Structure of PDB 3rbd Chain B

Receptor sequence

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

GIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

3D structure

• PDB: 3rbd Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions.
• Chain: B
• Resolution: 2.502 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	E1106 G1185 G1187 I1189 T1190 V1296 S1297 R1298 T1301	E106 G185 G187 I189 T190 V296 S297 R298 T301
BS02	dna	B	V1032 A1042 A1220 R1242 K1243 S1244 I1245 G1246 R1247 I1248 T1250 R1332 R1336	V32 A42 A220 R242 K243 S244 I245 G246 R247 I248 T250 R332 R336
BS03	DGT	B	Y1010 F1011 Y1012 A1044 T1045 Y1048 R1051 D1105	Y10 F11 Y12 A44 T45 Y48 R51 D105
BS04	CA	B	D1007 D1105 E1106	D7 D105 E106
BS05	CA	B	D1007 F1008 D1105	D7 F8 D105
BS06	CA	B	A1181 I1186	A181 I186

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:3rbd, PDBe:3rbd, PDBj:3rbd
• PDBsum: 3rbd
• PubMed: 21645853
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)