Structure of PDB 7yel Chain A

Receptor sequence

>7yelA (length=456) Species: 192952 (Methanosarcina mazei Go1)

PRGSHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEA
NVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDP
GEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVV
PCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPETLSDVLET
GVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVMESFIADRLDSYGALR
NDPTKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAFLDEILIWK
EISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEEFEAGKTH
DPLWNASQMELLSTGKMHGYTRMYWAKKILEWSESPEKALEIAICLNDRY
ELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRKFDVKL
YIEKYS

3D structure

• PDB: 7yel Visualizing the DNA repair process by a photolyase at atomic resolution
• Chain: A
• Resolution: 2.5 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	A	A160 H161 R164 R256 E301 W305 Y376 M379 R429 W431 R441 Y442 M443 G447 K451	A163 H164 R167 R250 E295 W299 Y370 M373 R423 W425 R435 Y436 M437 G441 K445
BS02	dna	A	Y158 R429 A430 W431 G432 E433 K439	Y161 R423 A424 W425 G426 E427 K433
BS03	FAD	A	Y252 L264 S265 N266 S268 L271 F298 E301 I302 W305 K306 K372 R378 N403 D409 N414 G415	Y246 L258 S259 N260 S262 L265 F292 E295 I296 W299 K300 K366 R372 N397 D403 N408 G409

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:7yel, PDBe:7yel, PDBj:7yel
• PDBsum: 7yel
• PubMed: 38033054
• UniProt: Q8PYK9