Structure of PDB 3khh Chain B

Receptor sequence

>3khhB (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: B
• 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	B	P1184 G1185 G1187 I1189 T1190 V1296 S1297 R1298 R1300 T1301 K1339	P184 G185 G187 I189 T190 V296 S297 R298 R300 T301 K339
BS02	dna	B	V1032 S1034 F1037 G1041 A1042 R1242 K1243 S1244 G1246 R1247 I1248 T1250 R1331 R1332 R1336	V32 S34 F37 G41 A42 R242 K243 S244 G246 R247 I248 T250 R331 R332 R336
BS03	DGT	B	Y1010 R1051 G1058 D1105 K1159	Y10 R51 G58 D105 K159
BS04	CA	B	D1105 E1106	D105 E106
BS05	CA	B	D1007 F1008 D1105	D7 F8 D105
BS06	CA	B	A1181 V1183 I1186	A181 V183 I186
BS07	AF	B	L1293 R1332	L293 R332

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)