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Protein

Dihydropyrimidine dehydrogenase [NADP(+)]

Gene

DPYD

Organism
Sus scrofa (Pig)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine.3 Publications

Catalytic activityi

5,6-dihydrouracil + NADP+ = uracil + NADPH.2 Publications

Cofactori

Protein has several cofactor binding sites:

Pathwayi: beta-alanine biosynthesis

This protein is involved in the pathway beta-alanine biosynthesis, which is part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the pathway beta-alanine biosynthesis and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi79Iron-sulfur 1 (4Fe-4S)1
Metal bindingi82Iron-sulfur 1 (4Fe-4S)1
Metal bindingi87Iron-sulfur 1 (4Fe-4S)1
Metal bindingi91Iron-sulfur 2 (4Fe-4S)1
Binding sitei129FAD; via carbonyl oxygen1 Publication1
Metal bindingi130Iron-sulfur 2 (4Fe-4S)1
Metal bindingi136Iron-sulfur 2 (4Fe-4S)1
Metal bindingi140Iron-sulfur 1 (4Fe-4S)1
Metal bindingi156Iron-sulfur 2 (4Fe-4S)1
Binding sitei235FAD1 Publication1
Binding sitei261FAD; via amide nitrogen and carbonyl oxygen1 Publication1
Binding sitei371NADP1 Publication1
Binding sitei550FMN1 Publication1
Binding sitei609Substrate1
Active sitei671Proton acceptor1 Publication1
Binding sitei709FMN1 Publication1
Binding sitei767FMN; via amide nitrogen1 Publication1
Metal bindingi953Iron-sulfur 3 (4Fe-4S)1
Metal bindingi956Iron-sulfur 3 (4Fe-4S)1
Metal bindingi959Iron-sulfur 3 (4Fe-4S)1
Metal bindingi963Iron-sulfur 3 (4Fe-4S)1
Metal bindingi986Iron-sulfur 4 (4Fe-4S)1
Metal bindingi989Iron-sulfur 4 (4Fe-4S)1
Metal bindingi992Iron-sulfur 4 (4Fe-4S)1
Metal bindingi996Iron-sulfur 4 (4Fe-4S)1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi194 – 198FAD1 Publication5
Nucleotide bindingi218 – 226FAD1 Publication9
Nucleotide bindingi340 – 343NADP1 Publication4
Nucleotide bindingi364 – 365NADP1 Publication2
Nucleotide bindingi437 – 439NADP1 Publication3
Nucleotide bindingi480 – 489FAD1 Publication10
Nucleotide bindingi481 – 487NADP1 Publication7
Nucleotide bindingi574 – 575FMN1 Publication2
Nucleotide bindingi793 – 795FMN1 Publication3
Nucleotide bindingi816 – 817FMN1 Publication2

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  • dihydropyrimidine dehydrogenase (NADP+) activity Source: UniProtKB
  • flavin adenine dinucleotide binding Source: UniProtKB
  • FMN binding Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • NADP binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

4Fe-4S, FAD, Flavoprotein, FMN, Iron, Iron-sulfur, Metal-binding, NADP, Nucleotide-binding

Enzyme and pathway databases

BRENDAi1.3.1.2. 6170.
UniPathwayiUPA00131.

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydropyrimidine dehydrogenase [NADP(+)] (EC:1.3.1.2)
Short name:
DHPDHase
Short name:
DPD
Alternative name(s):
Dihydrothymine dehydrogenase
Dihydrouracil dehydrogenase
Gene namesi
Name:DPYD
OrganismiSus scrofa (Pig)
Taxonomic identifieri9823 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaSuinaSuidaeSus
Proteomesi
  • UP000008227 Componenti: Unplaced

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi126C → A: No effect on enzyme activity. Reduced iron content. 1 Publication1
Mutagenesisi156Q → E: Loss of enzyme activity. Reduces iron content. 1 Publication1
Mutagenesisi235R → A or K: Loss of enzyme activity. Loss of FAD binding. 1 Publication1
Mutagenesisi670S → A: Strongly reduced affinity for uracil. Reduces enzyme activity by 30%. 1 Publication1
Mutagenesisi671C → A: Reduces catalytic activity by 99%. 1 Publication1
Mutagenesisi673H → Q: Reduces activity by 50%. 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
PropeptideiPRO_00000211161 – 33
ChainiPRO_00000211174 – 1025Dihydropyrimidine dehydrogenase [NADP(+)]Add BLAST1022

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei384N6-acetyllysineBy similarity1

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ28943.
PeptideAtlasiQ28943.
PRIDEiQ28943.

Interactioni

Subunit structurei

Homodimer.3 Publications

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000007333.

Structurei

Secondary structure

11025
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi10 – 15Combined sources6
Turni16 – 18Combined sources3
Beta strandi24 – 26Combined sources3
Helixi31 – 41Combined sources11
Helixi69 – 78Combined sources10
Helixi86 – 89Combined sources4
Helixi97 – 105Combined sources9
Helixi109 – 119Combined sources11
Helixi123 – 129Combined sources7
Helixi132 – 134Combined sources3
Helixi136 – 139Combined sources4
Helixi141 – 144Combined sources4
Helixi152 – 166Combined sources15
Helixi179 – 181Combined sources3
Helixi184 – 187Combined sources4
Beta strandi190 – 193Combined sources4
Helixi197 – 208Combined sources12
Beta strandi214 – 222Combined sources9
Helixi226 – 229Combined sources4
Turni233 – 235Combined sources3
Helixi238 – 249Combined sources12
Turni250 – 252Combined sources3
Beta strandi254 – 258Combined sources5
Helixi268 – 273Combined sources6
Beta strandi278 – 281Combined sources4
Helixi292 – 294Combined sources3
Turni299 – 302Combined sources4
Beta strandi303 – 305Combined sources3
Helixi306 – 317Combined sources12
Beta strandi322 – 324Combined sources3
Beta strandi333 – 338Combined sources6
Helixi342 – 353Combined sources12
Beta strandi357 – 362Combined sources6
Helixi367 – 369Combined sources3
Helixi374 – 382Combined sources9
Beta strandi386 – 388Combined sources3
Beta strandi390 – 399Combined sources10
Beta strandi402 – 413Combined sources12
Beta strandi419 – 430Combined sources12
Beta strandi432 – 436Combined sources5
Helixi445 – 450Combined sources6
Turni451 – 453Combined sources3
Beta strandi460 – 462Combined sources3
Turni466 – 468Combined sources3
Beta strandi476 – 478Combined sources3
Helixi481 – 483Combined sources3
Helixi489 – 510Combined sources22
Helixi527 – 530Combined sources4
Beta strandi535 – 537Combined sources3
Beta strandi540 – 548Combined sources9
Helixi552 – 554Combined sources3
Helixi557 – 566Combined sources10
Beta strandi569 – 572Combined sources4
Helixi579 – 581Combined sources3
Beta strandi590 – 592Combined sources3
Beta strandi607 – 609Combined sources3
Helixi618 – 631Combined sources14
Beta strandi635 – 641Combined sources7
Helixi647 – 659Combined sources13
Beta strandi663 – 668Combined sources6
Beta strandi678 – 680Combined sources3
Helixi684 – 686Combined sources3
Helixi688 – 701Combined sources14
Beta strandi706 – 710Combined sources5
Helixi717 – 727Combined sources11
Beta strandi730 – 734Combined sources5
Beta strandi738 – 740Combined sources3
Beta strandi750 – 752Combined sources3
Turni755 – 758Combined sources4
Beta strandi763 – 767Combined sources5
Helixi768 – 770Combined sources3
Helixi771 – 784Combined sources14
Beta strandi790 – 795Combined sources6
Helixi799 – 807Combined sources9
Beta strandi811 – 816Combined sources6
Helixi817 – 820Combined sources4
Helixi826 – 840Combined sources15
Helixi844 – 846Combined sources3
Beta strandi848 – 850Combined sources3
Beta strandi858 – 860Combined sources3
Turni869 – 873Combined sources5
Helixi880 – 899Combined sources20
Helixi921 – 924Combined sources4
Turni925 – 928Combined sources4
Helixi929 – 931Combined sources3
Helixi935 – 937Combined sources3
Beta strandi940 – 942Combined sources3
Beta strandi944 – 948Combined sources5
Turni950 – 952Combined sources3
Helixi958 – 966Combined sources9
Beta strandi971 – 973Combined sources3
Turni975 – 977Combined sources3
Beta strandi980 – 982Combined sources3
Helixi991 – 995Combined sources5
Turni999 – 1001Combined sources3
Beta strandi1002 – 1006Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GT8X-ray3.30A/B/C/D1-1025[»]
1GTEX-ray1.65A/B/C/D1-1025[»]
1GTHX-ray2.25A/B/C/D1-1025[»]
1H7WX-ray1.90A/B/C/D1-1025[»]
1H7XX-ray2.01A/B/C/D1-1025[»]
ProteinModelPortaliQ28943.
SMRiQ28943.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ28943.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini69 – 1004Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd BLAST32
Domaini944 – 9764Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd BLAST33
Domaini978 – 10074Fe-4S ferredoxin-type 3PROSITE-ProRule annotationAdd BLAST30

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni668 – 670Substrate binding3
Regioni736 – 737Substrate binding2

Sequence similaritiesi

Contains 3 4Fe-4S ferredoxin-type domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0399. Eukaryota.
COG0167. LUCA.
COG0493. LUCA.
COG1146. LUCA.
HOGENOMiHOG000007797.
HOVERGENiHBG004351.
InParanoidiQ28943.
KOiK00207.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.50.50.60. 2 hits.
InterProiIPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR013785. Aldolase_TIM.
IPR005720. Dihydroorotate_DH.
IPR028261. DPD_II.
IPR023753. FAD/NAD-binding_dom.
IPR009051. Helical_ferredxn.
[Graphical view]
PfamiPF01180. DHO_dh. 1 hit.
PF14691. Fer4_20. 1 hit.
PF07992. Pyr_redox_2. 1 hit.
[Graphical view]
SUPFAMiSSF46548. SSF46548. 1 hit.
TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.
PROSITEiPS00198. 4FE4S_FER_1. 1 hit.
PS51379. 4FE4S_FER_2. 3 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q28943-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPVLSKDVA DIESILALNP RTQSHAALHS TLAKKLDKKH WKRNPDKNCF
60 70 80 90 100
HCEKLENNFG DIKHTTLGER GALREAMRCL KCADAPCQKS CPTHLDIKSF
110 120 130 140 150
ITSISNKNYY GAAKMIFSDN PLGLTCGMVC PTSDLCVGGC NLYATEEGSI
160 170 180 190 200
NIGGLQQFAS EVFKAMNIPQ IRNPCLPSQE KMPEAYSAKI ALLGAGPASI
210 220 230 240 250
SCASFLARLG YSDITIFEKQ EYVGGLSTSE IPQFRLPYDV VNFEIELMKD
260 270 280 290 300
LGVKIICGKS LSENEITLNT LKEEGYKAAF IGIGLPEPKT DDIFQGLTQD
310 320 330 340 350
QGFYTSKDFL PLVAKSSKAG MCACHSPLPS IRGAVIVLGA GDTAFDCATS
360 370 380 390 400
ALRCGARRVF LVFRKGFVNI RAVPEEVELA KEEKCEFLPF LSPRKVIVKG
410 420 430 440 450
GRIVAVQFVR TEQDETGKWN EDEDQIVHLK ADVVISAFGS VLRDPKVKEA
460 470 480 490 500
LSPIKFNRWD LPEVDPETMQ TSEPWVFAGG DIVGMANTTV ESVNDGKQAS
510 520 530 540 550
WYIHKYIQAQ YGASVSAKPE LPLFYTPVDL VDISVEMAGL KFINPFGLAS
560 570 580 590 600
AAPTTSSSMI RRAFEAGWGF ALTKTFSLDK DIVTNVSPRI VRGTTSGPMY
610 620 630 640 650
GPGQSSFLNI ELISEKTAAY WCQSVTELKA DFPDNIVIAS IMCSYNKNDW
660 670 680 690 700
MELSRKAEAS GADALELNLS CPHGMGERGM GLACGQDPEL VRNICRWVRQ
710 720 730 740 750
AVQIPFFAKL TPNVTDIVSI ARAAKEGGAD GVTATNTVSG LMGLKADGTP
760 770 780 790 800
WPAVGAGKRT TYGGVSGTAI RPIALRAVTT IARALPGFPI LATGGIDSAE
810 820 830 840 850
SGLQFLHSGA SVLQVCSAVQ NQDFTVIQDY CTGLKALLYL KSIEELQGWD
860 870 880 890 900
GQSPGTESHQ KGKPVPRIAE LMGKKLPNFG PYLEQRKKII AEEKMRLKEQ
910 920 930 940 950
NAAFPPLERK PFIPKKPIPA IKDVIGKALQ YLGTFGELSN IEQVVAVIDE
960 970 980 990 1000
EMCINCGKCY MTCNDSGYQA IQFDPETHLP TVTDTCTGCT LCLSVCPIID
1010 1020
CIRMVSRTTP YEPKRGLPLA VNPVC
Length:1,025
Mass (Da):111,424
Last modified:November 1, 1997 - v1
Checksum:iB8D553AD862845D0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U09179 mRNA. Translation: AAA57475.1.
PIRiB54718.
RefSeqiNP_999209.1. NM_214044.2.
UniGeneiSsc.153.

Genome annotation databases

GeneIDi397109.
KEGGissc:397109.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U09179 mRNA. Translation: AAA57475.1.
PIRiB54718.
RefSeqiNP_999209.1. NM_214044.2.
UniGeneiSsc.153.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GT8X-ray3.30A/B/C/D1-1025[»]
1GTEX-ray1.65A/B/C/D1-1025[»]
1GTHX-ray2.25A/B/C/D1-1025[»]
1H7WX-ray1.90A/B/C/D1-1025[»]
1H7XX-ray2.01A/B/C/D1-1025[»]
ProteinModelPortaliQ28943.
SMRiQ28943.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000007333.

Proteomic databases

PaxDbiQ28943.
PeptideAtlasiQ28943.
PRIDEiQ28943.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi397109.
KEGGissc:397109.

Organism-specific databases

CTDi1806.

Phylogenomic databases

eggNOGiKOG0399. Eukaryota.
COG0167. LUCA.
COG0493. LUCA.
COG1146. LUCA.
HOGENOMiHOG000007797.
HOVERGENiHBG004351.
InParanoidiQ28943.
KOiK00207.

Enzyme and pathway databases

UniPathwayiUPA00131.
BRENDAi1.3.1.2. 6170.

Miscellaneous databases

EvolutionaryTraceiQ28943.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.50.50.60. 2 hits.
InterProiIPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR013785. Aldolase_TIM.
IPR005720. Dihydroorotate_DH.
IPR028261. DPD_II.
IPR023753. FAD/NAD-binding_dom.
IPR009051. Helical_ferredxn.
[Graphical view]
PfamiPF01180. DHO_dh. 1 hit.
PF14691. Fer4_20. 1 hit.
PF07992. Pyr_redox_2. 1 hit.
[Graphical view]
SUPFAMiSSF46548. SSF46548. 1 hit.
TIGRFAMsiTIGR01037. pyrD_sub1_fam. 1 hit.
PROSITEiPS00198. 4FE4S_FER_1. 1 hit.
PS51379. 4FE4S_FER_2. 3 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDPYD_PIG
AccessioniPrimary (citable) accession number: Q28943
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: November 2, 2016
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.