Reviewed, UniProtKB/Swiss-Prot Q12882 (DPYD_HUMAN)

Names and origin

Protein names

Recommended name:
    Dihydropyrimidine dehydrogenase [NADP+]
      Short name=DHPDHase
      Short name=DPD
    EC=1.3.1.2
Alternative name(s):
    Dihydrouracil dehydrogenase
    Dihydrothymine dehydrogenase

Gene names

Name:

DPYD

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	1025 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine. Also involved the degradation of the chemotherapeutic drug 5-fluorouracil.
Catalytic activity	5,6-dihydrouracil + NADP(+) = uracil + NADPH.
Cofactor	Binds 2 FAD. Binds 2 FMN. Binds 2 4Fe-4S clusters. Contains approximately 33 iron atoms per molecule.
Pathway	Amino-acid biosynthesis; beta-alanine biosynthesis.
Subunit structure	Homodimer.
Subcellular location	Cytoplasm.
Tissue specificity	Found in most tissues with greatest activity found in liver and peripheral blood mononuclear cells.
Involvement in disease	Defects in DPYD are the cause of dihydropyrimidine dehydrogenase deficiency (DPYD deficiency) [MIM:274270]; also known as hereditary thymine-uraciluria or familial pyrimidinemia. DPYD deficiency is a disease characterized by persistent urinary excretion of excessive amounts of uracil, thymine and 5-hydroxymethyluracil. Patients suffering from this disease show a severe reaction to the anticancer drug 5-fluorouracil. This reaction includes stomatitis, Leukopenia, thrombocytopenia, hair loss, diarrhea, fever, marked weight loss, cerebellar ataxia, and neurologic symptoms, progressing to semicoma.
Sequence similarities	Belongs to the dihydropyrimidine dehydrogenase family. Contains 3 4Fe-4S ferredoxin-type domains.

Ontologies

Keywords
Cellular component	Cytoplasm
Coding sequence diversity	Polymorphism
Disease	Disease mutation
Domain	Repeat
Ligand	4Fe-4S FAD FMN Flavoprotein Iron Iron-sulfur Metal-binding NADP
Molecular function	Oxidoreductase
PTM	Phosphoprotein
Technical term	Direct protein sequencing
Gene Ontology (GO)
Biological process	'de novo' pyrimidine base biosynthetic process Inferred from electronic annotation. Source: InterPro oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW purine base catabolic process Inferred from mutant phenotype. Source: UniProtKB thymidine catabolic process Ref.9 Inferred from direct assay. Source: UniProtKB thymine catabolic process Inferred from direct assay. Source: UniProtKB uracil catabolic process Ref.9 Inferred from direct assay. Source: UniProtKB
Cellular component	cytosol Ref.1 Inferred from direct assay. Source: UniProtKB
Molecular function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW FAD binding Inferred from sequence or structural similarity. Source: UniProtKB NADP binding Inferred from sequence or structural similarity. Source: UniProtKB dihydroorotate oxidase activity Inferred from electronic annotation. Source: InterPro dihydropyrimidine dehydrogenase (NADP+) activity Ref.1 Ref.9 Inferred from direct assay. Source: UniProtKB dihydrouracil dehydrogenase (NAD+) activity Ref.1 Inferred from Experiment. Source: Reactome electron carrier activity Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein homodimerization activity Ref.9 Inferred from direct assay. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Propeptide	1 – 3	3			PRO_0000021114
	Chain	4 – 1025	1022	Dihydropyrimidine dehydrogenase [NADP+]		PRO_0000021115
Regions
	Domain	69 – 100	32	4Fe-4S ferredoxin-type 1
	Domain	944 – 976	33	4Fe-4S ferredoxin-type 2
	Domain	978 – 1007	30	4Fe-4S ferredoxin-type 3
	Nucleotide binding	335 – 351	17	NADP Potential
	Nucleotide binding	471 – 481	11	FAD Potential
	Region	661 – 678	18	Uracil binding Potential
Sites
	Metal binding	953	1	Iron-sulfur 1 (4Fe-4S) Potential
	Metal binding	956	1	Iron-sulfur 1 (4Fe-4S) Potential
	Metal binding	959	1	Iron-sulfur 1 (4Fe-4S) Potential
	Metal binding	963	1	Iron-sulfur 1 (4Fe-4S) Potential
	Metal binding	986	1	Iron-sulfur 2 (4Fe-4S) Potential
	Metal binding	989	1	Iron-sulfur 2 (4Fe-4S) Potential
	Metal binding	992	1	Iron-sulfur 2 (4Fe-4S) Potential
	Metal binding	996	1	Iron-sulfur 2 (4Fe-4S) Potential
Amino acid modifications
	Modified residue	577	1	Phosphoserine
Natural variations
	Natural variant	29	1	C → R in allele DPYD*9A and allele DPYD*9B; loss of activity. dbSNP rs1801265.		VAR_005173
	Natural variant	235	1	R → W in allele DPYD*8; loss of activity. dbSNP rs1801266.		VAR_005174
	Natural variant	534	1	S → N in allele DPYD*4; low activity. dbSNP rs1801158.		VAR_005175
	Natural variant	543	1	I → V in allele DPYD*5. dbSNP rs1801159.		VAR_005176
	Natural variant	732	1	V → I: dbSNP rs1801160.		VAR_014760
	Natural variant	886	1	R → H in allele DPYD*9B; 25% of activity. dbSNP rs1801267.		VAR_005177
	Natural variant	995	1	V → F in allele DPYD*10; low activity. dbSNP rs1801268.		VAR_005178
Experimental info
	Sequence conflict	845	1	E → G in BAF83906. Ref.4
	Sequence conflict	910	1	N → S in AAA57474. Ref.1
	Sequence conflict	1024	1	V → G in AAI31779. Ref.6

Sequences

	Sequence		Length	Mass (Da)
	Q12882-1 [UniParc]. Last modified November 13, 2007. Version 2. Checksum: 0201943955AB2C21	FASTA	1,025	111,401
	10 20 30 40 50 60 MAPVLSKDSA DIESILALNP RTQTHATLCS TSAKKLDKKH WKRNPDKNCF NCEKLENNFD 70 80 90 100 110 120 DIKHTTLGER GALREAMRCL KCADAPCQKS CPTNLDIKSF ITSIANKNYY GAAKMIFSDN 130 140 150 160 170 180 PLGLTCGMVC PTSDLCVGGC NLYATEEGPI NIGGLQQFAT EVFKAMSIPQ IRNPSLPPPE 190 200 210 220 230 240 KMSEAYSAKI ALFGAGPASI SCASFLARLG YSDITIFEKQ EYVGGLSTSE IPQFRLPYDV 250 260 270 280 290 300 VNFEIELMKD LGVKIICGKS LSVNEMTLST LKEKGYKAAF IGIGLPEPNK DAIFQGLTQD 310 320 330 340 350 360 QGFYTSKDFL PLVAKGSKAG MCACHSPLPS IRGVVIVLGA GDTAFDCATS ALRCGARRVF 370 380 390 400 410 420 IVFRKGFVNI RAVPEEMELA KEEKCEFLPF LSPRKVIVKG GRIVAMQFVR TEQDETGKWN 430 440 450 460 470 480 EDEDQMVHLK ADVVISAFGS VLSDPKVKEA LSPIKFNRWG LPEVDPETMQ TSEAWVFAGG 490 500 510 520 530 540 DVVGLANTTV ESVNDGKQAS WYIHKYVQSQ YGASVSAKPE LPLFYTPIDL VDISVEMAGL 550 560 570 580 590 600 KFINPFGLAS ATPATSTSMI RRAFEAGWGF ALTKTFSLDK DIVTNVSPRI IRGTTSGPMY 610 620 630 640 650 660 GPGQSSFLNI ELISEKTAAY WCQSVTELKA DFPDNIVIAS IMCSYNKNDW TELAKKSEDS 670 680 690 700 710 720 GADALELNLS CPHGMGERGM GLACGQDPEL VRNICRWVRQ AVQIPFFAKL TPNVTDIVSI 730 740 750 760 770 780 ARAAKEGGAN GVTATNTVSG LMGLKSDGTP WPAVGIAKRT TYGGVSGTAI RPIALRAVTS 790 800 810 820 830 840 IARALPGFPI LATGGIDSAE SGLQFLHSGA SVLQVCSAIQ NQDFTVIEDY CTGLKALLYL 850 860 870 880 890 900 KSIEELQDWD GQSPATVSHQ KGKPVPRIAE LMDKKLPSFG PYLEQRKKII AENKIRLKEQ 910 920 930 940 950 960 NVAFSPLKRN CFIPKRPIPT IKDVIGKALQ YLGTFGELSN VEQVVAMIDE EMCINCGKCY 970 980 990 1000 1010 1020 MTCNDSGYQA IQFDPETHLP TITDTCTGCT LCLSVCPIVD CIKMVSRTTP YEPKRGVPLS VNPVC

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"cDNA cloning and chromosome mapping of human dihydropyrimidine dehydrogenase, an enzyme associated with 5-fluorouracil toxicity and congenital thymine uraciluria." Yokota H., Fernandez-Salguero P., Furuya H., Lin K., McBride O.W., Podschun B., Schnackerz K.D., Gonzalez F.J. J. Biol. Chem. 269:23192-23196(1994) [PubMed: 8083224] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Liver.
[2]	"Structural organization of the human dihydropyrimidine dehydrogenase gene." Johnson M.R., Wang K., Tillmanns S., Albin N., Diasio R.B. Cancer Res. 57:1660-1663(1997) [PubMed: 9135003] [Abstract] Cited for: NUCLEOTIDE SEQUENCE.
[3]	"Suicidal inactivation of human dihydropyrimidine dehydrogenase by (E)-5-(2-bromovinyl)uracil derived from the antiviral, sorivudine." Ogura K., Nishiyama T., Takubo H., Kato A., Okuda H., Arakawa K., Fukushima M., Nagayama S., Kawaguchi Y., Watabe T. Cancer Lett. 122:107-113(1998) [PubMed: 9464498] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[4]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ARG-29.
[5]	"The DNA sequence and biological annotation of human chromosome 1." Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R. Nature 441:315-321(2006) [PubMed: 16710414] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANTS VAL-543 AND ILE-732.
[7]	"A point mutation in an invariant splice donor site leads to exon skipping in two unrelated Dutch patients with dihydropyrimidine dehydrogenase deficiency." Vreken P., van Kuilenburg A.B.P., Meinsma R., Smit G.P.A., Bakker H.D., de Abreu R.A., van Gennip A.H. J. Inherit. Metab. Dis. 19:645-654(1996) [PubMed: 8892022] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 581-635. Tissue: Liver.
[8]	"Lack of correlation between phenotype and genotype for the polymorphically expressed dihydropyrimidine dehydrogenase in a family of Pakistani origin." Fernandez-Salguero P.M., Sapone A., Wei X., Holt J.R., Jones S., Idle J.R., Gonzalez F.J. Pharmacogenetics 7:161-163(1997) [PubMed: 9170156] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 581-635.
[9]	"Purification and characterization of dihydropyrimidine dehydrogenase from human liver." Lu Z.-H., Zhang R., Diasio R.B. J. Biol. Chem. 267:17102-17109(1992) [PubMed: 1512248] [Abstract] Cited for: CHARACTERIZATION, PARTIAL PROTEIN SEQUENCE. Tissue: Liver.
[10]	"Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column." Imami K., Sugiyama N., Kyono Y., Tomita M., Ishihama Y. Anal. Sci. 24:161-166(2008) [PubMed: 18187866] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-577, MASS SPECTROMETRY.
[11]	"Dihydropyrimidine dehydrogenase (DPD) deficiency: identification and expression of missense mutations C29R, R886H and R235W." Vreken P., van Kuilenburg A.B.P., Meinsma R., van Gennip A.H. Hum. Genet. 101:333-338(1997) [PubMed: 9439663] [Abstract] Cited for: VARIANTS ARG-29; TRP-235 AND HIS-886.
[12]	"Identification of novel point mutations in the dihydropyrimidine dehydrogenase gene." Vreken P., van Kuilenburg A.B.P., Meinsma R., van Gennip A.H. J. Inherit. Metab. Dis. 20:335-338(1997) [PubMed: 9266349] [Abstract] Cited for: VARIANTS ARG-29; TRP-235 AND HIS-886.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases
EMBLGenBankDDBJ	U09178 mRNA. Translation: AAA57474.1. U20938 mRNA. Translation: AAB51366.1. AB003063 mRNA. Translation: BAA89789.1. AK291217 mRNA. Translation: BAF83906.1. AC091608 Genomic DNA. No translation available. BC131777 mRNA. Translation: AAI31778.1. BC131778 mRNA. Translation: AAI31779.1. X95670 Genomic DNA. Translation: CAA64973.1. U57655 Genomic DNA. Translation: AAB07049.1.
PIR	A54718.
RefSeq	NP_000101.2.
UniGene	Hs.335034
3D structure databases
HSSP	HSSP built from PDB template 1GTE based on UniProtKB Q28943.
SMR	Q12882. Positions 2-1017.
ModBase	Search...
PTM databases
PhosphoSite	Q12882.
Genome annotation databases
Ensembl	ENSG00000188641. Homo sapiens. [Contig view]
GeneID	1806.
KEGG	hsa:1806.
Organism-specific databases
H-InvDB	HIX0000804.
HGNC	HGNC:3012. DPYD.
MIM	274270. gene+phenotype.
Orphanet	1675. Dihydropyrimidine dehydrogenase deficiency.
PharmGKB	PA145.
GenAtlas	Search...
GeneCards	Search...
Phylogenomic databases
HOGENOM	Q12882.
HOVERGEN	Q12882.
Enzyme and pathway databases
Reactome	REACT_1698. Nucleotide metabolism.
Gene expression databases
ArrayExpress	Q12882.
CleanEx