0006974 DNA damage response
• GO:0042276 error-prone translesion synthesis

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3khh, PDBe:3khh, PDBj:3khh
• PDBsum: 3khh
• PubMed: 20154704
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)