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Protein

Dihydropyrimidine dehydrogenase [NADP(+)]

Gene

DPYD

Organism
Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine (By similarity).By similarity

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:
  • [4Fe-4S] clusterBy similarityNote: Binds 4 [4Fe-4S] clusters. Contains approximately 16 iron atoms per subunit.By similarity
  • FADBy similarity
  • FMNBy similarity

Enzyme regulationi

Inactivated by 5-iodouracil.By similarity

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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi79 – 791Iron-sulfur 1 (4Fe-4S)By similarity
Metal bindingi82 – 821Iron-sulfur 1 (4Fe-4S)By similarity
Metal bindingi87 – 871Iron-sulfur 1 (4Fe-4S)By similarity
Metal bindingi91 – 911Iron-sulfur 2 (4Fe-4S)By similarity
Binding sitei129 – 1291FAD; via carbonyl oxygenBy similarity
Metal bindingi130 – 1301Iron-sulfur 2 (4Fe-4S)By similarity
Metal bindingi136 – 1361Iron-sulfur 2 (4Fe-4S)By similarity
Metal bindingi140 – 1401Iron-sulfur 1 (4Fe-4S)By similarity
Metal bindingi156 – 1561Iron-sulfur 2 (4Fe-4S)By similarity
Binding sitei235 – 2351FADBy similarity
Binding sitei261 – 2611FAD; via amide nitrogen and carbonyl oxygenBy similarity
Binding sitei371 – 3711NADPBy similarity
Binding sitei550 – 5501FMNBy similarity
Binding sitei609 – 6091SubstrateBy similarity
Active sitei671 – 6711Proton acceptorBy similarity
Binding sitei709 – 7091FMNBy similarity
Binding sitei767 – 7671FMN; via amide nitrogenBy similarity
Metal bindingi953 – 9531Iron-sulfur 3 (4Fe-4S)By similarity
Metal bindingi956 – 9561Iron-sulfur 3 (4Fe-4S)By similarity
Metal bindingi959 – 9591Iron-sulfur 3 (4Fe-4S)By similarity
Metal bindingi963 – 9631Iron-sulfur 3 (4Fe-4S)By similarity
Metal bindingi986 – 9861Iron-sulfur 4 (4Fe-4S)By similarity
Metal bindingi989 – 9891Iron-sulfur 4 (4Fe-4S)By similarity
Metal bindingi992 – 9921Iron-sulfur 4 (4Fe-4S)By similarity
Metal bindingi996 – 9961Iron-sulfur 4 (4Fe-4S)By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi194 – 1985FADBy similarity
Nucleotide bindingi218 – 2269FADBy similarity
Nucleotide bindingi340 – 3434NADPBy similarity
Nucleotide bindingi364 – 3652NADPBy similarity
Nucleotide bindingi437 – 4393NADPBy similarity
Nucleotide bindingi480 – 48910FADBy similarity
Nucleotide bindingi481 – 4877NADPBy similarity
Nucleotide bindingi574 – 5752FMNBy similarity
Nucleotide bindingi793 – 7953FMNBy similarity
Nucleotide bindingi816 – 8172FMNBy similarity

GO - Molecular functioni

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

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
OrganismiPongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
Taxonomic identifieri9601 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaePongo
Proteomesi
  • UP000001595 Componenti: Unplaced

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10251025Dihydropyrimidine dehydrogenase [NADP(+)]PRO_0000327503Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei384 – 3841N6-acetyllysineBy similarity
Modified residuei905 – 9051PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PRIDEiQ5R895.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi9601.ENSPPYP00000001308.

Structurei

3D structure databases

ProteinModelPortaliQ5R895.
SMRiQ5R895. Positions 2-1019.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini69 – 100324Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd
BLAST
Domaini944 – 976334Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd
BLAST
Domaini978 – 1007304Fe-4S ferredoxin-type 3PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni668 – 6703Substrate bindingBy similarity
Regioni736 – 7372Substrate bindingBy similarity

Sequence similaritiesi

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

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG0167. LUCA.
COG0493. LUCA.
COG1146. LUCA.
HOGENOMiHOG000007797.
HOVERGENiHBG004351.
InParanoidiQ5R895.
KOiK00207.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.50.50.60. 3 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.

Q5R895-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAPVLSKDSA DIESILALNP RTQTHATLRS TSAKKLDKKH WKRNPDKNCF
60 70 80 90 100
NCEKLENNFD DIKHTTLGER GALREAMRCL KCADAPCQKS CPTNLDIKSF
110 120 130 140 150
ITSIANKNYY GAAKMIFSDN PLGLTCGMVC PTPDLCVGGC NLYATEEGPI
160 170 180 190 200
NIGGLQQFAT EVFKAMSIPQ IRNPFLPPPE KMSEAYSAKI ALFGAGPASI
210 220 230 240 250
SCASFLARLG YSDITIFEKQ EYVGGLSTSE IPQFRLPYDV VNFEIELMKD
260 270 280 290 300
LGVKIICGKS LSVNEMTLST LKEKGYKAAF IGIGLPEPNK DAIFQGLTQD
310 320 330 340 350
QGFYTSKDFL PLVAKGSKAG MCACHSPLPS IRGVVIVLGA GDTAFDCATS
360 370 380 390 400
ALRCGARRVF IVFRKGFVNI RAVPEEMELA KEEKCEFLPF LSPRKVIVKG
410 420 430 440 450
GRIVAMQFVR TEQDETGKWN EDEDQMVHLK ADVVISAFGS VLSDPKVKEA
460 470 480 490 500
MSPIKFNRWG LPEVDPETMQ TSEAWVFAGG DVVGLANTTV ESVNDGKQAS
510 520 530 540 550
WYIHKYIQSQ YGASVSAKPE LPLFYTAIDL VDISVEMAGL KFINPFGLAS
560 570 580 590 600
ATPATSTSMI RRAFEAGWGF ALTKTFSLDK DIVTNVSPRI VRGTTSGPMY
610 620 630 640 650
GPGQSSFLNI ELISEKTAAY WCQSVTELKA DFPDNIVIAS IMCSYNKNDW
660 670 680 690 700
TELAKKSEDS GADALELNLS CPHGMGERGM GLACGQDPEL VRNICRWVRQ
710 720 730 740 750
AVQIPFFAKL TPNVTDIVSI ARAAKEGGAN GVTATNTVSG LMGLKSDGTP
760 770 780 790 800
WPAVGIAKRT TYGGVSGTAI RPIALRAVTS TARALPGFPI LATGGIDSAE
810 820 830 840 850
SGLQFLHSGA SVLQVCSAIQ NQDFTVIEDY CTGLKALLYL KSIEELQDWD
860 870 880 890 900
GQSPATVSHQ KGKPVPRIAE LMDKKLPSFG PYLEQRKKII AENKIRLKEQ
910 920 930 940 950
NIASSPHKRN CFIPKRPVPT IKDVIGKALQ YLGTFGELSN VEQVVAMIDE
960 970 980 990 1000
EMCINCGKCY MTCNDSGYQA IQFDPETHLP TITDTCTGCT LCLSVCPIVD
1010 1020
CIKMVSRTTP YEPKRGVPLS VNPVC
Length:1,025
Mass (Da):111,468
Last modified:December 21, 2004 - v1
Checksum:i39FAE483BA9983B6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR859859 mRNA. Translation: CAH92015.1.
RefSeqiNP_001126169.1. NM_001132697.1.
UniGeneiPab.11422.

Genome annotation databases

GeneIDi100173131.
KEGGipon:100173131.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR859859 mRNA. Translation: CAH92015.1.
RefSeqiNP_001126169.1. NM_001132697.1.
UniGeneiPab.11422.

3D structure databases

ProteinModelPortaliQ5R895.
SMRiQ5R895. Positions 2-1019.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9601.ENSPPYP00000001308.

Proteomic databases

PRIDEiQ5R895.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100173131.
KEGGipon:100173131.

Organism-specific databases

CTDi1806.

Phylogenomic databases

eggNOGiCOG0167. LUCA.
COG0493. LUCA.
COG1146. LUCA.
HOGENOMiHOG000007797.
HOVERGENiHBG004351.
InParanoidiQ5R895.
KOiK00207.

Enzyme and pathway databases

UniPathwayiUPA00131.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
3.50.50.60. 3 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...

Publicationsi

  1. The German cDNA consortium
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Kidney.

Entry informationi

Entry nameiDPYD_PONAB
AccessioniPrimary (citable) accession number: Q5R895
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 8, 2008
Last sequence update: December 21, 2004
Last modified: July 6, 2016
This is version 80 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.