CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-016879
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Dihydropyrimidine dehydrogenase [NADP(+)] 
Protein Synonyms/Alias
 DHPDHase; DPD; Dihydrothymine dehydrogenase; Dihydrouracil dehydrogenase 
Gene Name
 Dpyd 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Mus musculus (Mouse) 
NCBI Taxa ID
 10090 
Lysine Modification
Position
Peptide
Type
References
54KNCFTCEKLESNFDDubiquitination[1]
63ESNFDDIKHTTLGERubiquitination[1]
89CADAPCQKSCPTSLDubiquitination[1]
98CPTSLDIKSFITSIAubiquitination[1]
107FITSIANKNYYGAAKubiquitination[1]
254LMKDLGVKIICGKSLubiquitination[1]
259GVKIICGKSLSTDEMubiquitination[1]
272EMTLSSLKENGYRAAubiquitination[1]
289GIGLPEPKKDHIFQGubiquitination[1]
290IGLPEPKKDHIFQGLubiquitination[1]
307VQGFYTSKDFLPLVAubiquitination[1]
315DFLPLVAKSSKTGMCubiquitination[1]
318PLVAKSSKTGMCACHubiquitination[1]
381PEEMELAKEEKCEFLubiquitination[1]
384MELAKEEKCEFLPFLacetylation[2, 3, 4, 5]
384MELAKEEKCEFLPFLubiquitination[1]
402KVIVKDGKIVAMQFVubiquitination[1]
446GSVLEDPKVKEALSPubiquitination[1]
448VLEDPKVKEALSPIKubiquitination[1]
455KEALSPIKFNRWGLPubiquitination[1]
580TKTFSLDKDIVTNVSubiquitination[1]
709VRVPFFAKLTPNVTDubiquitination[1]
725VSIARAAKEGGADGVubiquitination[1]
861PPIISHQKGKPVPRVubiquitination[1]
875VAELMGQKLPSFGPYubiquitination[1]
894KKIIAASKIRQKDQNubiquitination[1]
898AASKIRQKDQNTACSubiquitination[1]
910ACSPLQRKHFNSQKPubiquitination[1]
916RKHFNSQKPIPAIKDubiquitination[1]
922QKPIPAIKDVIGKSLubiquitination[1]
1022RGLPLAVKPVC****ubiquitination[1]
Reference
 [1] Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues.
 Wagner SA, Beli P, Weinert BT, Schölz C, Kelstrup CD, Young C, Nielsen ML, Olsen JV, Brakebusch C, Choudhary C.
 Mol Cell Proteomics. 2012 Dec;11(12):1578-85. [PMID: 22790023]
 [2] Quantitative assessment of the impact of the gut microbiota on lysine epsilon-acetylation of host proteins using gnotobiotic mice.
 Simon GM, Cheng J, Gordon JI.
 Proc Natl Acad Sci U S A. 2012 Jul 10;109(28):11133-8. [PMID: 22733758]
 [3] Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome.
 Hebert AS, Dittenhafer-Reed KE, Yu W, Bailey DJ, Selen ES, Boersma MD, Carson JJ, Tonelli M, Balloon AJ, Higbee AJ, Westphall MS, Pagliarini DJ, Prolla TA, Assadi-Porter F, Roy S, Denu JM, Coon JJ.
 Mol Cell. 2013 Jan 10;49(1):186-99. [PMID: 23201123]
 [4] Circadian acetylome reveals regulation of mitochondrial metabolic pathways.
 Masri S, Patel VR, Eckel-Mahan KL, Peleg S, Forne I, Ladurner AG, Baldi P, Imhof A, Sassone-Corsi P.
 Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3339-44. [PMID: 23341599]
 [5] Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation.
 Still AJ, Floyd BJ, Hebert AS, Bingman CA, Carson JJ, Gunderson DR, Dolan BK, Grimsrud PA, Dittenhafer-Reed KE, Stapleton DS, Keller MP, Westphall MS, Denu JM, Attie AD, Coon JJ, Pagliarini DJ.
 J Biol Chem. 2013 Jul 17;. [PMID: 23864654] 
Functional Description
 Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine (By similarity). 
Sequence Annotation
 DOMAIN 69 100 4Fe-4S ferredoxin-type 1.
 DOMAIN 944 976 4Fe-4S ferredoxin-type 2.
 DOMAIN 978 1007 4Fe-4S ferredoxin-type 3.
 NP_BIND 194 198 FAD (By similarity).
 NP_BIND 218 226 FAD (By similarity).
 NP_BIND 340 343 NADP (By similarity).
 NP_BIND 364 365 NADP (By similarity).
 NP_BIND 437 439 NADP (By similarity).
 NP_BIND 480 489 FAD (By similarity).
 NP_BIND 481 487 NADP (By similarity).
 NP_BIND 574 575 FMN (By similarity).
 NP_BIND 793 795 FMN (By similarity).
 NP_BIND 816 817 FMN (By similarity).
 REGION 668 670 Substrate binding (By similarity).
 REGION 736 737 Substrate binding (By similarity).
 ACT_SITE 671 671 Proton acceptor (By similarity).
 METAL 79 79 Iron-sulfur 1 (4Fe-4S) (By similarity).
 METAL 82 82 Iron-sulfur 1 (4Fe-4S) (By similarity).
 METAL 87 87 Iron-sulfur 1 (4Fe-4S) (By similarity).
 METAL 91 91 Iron-sulfur 2 (4Fe-4S) (By similarity).
 METAL 130 130 Iron-sulfur 2 (4Fe-4S) (By similarity).
 METAL 136 136 Iron-sulfur 2 (4Fe-4S) (By similarity).
 METAL 140 140 Iron-sulfur 1 (4Fe-4S) (By similarity).
 METAL 156 156 Iron-sulfur 2 (4Fe-4S) (By similarity).
 METAL 953 953 Iron-sulfur 3 (4Fe-4S) (By similarity).
 METAL 956 956 Iron-sulfur 3 (4Fe-4S) (By similarity).
 METAL 959 959 Iron-sulfur 3 (4Fe-4S) (By similarity).
 METAL 963 963 Iron-sulfur 3 (4Fe-4S) (By similarity).
 METAL 986 986 Iron-sulfur 4 (4Fe-4S) (By similarity).
 METAL 989 989 Iron-sulfur 4 (4Fe-4S) (By similarity).
 METAL 992 992 Iron-sulfur 4 (4Fe-4S) (By similarity).
 METAL 996 996 Iron-sulfur 4 (4Fe-4S) (By similarity).
 BINDING 129 129 FAD; via carbonyl oxygen (By similarity).
 BINDING 235 235 FAD (By similarity).
 BINDING 261 261 FAD; via amide nitrogen and carbonyl
 BINDING 371 371 NADP (By similarity).
 BINDING 550 550 FMN (By similarity).
 BINDING 609 609 Substrate (By similarity).
 BINDING 709 709 FMN (By similarity).
 BINDING 767 767 FMN; via amide nitrogen (By similarity).
 MOD_RES 384 384 N6-acetyllysine (By similarity).  
Keyword
 4Fe-4S; Acetylation; Complete proteome; Cytoplasm; FAD; Flavoprotein; FMN; Iron; Iron-sulfur; Metal-binding; NADP; Nucleotide-binding; Oxidoreductase; Reference proteome; Repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1025 AA 
Protein Sequence
MAGVLSRDAP DIESILALNP RVQAHATLRS TAAKKLDKKH WKRNTDKNCF TCEKLESNFD 60
DIKHTTLGER GALREAVRCL KCADAPCQKS CPTSLDIKSF ITSIANKNYY GAAKLIFSDN 120
PLGLTCGMVC PTSDLCVGGC NLHAAEEGPI NIGGLQQFAT EVFKAMNIPQ IRNPSLPPPE 180
HMPEAYSAKI ALFGAGPASI SCASFLARLG YSNITIFEKQ EYVGGLSTSE IPQFRLPYDV 240
VNFEIELMKD LGVKIICGKS LSTDEMTLSS LKENGYRAAF IGIGLPEPKK DHIFQGLTQV 300
QGFYTSKDFL PLVAKSSKTG MCACHSPLPS IRGAVIVLGA GDTAFDCATS ALRCGALRVF 360
IVFRKGFVNI RAVPEEMELA KEEKCEFLPF LSPRKVIVKD GKIVAMQFVR TEQDETGNWV 420
EDEEQTVRLK ADVVISAFGS VLEDPKVKEA LSPIKFNRWG LPEVNPETMQ TSEPWVFAGG 480
DVVGMANTTV ESVNDGKQAS WYIHKHIQAQ YGTSVPSQPT MPLFYTPVDL VDISVEMAGL 540
RFPNPFGLAS ATPATSTPMI RRAFEAGWGF ALTKTFSLDK DIVTNVSPRI IRGTTSGPLY 600
GPGQSSFLNI ELISEKTAAY WCHSVTELKA DFPDNILIAS IMCSYNKSDW MELSKMAEAS 660
GADALELNLS CPHGMGERGM GLACGQDPEL VRNICRWVRQ AVRVPFFAKL TPNVTDIVSI 720
ARAAKEGGAD GVTATNTVSG LMGLKADGTP WPAVGIGRRT TYGGVSGTAI RPIALRAVTA 780
IARALPGFPI LATGGIDSAE SGLQFLHSGA SVLQVCSAIQ NQDFTVIEDY CTGLKALLYL 840
KSIEELADWD GQSPPIISHQ KGKPVPRVAE LMGQKLPSFG PYLEQRKKII AASKIRQKDQ 900
NTACSPLQRK HFNSQKPIPA IKDVIGKSLQ YLGTFGEMSI MEQVVALIDE EMCINCGKCY 960
MTCNDSGYQA IQFDPETHLP TVSDTCTGCT LCLSVCPIMD CIRMVSRATP YQPKRGLPLA 1020
VKPVC 1025 
Gene Ontology
 GO:0005829; C:cytosol; IDA:MGI.
 GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
 GO:0004158; F:dihydroorotate oxidase activity; IEA:InterPro.
 GO:0017113; F:dihydropyrimidine dehydrogenase (NADP+) activity; ISS:UniProtKB.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
 GO:0019483; P:beta-alanine biosynthetic process; IEA:UniProtKB-UniPathway.
 GO:0006145; P:purine nucleobase catabolic process; IEA:Compara.
 GO:0006214; P:thymidine catabolic process; ISS:UniProtKB.
 GO:0006210; P:thymine catabolic process; IEA:Compara.
 GO:0006222; P:UMP biosynthetic process; IEA:InterPro.
 GO:0006212; P:uracil catabolic process; ISS:UniProtKB. 
Interpro
 IPR001450; 4Fe4S-bd_dom.
 IPR017896; 4Fe4S_Fe-S-bd.
 IPR017900; 4Fe4S_Fe_S_CS.
 IPR013785; Aldolase_TIM.
 IPR005720; Dihydroorotate_DH.
 IPR012135; Dihydroorotate_DH_1_2.
 IPR012285; Fum_reductase_C.
 IPR009051; Helical_ferredxn. 
Pfam
 PF01180; DHO_dh
 PF12838; Fer4_7 
SMART
  
PROSITE
 PS00198; 4FE4S_FER_1
 PS51379; 4FE4S_FER_2 
PRINTS