Structure of PDB 8oy3 Chain B

Receptor sequence

>8oy3B (length=427) Species: 192952 (Methanosarcina mazei Go1)

MNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEANVPVV
VVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDPGEKIS
RFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVVPCWEA
SQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTDPLFEPWHFEPGEKA
AKKVMESFIADRLDSYGALRNDPTKNMLSNLSPYLHFGQISSQRVVLEVE
KAESNPGSKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSWAKESLNAH
RNDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYMRMYWAKKIL
EWSESPEKALEIAICLNDRYELDGRDPNGYAGIAWSIGGVHDRAWGEREV
TGKIRYMSYEGCKRKFDVKLYIEKYSA

3D structure

• PDB: 8oy3 Time-resolved crystallography captures light-driven DNA repair
• Chain: B
• Resolution: 2.16 Å

Enzymatic activity

• Enzyme Commision number: 4.1.99.3: deoxyribodipyrimidine photo-lyase.

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	A160 H161 R256 N257 E301 W305 Y376 M379 W421 R429 W431 R441 Y442 M443 S444 E446 G447 R450 K451	A158 H159 R220 N221 E265 W269 Y340 M343 W385 R393 W395 R405 Y406 M407 S408 E410 G411 R414 K415
BS02	dna	B	Y158 R429 A430 W431 G432 E433 K439 R450	Y156 R393 A394 W395 G396 E397 K403 R414
BS03	FDA	B	Y252 L264 S265 N266 S268 F298 E301 I302 W305 K306 K372 R378 M379 N403 D409 N414 G415	Y216 L228 S229 N230 S232 F262 E265 I266 W269 K270 K336 R342 M343 N367 D373 N378 G379

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003677 DNA binding
• GO:0003904 deoxyribodipyrimidine photo-lyase activity
• GO:0016829 lyase activity

Biological Process

• GO:0000719 photoreactive repair
• GO:0006281 DNA repair

External links

• PDB: RCSB:8oy3, PDBe:8oy3, PDBj:8oy3
• PDBsum: 8oy3
• PubMed: 38033070
• UniProt: Q8PYK9