Structure of PDB 5zcw Chain A

Receptor sequence

>5zcwA (length=459) Species: 2209 (Methanosarcina mazei)

PRGSHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEA
NVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDP
GEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVV
PCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPEMVETLSDV
LETGVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVMESFIADRLDSYG
ALRNDPTKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAFLDEIL
IWKEISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEEFEAG
KTHDPLWNASQMELLSTGKMHGYTRMYWAKKILEWSESPEKALEIAICLN
DRYELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRKFD
VKLYIEKYS

3D structure

• PDB: 5zcw Twist and turn: a revised structural view on the unpaired bubble of class II CPD photolyase in complex with damaged DNA.
• Chain: A
• Resolution: 2.7 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 E301 W305 Y376 M379 W421 W431 R441 Y442 M443 S444 R450 K451	A163 E298 W302 Y373 M376 W418 W428 R438 Y439 M440 S441 R447 K448
BS02	dna	A	Y158 W328 R429 W431 K439	Y161 W325 R426 W428 K436
BS03	FAD	A	Y252 L264 S265 N266 S268 F298 E301 W305 K306 K372 G375 R378 M379 N403 D409 N414 G415 S422	Y249 L261 S262 N263 S265 F295 E298 W302 K303 K369 G372 R375 M376 N400 D406 N411 G412 S419

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:5zcw, PDBe:5zcw, PDBj:5zcw
• PDBsum: 5zcw
• PubMed: 30224964
• UniProt: Q8PYK9