Structure of PDB 7ydz Chain B

Receptor sequence

>7ydzB (length=432) Species: 192952 (Methanosarcina mazei Go1)

LVPRGSHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAK
EANVPVVVVFCLTDEFLGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDP
GEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVV
PCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPDPLFEPWHF
EPGEKAAKKVMESFIADRLDSYGALRNDPTKNMLSNLSPYLHFGQISSQR
VVLEVEKAESNPGSKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSWAK
ESLNAHRNDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYTRMY
WAKKILEWSESPEKALEIAICLNDRYELDGRDPNGYAGIAWSIGGVHDRA
WGEREVTGKIRYMSYEGCKRKFDVKLYIEKYS

3D structure

• PDB: 7ydz Visualizing the DNA repair process by a photolyase at atomic resolution
• Chain: B
• Resolution: 2.23 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 R450 K451	A163 H164 R226 N227 E271 W275 Y346 M349 W391 R399 W401 R411 Y412 M413 S414 R420 K421
BS02	dna	B	Y158 T162 R429 A430 W431 E433 K439 R450	Y161 T165 R399 A400 W401 E403 K409 R420
BS03	FAD	B	Y252 L264 S265 N266 S268 E301 I302 W305 K306 K372 R378 N403 D409 N414 G415 G418	Y222 L234 S235 N236 S238 E271 I272 W275 K276 K342 R348 N373 D379 N384 G385 G388

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