Structure of PDB 8f61 Chain C

Receptor sequence

>8f61C (length=1016) Species: 9823 (Sus scrofa)

APVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFH
CEKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFI
TSISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSIN
IGGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASIS
CASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDL
GVKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQ
GFYTSKDFLPLVAKSSKAGMCACHSPLPSIRGAVIVLGAGDTAFDCATSA
LRCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGG
RIVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEAL
SPIKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASW
YIHKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASA
APTTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYG
PGQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWM
ELSRKAEASGADALELNLSSPHGMGERGMGLACGQDPELVRNICRWVRQA
VQIPFFAKLTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPW
PAVGAGKRTTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAES
GLQFLHSGASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDG
QSPGTESHQKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQN
AAFPPLERKPFIPKKPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEE
MCINCGKCYMTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDC
IRMVSRTTPYEPKRGL

3D structure

• PDB: 8f61 Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes.
• Chain: C
• 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	C	C91 I97 C126 C130 T132 L135 C136 Q156	C90 I96 C125 C129 T131 L134 C135 Q155
BS02	SF4	C	C79 L80 K81 C82 C87 C140 N141 L142 I150 I152	C78 L79 K80 C81 C86 C139 N140 L141 I149 I151
BS03	SF4	C	C953 I954 N955 C956 G957 C959 P980 C996 P997 C1001 I1002	C952 I953 N954 C955 G956 C958 P979 C995 P996 C1000 I1001
BS04	SF4	C	C963 I971 C986 G988 C989 T990 C992	C962 I970 C985 G987 C988 T989 C991
BS05	FAD	C	V129 G194 G196 P197 A198 E218 K219 G225 L226 I231 R235 L261 I283 G284 T343 G480 D481 T488 T489 S492	V128 G193 G195 P196 A197 E217 K218 G224 L225 I230 R234 L260 I282 G283 T342 G479 D480 T487 T488 S491
BS06	FMN	C	S550 A551 K574 T575 N609 N668 K709 T737 S766 G767 T793 G794 G795 C816 S817	S549 A550 K573 T574 N608 N667 K708 T736 S765 G766 T792 G793 G794 C815 S816
BS07	XH5	C	N609 E611 N668 N736	N608 E610 N667 N735

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)