Structure of PDB 8f6n Chain C

Receptor sequence

>8f6nC (length=1002) Species: 9823 (Sus scrofa)

APVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFH
CEKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFI
TSISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSIN
IGGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASIS
CASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDL
GVKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQ
GFYTSKDFLPLVAKSSKAGMCASPLPSIRGAVIVLGAGDTAFDCATSALR
CGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGRI
VAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALSP
IKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWYI
HKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAAP
TTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGPG
QSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWMEL
SRKAEASGADALELNLSSPHGMGLACGQDPELVRNICRWVRQAVQIPFFA
KLTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGK
RTTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQFLHS
GASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSPGTES
HQKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQERKPFIPK
KPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGKCYMTCND
SGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTTPYEPKR
GL

3D structure

• PDB: 8f6n Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes.
• Chain: C
• 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	C	C91 C130 C136 Q156	C90 C129 C135 Q155
BS02	SF4	C	C79 L80 K81 C82 C87 C140 N141 I150	C78 L79 K80 C81 C86 C139 N140 I149
BS03	SF4	C	C953 C956 C959 C996 I1002	C938 C941 C944 C981 I987
BS04	SF4	C	C963 I971 C986 T987 G988 C989 T990 C992	C948 I956 C971 T972 G973 C974 T975 C977
BS05	FMN	C	S550 A551 K574 I590 N609 N668 K709 T737 S766 G767 T793 G794 G795 C816 S817 Q820	S547 A548 K571 I587 N606 N665 K701 T729 S758 G759 T785 G786 G787 C808 S809 Q812
BS06	FAD	C	V129 G194 G196 P197 E218 K219 G225 L226 E230 I231 R235 L261 I283 D342 T343 G480 D481 N487 T488 T489 S492	V128 G193 G195 P196 E217 K218 G224 L225 E229 I230 R234 L260 I282 D339 T340 G477 D478 N484 T485 T486 S489
BS07	TDR	C	N609 L612 N736 T737	N606 L609 N728 T729

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)