Structure of PDB 1gth Chain B

Receptor sequence

>1gthB (length=1012) Species: 9823 (Sus scrofa)

APVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFH
CEKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFI
TSISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSIN
IGGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASIS
CASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDL
GVKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQ
GFYTSKDFLPLVAKSSKAGMCACHSPLPSIRGAVIVLGAGDTAFDCATSA
LRCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGG
RIVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEAL
SPIKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASW
YIHKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASA
APTTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYG
PGQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWM
ELSRKAEASGADALELNLSCPHGMGERGMGLACGQDPELVRNICRWVRQA
VQIPFFAKLTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPW
PAVGAGKRTTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAES
GLQFLHSGASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDG
QSPGTESHQKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQE
RKPFIPKKPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGK
CYMTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRT
TPYEPKRGLPLA

3D structure

• PDB: 1gth Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.
• Chain: B
• Resolution: 2.25 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K574 G601 S605 C671 H673 G674 K709 T735
• Catalytic site (residue number reindexed from 1): K573 G600 S604 C670 H672 G673 K708 T734
• 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 I97 C126 C130 T132 L135 C136 I152 Q156	C90 L94 I96 C125 C129 T131 L134 C135 I151 Q155
BS02	SF4	B	C79 L80 K81 C82 P86 C87 C140 N141 L142 I150 I152	C78 L79 K80 C81 P85 C86 C139 N140 L141 I149 I151
BS03	SF4	B	I948 C953 I954 N955 C956 G957 C959 P980 C996 P997 C1001 I1002	I940 C945 I946 N947 C948 G949 C951 P972 C988 P989 C993 I994
BS04	SF4	B	C963 Y968 I971 C986 T987 G988 C989 T990 C992	C955 Y960 I963 C978 T979 G980 C981 T982 C984
BS05	FMN	B	S550 A551 K574 T575 I590 N609 N668 K709 N736 S766 G767 T793 G794 G795 C816 S817 Q820	S549 A550 K573 T574 I589 N608 N667 K708 N735 S765 G766 T792 G793 G794 C815 S816 Q819
BS06	FAD	B	V129 G194 G196 P197 A198 E218 K219 G225 L226 E230 I231 R235 S260 L261 I283 G480 D481 T488 T489 S492	V128 G193 G195 P196 A197 E217 K218 G224 L225 E229 I230 R234 S259 L260 I282 G479 D480 T487 T488 S491
BS07	NDP	B	P131 A340 G341 D342 T343 R364 K365 R371 A437 F438 G439 N487	P130 A339 G340 D341 T342 R363 K364 R370 A436 F437 G438 N486
BS08	IDH	B	N609 E611 L612 I613 C671 H673 N736 T737	N608 E610 L611 I612 C670 H672 N735 T736

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:1gth, PDBe:1gth, PDBj:1gth
• PDBsum: 1gth
• PubMed: 11796730
• UniProt: Q28943|DPYD_PIG Dihydropyrimidine dehydrogenase [NADP(+)] (Gene Name=DPYD)