Structure of PDB 8f61 Chain D

Receptor sequence

>8f61D (length=1016) Species: 9823 (Sus scrofa)

PVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFHC
EKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFIT
SISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSINI
GGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASISC
ASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDLG
VKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQG
FYTSKDFLPLVAKSSKAGMCACHSPLPSIRGAVIVLGAGDTAFDCATSAL
RCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGR
IVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALS
PIKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWY
IHKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAA
PTTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGP
GQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWME
LSRKAEASGADALELNLSSPHGMGERGMGLACGQDPELVRNICRWVRQAV
QIPFFAKLTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWP
AVGAGKRTTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESG
LQFLHSGASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQ
SPGTESHQKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQNA
AFPPLERKPFIPKKPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEM
CINCGKCYMTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCI
RMVSRTTPYEPKRGLP

3D structure

• PDB: 8f61 Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes.
• Chain: D
• Resolution: 2.14 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	D	C79 L80 K81 C82 C87 C140 N141 L142 I150 I152	C77 L78 K79 C80 C85 C138 N139 L140 I148 I150
BS02	SF4	D	C91 L95 I97 C130 T132 L135 C136 Q156	C89 L93 I95 C128 T130 L133 C134 Q154
BS03	SF4	D	A946 C963 I971 C986 T987 G988 C989 T990 C992	A944 C961 I969 C984 T985 G986 C987 T988 C990
BS04	SF4	D	I948 C953 I954 C956 G957 C959 P980 C996 P997 C1001 I1002	I946 C951 I952 C954 G955 C957 P978 C994 P995 C999 I1000
BS05	FAD	D	V129 G196 P197 E218 K219 G225 L226 I231 R235 S260 L261 I283 G284 T343 D346 G480 D481 T488 T489 S492	V127 G194 P195 E216 K217 G223 L224 I229 R233 S258 L259 I281 G282 T341 D344 G478 D479 T486 T487 S490
BS06	TDR	D	N609 E611 N668 N736 T737	N607 E609 N666 N734 T735
BS07	FNR	D	S550 A551 K574 T575 I590 N609 N668 K709 N736 S766 G767 T793 G795 C816 S817	S548 A549 K572 T573 I588 N607 N666 K707 N734 S764 G765 T791 G793 C814 S815

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:8f61, PDBe:8f61, PDBj:8f61
• PDBsum: 8f61
• PubMed: 36681231
• UniProt: Q28943|DPYD_PIG Dihydropyrimidine dehydrogenase [NADP(+)] (Gene Name=DPYD)