Structure of PDB 8f6n Chain B

Receptor sequence

>8f6nB (length=1001) Species: 9823 (Sus scrofa)

PVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFHC
EKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFIT
SISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSINI
GGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASISC
ASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDLG
VKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQG
FYTSKDFLPLVAKSSKAGMCACHSPLPSIRGAVIVLGAGDTAFDCATSAL
RCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGR
IVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALS
PIKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWY
IHKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAA
PTTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGP
GQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWME
LSRKAEASGADALELNLSSPHMGLACGQDPELVRNICRWVRQAVQIPFFA
KLTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGK
RTTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQFLHS
GASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSPGTES
HQKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKERKPFIPKKP
IPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGKCYMTCNDSG
YQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTTPYEPKRGL
P

3D structure

• PDB: 8f6n Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes.
• Chain: B
• 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	B	C91 L95 C130 L135 C136 Q156 V490	C89 L93 C128 L133 C134 Q154 V488
BS02	SF4	B	C79 L80 K81 C82 C87 C140 N141 I150	C77 L78 K79 C80 C85 C138 N139 I148
BS03	SF4	B	C953 I954 C956 C959 C996 P997 C1001	C936 I937 C939 C942 C979 P980 C984
BS04	SF4	B	C963 C986 G988 C989 T990 C992	C946 C969 G971 C972 T973 C975
BS05	FMN	B	S550 A551 K574 N609 N668 K709 T737 S766 G767 T793 G794 G795 C816 S817 Q820	S548 A549 K572 N607 N666 K701 T729 S758 G759 T785 G786 G787 C808 S809 Q812
BS06	FAD	B	V129 G194 G196 P197 A198 E218 K219 G225 L226 R235 S260 L261 I283 D342 G480 D481 T488 T489 S492	V127 G192 G194 P195 A196 E216 K217 G223 L224 R233 S258 L259 I281 D340 G478 D479 T486 T487 S490
BS07	TDR	B	N609 E611 L612 N668 N736 T737	N607 E609 L610 N666 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)