Structure of PDB 1ryr Chain A

Receptor sequence

>1ryrA (length=341) Species: 2287 (Saccharolobus solfataricus)

MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEA
RKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIE
IASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVF
AKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGIN
KLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVT
MKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGR
TFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI

3D structure

• PDB: 1ryr Replication of a Cis-Syn Thymine Dimer at Atomic Resolution
• Chain: A
• Resolution: 2.28 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	G185 G187 I189 T190 V296 S297 R298 T301 K339	G185 G187 I189 T190 V296 S297 R298 T301 K339
BS02	dna	A	G41 A42 G58 I59 P60 G218 K221 R242 S244 G246 R247 I248 L293 R332 R336	G41 A42 G58 I59 P60 G218 K221 R242 S244 G246 R247 I248 L293 R332 R336
BS03	CA	A	D7 F8 D105	D7 F8 D105
BS04	ATP	A	D7 Y10 A44 R51 K159	D7 Y10 A44 R51 K159

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:1ryr, PDBe:1ryr, PDBj:1ryr
• PDBsum: 1ryr
• PubMed: 12904819
• UniProt: Q97W02|DPO4_SACS2 DNA polymerase IV (Gene Name=dbh)