Structure of PDB 8f6n Chain A

Receptor sequence

>8f6nA (length=996) Species: 9823 (Sus scrofa)

APVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFH
CEKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFI
TSISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSIN
IGGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASIS
CASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDL
GVKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQ
GFYTSKDFLPLVAKSSKGMCPLSIRGAVIVLGAGDTAFDCATSALRCGAR
RVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGRIVAVQ
FVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALSPIKFN
RWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWYIHKYI
QAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAAPTTSS
SMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGPGQSSF
LNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWMELSRKA
EASGADALELNLSSPHGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTP
NVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKRTTY
GGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQFLHSGASV
LQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSPGTESHQKG
KPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKERKPFIPKKPIPAI
KDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGKCYMTCNDSGYQAI
QFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTTPYEPKRGL

3D structure

• PDB: 8f6n Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes.
• Chain: A
• Resolution: 2.12 Å

Enzymatic activity

• Enzyme Commision number: 1.3.1.2: dihydropyrimidine dehydrogenase (NADP(+)).

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	SF4	A	C91 L95 I97 C130 C136 Q156	C90 L94 I96 C129 C135 Q155
BS02	SF4	A	C79 K81 C82 C87 C140 N141 I150 I152	C78 K80 C81 C86 C139 N140 I149 I151
BS03	SF4	A	C953 I954 C956 G957 C959 C996 C1001	C932 I933 C935 G936 C938 C975 C980
BS04	SF4	A	C963 I971 C986 G988 C989 T990 C992	C942 I950 C965 G967 C968 T969 C971
BS05	FMN	A	S550 A551 K574 T575 N609 N668 K709 S766 G767 T793 G794 G795 C816 S817	S543 A544 K567 T568 N602 N661 K697 S754 G755 T781 G782 G783 C804 S805
BS06	FAD	A	V129 G194 G196 P197 A198 E218 K219 G225 L226 I231 R235 S260 L261 I283 G284 D342 T343 G480 D481 T488 T489 S492	V128 G193 G195 P196 A197 E217 K218 G224 L225 I230 R234 S259 L260 I282 G283 D335 T336 G473 D474 T481 T482 S485
BS07	TDR	A	N609 E611 N736 T737	N602 E604 N724 T725

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0002058 uracil binding
• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity
• GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
• GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity
• GO:0042803 protein homodimerization activity
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding
• GO:0050661 NADP binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0006210 thymine catabolic process
• GO:0006212 uracil catabolic process
• GO:0006214 thymidine catabolic process
• GO:0019483 beta-alanine biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:8f6n, PDBe:8f6n, PDBj:8f6n
• PDBsum: 8f6n
• PubMed: 36681231
• UniProt: Q28943|DPYD_PIG Dihydropyrimidine dehydrogenase [NADP(+)] (Gene Name=DPYD)