KEGG   ENZYME: 1.14.99.46
Entry
EC 1.14.99.46               Enzyme                                 
Name
pyrimidine oxygenase;
rutA (gene name)
Class
Oxidoreductases;
Acting on paired donors, with incorporation or reduction of molecular oxygen;
Miscellaneous
Sysname
uracil,FMNH2:oxygen oxidoreductase (uracil hydroxylating, ring-opening)
Reaction(IUBMB)
(1) uracil + FMNH2 + O2 + NADH = (Z)-3-ureidoacrylate + H2O + FMN + NAD+ + H+ (overall reaction) [RN:R12544];
(1a) FMNH2 + O2 = FMN-N5-peroxide [RN:R12756];
(1b) uracil + FMN-N5-peroxide = (Z)-3-ureidoacrylate + FMN-N5-oxide [RN:R12545];
(1c) FMN-N5-oxide + NADH = FMN + H2O + NAD+ + H+ (spontaneous) [RN:R12539];
(2) thymine + FMNH2 + O2 + NADH = (Z)-2-methylureidoacrylate + H2O + FMN + NAD+ + H+ (overall reaction) [RN:R12546];
(2a) FMNH2 + O2 = FMN-N5-peroxide;
(2b) thymine + FMN-N5-peroxide = (Z)-2-methylureidoacrylate + FMN-N5-oxide [RN:R12547];
(2c) FMN-N5-oxide + NADH = FMN + H2O + NAD+ + H+ (spontaneous)
Reaction(KEGG)
Substrate
uracil [CPD:C00106];
FMNH2 [CPD:C01847];
O2 [CPD:C00007];
NADH [CPD:C00004];
FMN-N5-peroxide [CPD:C22379];
FMN-N5-oxide [CPD:C22238];
thymine [CPD:C00178]
Product
(Z)-3-ureidoacrylate [CPD:C20254];
H2O [CPD:C00001];
FMN [CPD:C00061];
NAD+ [CPD:C00003];
H+ [CPD:C00080];
FMN-N5-peroxide [CPD:C22379];
FMN-N5-oxide [CPD:C22238];
(Z)-2-methylureidoacrylate [CPD:C20256]
Comment
The enzyme participates in the Rut pyrimidine catabolic pathway. The flavin-N5-oxide that is formed by the enzyme reacts spontaneously with NADH to give oxidized flavin, releasing a water molecule.
History
EC 1.14.99.46 created 2012, modified 2019
Pathway
ec00240  Pyrimidine metabolism
ec01100  Metabolic pathways
Orthology
K09018  pyrimidine oxygenase
Genes
ECOb1012(rutA)
ECJJW0997(ycdM)
ECDECDH10B_1084(rutA)
EBWBWG_0866(rutA)
ECOKECMDS42_0857(ycdM)
ECEZ1511
ECSECs_1258(rutA)
ECFECH74115_1249
ETWECSP_1181
ELXCDCO157_1203
EOIECO111_1201(ycdM)
EOJECO26_1250(ycdM)
EOHECO103_1058(ycdM)
ECOOECRM13514_1189(rutA)
ECOHECRM13516_1118(rutA)
ESLO3K_15925
ESOO3O_09370
ESMO3M_15900
ECKEC55989_1123(rutA)
ECGE2348C_1063(rutA)
EOKG2583_1245(rutA)
ELRECO55CA74_06090
ELHETEC_1081
ECWEcE24377A_1130
EUNUMNK88_1167
ECPECP_1011
ENAECNA114_1083
ECOSEC958_1209(ycdM)
ECVAPECO1_103(ycdM)
ECOAAPECO78_09050
ECXEcHS_A1127
ECMEcSMS35_2113
ECYECSE_1074
ECRECIAI1_1057(rutA)
ECQECED1_1168(rutA)
EUMECUMN_1195(rutA)
ECTECIAI39_2143(rutA)
EOCCE10_1090(rutA)
EBRECB_01015(ycdM)
EBLECD_01015(rutA)
EBEB21_01022(rutA)
EBDECBD_2582
ECIUTI89_C1075(ycdM)
EIHECOK1_1064
ECZECS88_1028(rutA)
ECCc1149
ELOEC042_1087(rutA)
ELNNRG857_04905
ESEECSF_0918
ECLEcolC_2583
EKOEKO11_2818
EKFKO11_17660(rutA)
EABECABU_c10390(rutA)
EDHEcDH1_2630
EDJECDH1ME8569_0966(rutA)
ELUUM146_12550
ELWECW_m1122(rutA)
ELLWFL_05475(rutA)
ELCi14_1049
ELDi02_1049
ELPP12B_c0997(ycdM)
ELFLF82_2049(rutA)
ECOLLY180_05300
ECOIECOPMV1_01034(rutA)
ECOJP423_05500
ESZFEM44_19940(rutA)
SFLSF1015
SFXS1085
SFVSFV_1024
SFESFxv_1101(rutA)
SFNSFy_1390
SFSSFyv_1433
SFTNCTC1_01054(rutA)
SBOSBO_2045
SBCSbBS512_E2306
SDYSDY_0987
SDZAsd1617_01250
SHQA0259_09190
ENCECL_02622(rutA)
ENLA3UG_08165
ECLGEC036_15740
ECLEECNIH2_08810
ECLNECNIH4_14485
ECLIECNIH5_07855
ECLXLI66_07890
ECLYLI62_08680
ECLZLI64_08215
EHMAB284_17095
EXFBFV63_07825
ECLAECNIH3_07870
ECLCECR091_07845
EAUDI57_10690
EKBBFV64_08135
ENOECENHK_08170
EECEcWSU1_01610(rutA)
ELGBH714_04140
ERNBFV67_07755
ECLSLI67_009230
ECHGFY206_09415(rutA)
ESHC1N69_08300(rutA)
ENTEnt638_1525
EASEntas_1550
ENXNI40_007670
ENFAKI40_2539(rutA)
LNICWR52_04065(rutA)
EBGFAI37_21405(rutA)
ENDA4308_12860
ENZG0034_07985(rutA)
ENSHWQ15_16315(rutA)
ENKLOC22_18605(rutA)
EHUD5067_0014620(rutA)
EMORL6Y89_07905(rutA)
ENBELK40_08555(rutA)
ESAESA_02361
CSKES15_2461(rutA)
CSZCSSP291_10995
CSJCSK29544_03670
CCONAFK62_07355
CDMAFK67_07585
CSIP262_03590
CMJAFK66_012350
CUIAFK65_07345
CMWAFK63_11270
CTUCTU_15930(rutA)
KPNKPN_01038(ycdM)
KPUKP1_2027(ycdM)
KPMKPHS_19140
KPPA79E_3194
KPHKPNIH24_18945
KPZKPNIH27_09050
KPVKPNIH29_09575
KPWKPNIH30_10090
KPYKPNIH31_09465
KPGKPNIH32_09930
KPCKPNIH10_09580
KPQKPR0928_09755
KPTVK055_1439(rutA)
KPOKPN2242_08260
KPRKPR_3485(rutA)
KPJN559_3248
KPID364_05395
KPAKPNJ1_03488
KPSKPNJ2_03477
KPXPMK1_03378(rutA)
KPBFH42_01045
KPNEKU54_016570
KPNULI86_16880
KPNKBN49_2127(rutA)
KVAKvar_3341
KPEKPK_3520
KPKA593_19690
KVDKR75_17360
KVQSP68_23735
KOXKOX_17000
KOEA225_2250
KOYJ415_20535
KOMHR38_15525
KOKKONIH1_11005
KOCAB185_25130
KQUAVR78_14230
EAEEAE_16035
EARCCG30700
KQVB8P98_18060(rutA)
KLLBJF97_11280
KLWDA718_17555(rutA)
KARLGL98_16035(rutA)
KGRJJJ10_17520(rutA)
KPASLUW96_17625(rutA)
RORRORB6_09465
RONTE10_11095
RPLNB1209_17360
RAODSD31_16095(rutA)
RTGNCTC13098_04743(rutA)
REEelectrica_03235(rutA)
PGELG71_19240
KORAWR26_15860(rutA)
KRDA3780_08430
LAXAPT61_14385
LEIC2U54_13140(rutA)
LEHC3F35_03165(rutA)
LEEDVA44_15420(rutA)
LERGNG29_08310(rutA)
LEAGNG26_07930(rutA)
LPNUKQ929_12895(rutA)
LEFLJPFL01_1557
LEWDAI21_18780(rutA)
BUFD8682_07195(rutA)
BAGEBADSM9389_26670(rutA)
BFTMNO13_16125(rutA)
METYMRY16398_36470(rutA)
KINAB182_16015
PDZHHA33_18600(rutA)
IZHFEM41_12165(rutA)
EBCC2U52_26760(rutA)
EBUCUC76_06065(rutA)
PSTSE05_37920
YENYE1950(ssuD)
YEWCH47_1382(rutA)
YEFFORC2_2482
YEEYE5303_22861(ssuD)
YAKACZ76_00785
YMADA391_09485(rutA)
SPESpro_1823
SRRSerAS9_1768
SRLSOD_c16480(rutA)
SRYM621_09130
SPLYQ5A_009030(rutA)
SRSSerAS12_1768
SRASerAS13_1769
SLQM495_08455
SQUE4343_07070(rutA)
SFJSAMEA4384070_1850(rutA)
SENPKHA73_09110(rutA)
RAHRahaq_3017
RACEJHW33_09275(rutA)
RAQRahaq2_3045
RAAQ7S_15215
ROXBV494_10020
RVCJ9880_00925(rutA)
GQUAWC35_20505
EAMEGXP68_07350(rutA)
RBADH2866_14920(rutA)
RCBO1V66_10845(rutA)
LPOPI6N93_14380
EBIEbC_11600 EbC_15660(rutA)
EGEEM595_1350(rutA)
EPECI789_10745(rutA)
ERWIGN242_13265(rutA)
ERPLJN55_07860(rutA)
PAMPANA_4033(ycdM)
PLFPANA5342_p10175(rutA3)
PAJPAJ_p0253(ycdM)
PAQPAGR_p120
PVAPvag_0805(ycdM)
PAGGAL522_11305(rutA)
PAOPat9b_1395
KLNLH22_15225
PANTPSNIH1_11545
PANPPSNIH2_10710
PAGCBEE12_13795
PSTWDSJ_25275
PALHB1H58_20130
PANSFCN45_07195(rutA)
PEYEE896_12565(rutA)
PDISD8B20_06590(rutA)
PERLAC65_05790(rutA)
PJIKTJ90_12440(rutA)
PGZC2E15_07960(rutA)
PCDC2E16_07865(rutA)
TCIA7K98_09280
KPIEN5580_11205(rutA)
PLUplu3815
PLUMA4R40_18980
PAYPAU_00991
PTTVY86_03085
PAKHB0X70_19005
PLUICE143_19040
XBOXBJ1_1586
XBVXBW1_0887
VZIG5S32_21240(rutA)
VOSKNV97_09985(rutA)
PSTPSPTO_1157
PSBPsyr_0999
PSYRN018_20685
PSPPSPPH_1048
PSAVPSA3335_08755
PAMGBKM19_007705(rutA)
PAVLBKM03_06650(rutA)
PVDCFBP1590__4358(rutA)
PCABJGS08_05410(rutA)
PSYIMME58_04935(rutA)
PASTN015_05620(rutA)
PLULFOB45_22260(rutA)
PRHLT40_19385
PSESPSCI_0304
PPSLBJP27_10350
PEZHWQ56_15555(rutA)
PSAPST_3597
PSZPSTAB_3567
PSRPSTAA_3692
PSCA458_03440
PSTUUIB01_03255
PSTTCH92_21415
PCHLLLJ08_03335(rutA)
PKGLW136_03325(rutA)
SDEGGOM96_02820
HPEGEAO82_01540(rutA)
HAESLO767_00615(rutA)
HARRHV822_10655(rutA)
MSRAU15_03000
MPQABA45_09600
ACCBDGL_002277(rutA)
ACALBUM88_16245
ACIACIAD0027
AEIAOY20_13225
AJORZ95_09030
ACWA0J50_03130
ASOLBEN76_13385
ASJAsACE_CH00966(rutA)
ARJDOM24_07655(rutA)
ACUMC9E88_009225(rutA)
AGUAS4_29280(rutA)
AUGURS_1156
ALWFOB21_15240(rutA)
ABERBSR55_14115
ATNFM020_07950(rutA)
AWGGFH30_04570(rutA)
ASHAG8E00_05340(rutA)
AVBRYU24_20540(rutA)
ABOUACBO_20440(rutA)
MOSAXE82_11210
AMCMADE_000001022910
AMHI633_17760
AMAAamad1_17300
AMALI607_16325
AMAEI876_16630
AMAOI634_16580
AMADI636_16515
AMAII635_17260
AMAGI533_16145
AMACMASE_16140
AMGAMEC673_16435
AALEP13_18370
AAUSEP12_19150
GPSC427_0832
HAAA5892_14200
MMEMarme_1361
CUHBJN34_36115
PGPCUJ91_33805
PTSCUJ90_27805
PLGNCTC10937_03397(rutA)
VAPVapar_4838
VPDVAPA_1c50080(rutA)
VAMC4F17_21770(rutA)
RGUA4W93_25205
XYKGT347_11520(rutA)
HOHHoch_3938
MESOBSQ44_10080
PLAPlav_0991
ATUAtu2500(rutA)
ARAArad_7073
ATAAWN88_17375
AGRAGROH133_08499(rutA)
ATFAch5_23700(rutA)
AVIAvi_7126
AGCBSY240_839(rutA)
AROB0909_00430(rutA)
AGTEYD00_10560(rutA)
ALFCFBP5473_19085(rutA)
ARUIG6M88_16290(rutA) G6M88_19500(rutA)
AVQHRR99_16120(rutA) HRR99_19305(rutA)
RIRBN877_I2581(rutA)
RPUSCFBP5875_10895(rutA)
RHVBA939_06935
ROYG3A56_13450(rutA)
RLSHB780_12135(rutA)
RROSD4A92_16410(rutA)
NENNCHU2750_47470(rutA)
BBTBBta_1128(ycdM)
TRBHB776_24815(rutA)
APRAG3A50_08470
MEAMex_1p1664
MDIMETDI2412
MEXMext_1738
MCHMchl_2057
MPOMpop_1075
MZAB2G69_16360
MRDMrad2831_1584
MORMOC_1964(rutA)
METAY590_08280
MAQUMaq22A_c18500
MPHYMCBMB27_01224
MEEDA075_20040(rutA)
METXA3862_22955
METIDK427_02030(rutA)
MMESMMSR116_30935(rutA)
MINDmvi_25510(rutA)
MOGMMB17_22310(rutA)
MTADM6G65_08160(rutA)
DEIC4375_16505(rutA) C4375_16510(rutA) C4375_16515(rutA) C4375_16520(rutA)
CCRCC_1169 CC_2798
CCSCCNA_01227 CCNA_02888
CAKCaul_1792 Caul_3982
CSECseg_1789 Cseg_1893 Cseg_2081
CHQAQ619_03875 AQ619_04205
CFHC1707_01420(rutA) C1707_01770 C1707_03645
CAUFCSW63_09150 CSW63_19500(rutA)
CAULKCG34_19140
BGOEIFJ75_12350(rutA)
KVLKVU_1293 KVU_1872(rutA)
KVUEIO_1827
KROBVG79_02009(rutA)
CIDP73_1975
YPACCEW88_14425(rutA)
YANAYJ57_05560 AYJ57_10120
LSALKBK07_09960(rutA)
LVSLOKVESSMR4R_02448(rutA)
HMLHmaOT1_07750(rutA)
PSHQF3W81_03045(rutA) F3W81_03050(rutA)
FAPGR316_12320(rutA)
HNEHNE_1252
HBAHbal_2538
NPPPP1Y_AT10762
NPNJI59_06555
NREBES08_16575 BES08_19315 BES08_19380
NOVTQ38_014325(rutA) TQ38_022325(rutA) TQ38_022440
NOGGKE62_04895
NDRHT578_04665 HT578_19540(rutA)
SPHQBWQ93_13765
SWISwit_1168 Swit_4216
SPHDHY78_20735
SPHITS85_05045 TS85_06060
SSANNX02_15970 NX02_23365
SPANAWL63_12465
SPLMBXU08_06035
SPAPH3Z74_01520(rutA)
SPAIFPZ24_08920(rutA)
SARIH5J25_15430(rutA)
SPHRBSY17_3628(rutA)
SUFLFIL70_08440 FIL70_25155
SFLASPHFLASMR4Y_01888(rutA)
SPZRG5C33_08835(rutA)
AAYWYH_00064(rutA)
RGIRGI145_06135 RGI145_14655
ROSCTJ15_11265(rutA) CTJ15_21285(rutA)
RMUCFOB66_07945(rutA) FOB66_16700(rutA)
RMTIAI58_12850(rutA)
LCKHN018_01900
SRFLHU95_09130(rutA) LHU95_22010(rutA)
NAOY958_23495
NCBC0V82_24835(rutA)
TAPGZ22_02440
PBKBack11_38080
AACOK1I37_05850
MMAMK3U93_16435
MTHN4412656_02908(rutA_4)
NNONONO_c26560
RBYCEJ39_09950(rutA)
RAVAAT18_09645
RRZCS378_24480(rutA)
RHQIM25_13355
RRT4535765_00373(rutA_2)
RKOJWS14_38955
GJIH1R19_08930
SLCSL103_22515
SCLFBB341_01515
SLSSLINC_2834 SLINC_6196
SGDELQ87_01640
SQZFQU76_31570(rutA)
SCYAEJ357_22520(rutA)
STSUB7R87_31380
SFEUIM697_01760(rutA)
SLFJEQ17_05090(rutA)
ABRYNYE86_22435
LEIFHF024_01940
MBINLXM64_06920
CUBBJK06_04380 BJK06_11565
CARTPA27867_1036 PA27867_2671
CPHYB5808_01655
SALCC2138_01880 C2138_11300
SALDFVA74_02570
HUMDVJ78_01010
HEAHL652_06285 HL652_16070
SUBALQ955_13165
PUEFV140_02030
SKESked_02080
AEFGEV26_06470 GEV26_06495
NDANdas_4506
NEXNE857_02985
SNAHOUQ99_29520
KRAKrad_3110
PDXPsed_6202 Psed_6730
PSEAWY02_01035
PSEEFRP1_17015
PSEQAD006_24465
PECQAD017_04055
PAUTPdca_22210(rutA_1) Pdca_66760(rutA_2)
APRECNX65_13320
AMIAmir_2625
ACTNL083_3836
DFUDfulv_35240(rutA)
 » show all
Reference
1  [PMID:20369853]
  Authors
Mukherjee T, Zhang Y, Abdelwahed S, Ealick SE, Begley TP
  Title
Catalysis of a flavoenzyme-mediated amide hydrolysis.
  Journal
J Am Chem Soc 132:5550-1 (2010)
DOI:10.1021/ja9107676
  Sequence
[eco:b1012]
Reference
2  [PMID:20400551]
  Authors
Kim KS, Pelton JG, Inwood WB, Andersen U, Kustu S, Wemmer DE
  Title
The Rut pathway for pyrimidine degradation: novel chemistry and toxicity problems.
  Journal
J Bacteriol 192:4089-102 (2010)
DOI:10.1128/JB.00201-10
  Sequence
[eco:b1012]
Reference
3  [PMID:28661684]
  Authors
Adak S, Begley TP
  Title
RutA-Catalyzed Oxidative Cleavage of the Uracil Amide Involves Formation of a Flavin-N5-oxide.
  Journal
Biochemistry 56:3708-3709 (2017)
DOI:10.1021/acs.biochem.7b00493
Reference
4  [PMID:28784589]
  Authors
Adak S, Begley TP
  Title
Flavin-N5-oxide: A new, catalytic motif in flavoenzymology.
  Journal
Arch Biochem Biophys 632:4-10 (2017)
DOI:10.1016/j.abb.2017.08.001
Reference
5  [PMID:32066967]
  Authors
Matthews A, Saleem-Batcha R, Sanders JN, Stull F, Houk KN, Teufel R.
  Title
Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases.
  Journal
Nat Chem Biol 16:556-563 (2020)
DOI:10.1038/s41589-020-0476-2
Other DBs
ExplorEnz - The Enzyme Database: 1.14.99.46
IUBMB Enzyme Nomenclature: 1.14.99.46
ExPASy - ENZYME nomenclature database: 1.14.99.46
BRENDA, the Enzyme Database: 1.14.99.46

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