KEGG   ENZYME: 1.14.11.47Help
Entry
EC 1.14.11.47               Enzyme                                 

Name
[50S ribosomal protein L16]-arginine 3-hydroxylase;
ycfD (gene name)
Class
Oxidoreductases;
Acting on paired donors, with incorporation or reduction of molecular oxygen;
With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
BRITE hierarchy
Sysname
[50S ribosomal protein L16]-L-Arg81,2-oxoglutarate:oxygen oxidoreductase (3R-hydroxylating)
Reaction(IUBMB)
[50S ribosomal protein L16]-L-Arg81 + 2-oxoglutarate + O2 = [50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81 + succinate + CO2
Substrate
[50S ribosomal protein L16]-L-Arg81;
2-oxoglutarate [CPD:C00026];
O2 [CPD:C00007]
Product
[50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg81;
succinate [CPD:C00042];
CO2 [CPD:C00011]
Comment
The enzyme, characterized from the bacterium Escherichia coli, hydroxylates an arginine residue on the 50S ribosomal protein L16, and is involved in regulation of bacterial ribosome assembly.
History
EC 1.14.11.47 created 2014
Orthology
K18850  50S ribosomal protein L16 3-hydroxylase
Genes
ECO: b1128(roxA)
ECJ: JW1114(ycfD)
ECD: ECDH10B_1200(ycfD)
EBW: BWG_0976(ycfD)
ECOK: ECMDS42_0949(ycfD)
ECE: Z1833(ycfD)
ECS: ECs1573
ECF: ECH74115_1569
ETW: ECSP_1488(ycfD)
ELX: CDCO157_1505
EOJ: ECO26_1645(ycfD)
EOI: ECO111_1476(ycfD)
EOH: ECO103_1235(ycfD)
ECG: E2348C_1269(ycfD)
EOK: G2583_1386(ycfD)
ESO: O3O_10700
ESM: O3M_14895
ESL: O3K_14920
ELH: ETEC_1252
ECC: c1480(ycfD)
ECP: ECP_1123
ECV: APECO1_210(ycfD)
ECY: ECSE_1194
ECR: ECIAI1_1166(ycfD)
ECQ: ECED1_1272(ycfD)
ECK: EC55989_1241(ycfD)
ECT: ECIAI39_2028(ycfD)
EOC: CE10_1209(ycfD)
EUM: ECUMN_1372(ycfD)
ECZ: ECS88_1143(ycfD)
ESE: ECSF_1028
EBR: ECB_01126(ycfD)
EBD: ECBD_2471
EKF: KO11_17080(ycfD)
EAB: ECABU_c13420(ycfD)
EDJ: ECDH1ME8569_1063(ycfD)
ENA: ECNA114_1186(ycfD)
ELW: ECW_m1236(ycfD)
ELL: WFL_06040(ycfD)
ELC: i14_1350(ycfD)
ELD: i02_1350(ycfD)
ELP: P12B_c1978(ycfD)
EBL: ECD_01126(roxA)
EBE: B21_01134(ycfD)
ELF: LF82_2717(ycfD)
ECOJ: P423_06055
ECOS: EC958_1325
EFE: EFER_1802(ycfD)
STY: STY1269
STT: t1691
STM: STM1229(ycfD)
SEO: STM14_1407(ycfD)
SEY: SL1344_1167(ycfD)
SEJ: STMUK_1197(ycfD)
SEB: STM474_1227(ycfD)
SENI: CY43_06270
SPT: SPA1621(ycfD)
SEK: SSPA1506
SEI: SPC_2515(ycfD)
SEC: SCH_1180(ycfD)
SHB: SU5_01855
SENS: Q786_09115
SED: SeD_A2137
SEG: SG1892(ycfD)
SEL: SPUL_1033
SET: SEN1820(ycfD)
SENA: AU38_09425
SENO: AU37_09430
SENV: AU39_09435
SENQ: AU40_10530
SENL: IY59_09685
SEEP: I137_04735
SENB: BN855_12550(ycfD)
SENE: IA1_06065
SBG: SBG_1065
SBZ: A464_1165
SFL: SF1130(ycfD)
SFX: S1210(ycfD)
SFV: SFV_1146(ycfD)
SFE: SFxv_1283(ycfD)
SFN: SFy_1621
SFS: SFyv_1673
SFT: NCTC1_01184(ycfD)
SSN: SSON_1146(ycfD)
SBO: SBO_1911(ycfD)
SDY: SDY_2024(ycfD)
EEC: EcWSU1_00517(ycfD) EcWSU1_01722(ycfD)
CSK: ES15_2361
CTU: CTU_17050(ycfD) Ctu_1p00940(ycfD)
KPN: KPN_01134(ycfD) KPN_04743
KPU: KP1_0694 KP1_2135(ycfD)
KPX: PMK1_02199(ycfD_1) PMK1_03474(ycfD_2)
CKO: CKO_01925
CRO: ROD_12171
CAMA: F384_05590
HDE: HDEF_0169
EBT: EBL_c23760(ycfD)
AHN: NCTC12129_00642(ycfD_1) NCTC12129_02157(ycfD_2) NCTC12129_02158(ycfD_3) NCTC12129_02159(ycfD_4) NCTC12129_02160(ycfD_5)
YPE: YPO1632
YPK: y1792
YPH: YPC_1734
YPA: YPA_1892
YPN: YPN_1999
YPM: YP_1762
YPZ: YPZ3_2060
YPD: YPD4_2101
YPX: YPD8_2100
YPW: CH59_205
YPJ: CH55_207
YPV: BZ15_1919
YPL: CH46_3493
YRU: BD65_81
SRL: SOD_c18460(ycfD)
SPLY: Q5A_010090(roxA)
SMAF: D781_1857
SMW: SMWW4_v1c20420(ycfD)
SMAR: SM39_1491
SERF: L085_18560
SGL: SG1080
SOD: Sant_2455(ycfD)
ETA: ETA_19720(ycfD)
EPY: EpC_20960(ycfD)
EPR: EPYR_02253(ycfD)
EAM: EAMY_1529(ycfD)
EAY: EAM_1512
EBI: EbC_16860(ycfD)
ERJ: EJP617_26280(ycfD)
EGE: EM595_1478(ycfD)
PAM: PANA_1510(ycfD)
PLF: PANA5342_2713(ycfD)
PAJ: PAJ_0855(ycfD)
PVA: Pvag_0932(ycfD)
PSTW: DSJ_10790
PLU: plu2809
PAY: PAU_01732(ycfD)
PMR: PMI0883
PHAU: PH4a_13735
XBO: XBJ1_2837(ycfD)
XBV: XBW1_2466
XNE: XNC1_2711(ycfD)
XNM: XNC2_2609(ycfD)
XDO: XDD1_2482
XPO: XPG1_1348
PSI: S70_01480
PSX: DR96_3462
PRG: RB151_025300(ycfD)
ANS: ArsFIN_24560(roxA)
ETR: ETAE_2061
ETD: ETAF_1860
ETE: ETEE_0049
HIN: HI0396
HIT: NTHI0517
HIP: CGSHiEE_01015(xseA)
HIU: HIB_05070
HIA: H733_0290
HDU: HD_1945
HAP: HAPS_1493(xseA)
HPAZ: K756_10800
HPAS: JL26_09350
HPAK: JT17_07005
PMU: PM0167
PMP: Pmu_11460
PMUL: DR93_1899
MSU: MS0559
MHT: D648_2610
MHAT: B824_24020
MHAE: F382_06820
MHAM: J450_08220
MHAO: J451_09405
MHAL: N220_01265
MHAQ: WC39_12800
MHAY: VK67_12805
MVI: X808_1780
MVG: X874_1860
APL: APL_1790
APJ: APJL_1826
APA: APP7_1876
AAT: D11S_1466
AAN: D7S_02035
AACN: AANUM_2290
BTO: WQG_3250
BTRE: F542_18710
BTRH: F543_20590
BTRA: F544_3660
XFA: XF_1552
XFT: PD_0761
XCC: XCC1489
XCB: XC_2747
XCP: XCR_1754
XCV: XCV1580
XAX: XACM_1508
XAC: XAC1537
XOO: XOO2046
XOM: XOO1927(XOO1927)
XOP: PXO_01200(jmjC)
XOR: XOC_1755
XAL: XALC_1666
XPH: XppCFBP6546_03745(XppCFBP6546P_03745)
SML: Smlt3195
SMT: Smal_2628
SMZ: SMD_2772
PSUW: WQ53_14480
PSD: DSC_07970
LEZ: GLE_2719
LEM: LEN_2306
DKO: I596_2347
RBD: ALSL_0630
VSP: VS_1063
VSC: VSVS12_02093(ycfD)
VTA: A1662(ycfD)
VFI: VF_1592(ycfD)
PPR: PBPRA1139(YCFD)
PAE: PA2630
PAEV: N297_2710
PAEI: N296_2710
PAEP: PA1S_12455
PAEM: U769_12020
PAEL: T223_12605
PAEG: AI22_21455
PAEC: M802_2707
PAEO: M801_2576
PMY: Pmen_2403
PMK: MDS_2366
PPSE: BN5_1857
PCQ: PcP3B5_38090(ycfD)
PPU: PP_4017
PPF: Pput_1816
PPT: PPS_3427
PPI: YSA_08736
PPX: T1E_0543(ycfD)
PPUH: B479_17050
PPUT: L483_22495
PPUN: PP4_17360
PPUD: DW66_3874
PMON: X969_16330
PMOT: X970_15975
PSB: Psyr_3193
PSYR: N018_16050
PFL: PFL_3894
PPRO: PPC_3992
PFS: PFLU_3814
PFE: PSF113_2163(ycfD)
PFB: VO64_0904
PMAN: OU5_1182
PEN: PSEEN2197
PSA: PST_2307
PSTT: CH92_09155
PKC: PKB_3388
PSES: PSCI_5419
PSEM: TO66_20185
PSOS: POS17_4014
PANR: A7J50_3449
PSET: THL1_2468
PSIL: PMA3_19630
PAR: Psyc_1247
PALI: A3K91_1104
PSYA: AOT82_224
ACB: A1S_1541
ABM: ABSDF1707
ABY: ABAYE2093
ABN: AB57_1784
ABX: ABK1_2046
ABH: M3Q_1939
ABAD: ABD1_15490
ABAZ: P795_9465
ABAU: IX87_02420
ABAA: IX88_09720
ACC: BDGL_000930(xseA)
ACI: ACIAD1933
MCT: MCR_1176
MCS: DR90_735
SON: SO_2636
SDN: Sden_1825
SFR: Sfri_2263
SAZ: Sama_2065
SLO: Shew_1557
SSE: Ssed_2408
SHL: Shal_2301
ILO: IL1313
CPS: CPS_2133
PHA: PSHAa1693
PAT: Patl_2383
PSM: PSM_A1665
PSEO: OM33_10335
PSPO: PSPO_a1538
PART: PARC_a1817
PSEN: PNC201_09485(ycfD)
PAGA: PAGA_a1797
MAQ: Maqu_1765
MHC: MARHY1541
MAD: HP15_2089
MBS: MRBBS_2377(ycfD)
AMAL: I607_08490
AMAE: I876_08790
AMAO: I634_08870
AMAD: I636_09300
AMAI: I635_09600
AMAG: I533_08870
AMAC: MASE_08470
AAUS: EP12_09190
GNI: GNIT_2133
GPS: C427_1996
PIN: Ping_0960
FBL: Fbal_1997
MVS: MVIS_3307
MYA: MORIYA_4172(roxA)
CJA: CJA_2493
SDE: Sde_1674
SAGA: M5M_03170
MICC: AUP74_02592(ycfD)
LPN: lpg1901
LPH: LPV_2174
LPO: LPO_1971
LPM: LP6_1880
LPF: lpl1865
LPP: lpp1874
LPC: LPC_1351
LPA: lpa_02747
LPE: lp12_1840
LLO: LLO_1249
LFA: LFA_0747
LHA: LHA_1481
LCD: clem_07495(ycfD)
TMC: LMI_1867
TCX: Tcr_1132
MEJ: Q7A_1245
MEC: Q7C_632
TGR: Tgr7_1850
TKM: TK90_1274
TNI: TVNIR_1569(ycfD_[H])
TVR: TVD_06805
GAI: IMCC3135_24690(roxA)
HCH: HCH_02330
CSA: Csal_2447
HEL: HELO_3068(roxA)
HAM: HALO3351
HCO: LOKO_02688(ycfD)
HBE: BEI_2461
ABO: ABO_1272
ADI: B5T_01975
APAC: S7S_08885
AXE: P40_09395
KKO: Kkor_1045
KGE: TQ33_1262
TOL: TOL_1899
OAI: OLEAN_C18570(jmjC)
AHA: AHA_1412
ASA: ASA_1388
AVR: B565_1155
AMED: B224_1247
ASR: WL1483_1905(roxA)
TAU: Tola_1533
OCE: GU3_07355
TBN: TBH_C1493
ENM: EBS_1090
CVI: CV_3581
LHK: LHK_02631
PSE: NH8B_0809
AMAH: DLM_3072
RSO: RSc1148
RSE: F504_1175
RSY: RSUY_15660(ycfD)
RPI: Rpic_0990
REH: H16_A1207(h16_A1207)
RME: Rmet_1072
CGD: CR3_0984(ycfD)
BMAL: DM55_312
BMAE: DM78_1972
BMAQ: DM76_291
BMAI: DM57_485
BMAF: DM51_1361
BMAZ: BM44_1696
BMAB: BM45_1258
BPS: BPSL2255
BPSE: BDL_3234
BPSM: BBQ_1058
BPSU: BBN_1185
BPSD: BBX_1635
BPK: BBK_2703
BPSH: DR55_2266
BPSA: BBU_3308
BPSO: X996_1911
BUT: X994_182
BTE: BTH_I1910
BTQ: BTQ_2005
BTJ: BTJ_314
BTZ: BTL_1614
BTD: BTI_1382
BTV: BTHA_1713
BTHE: BTN_3155
BTHM: BTRA_1834
BTHA: DR62_3300
BTHL: BG87_1814
BOK: DM82_1859
BOC: BG90_2853
BVE: AK36_1796
BCN: Bcen_5986
BCJ: BCAL2163
BCEN: DM39_2165
BCEW: DM40_2731
BCEO: I35_2091
BAM: Bamb_2127
BMU: Bmul_1183
BMK: DM80_2875
BMUL: NP80_2210
BCT: GEM_1336
BCED: DM42_2996
BDL: AK34_1015
BCON: NL30_12315
BUB: BW23_2824
BLAT: WK25_10125
BTEI: WS51_20805
BSEM: WJ12_10550
BPSL: WS57_29045
BMEC: WJ16_10790
BSTG: WT74_10935
BGU: KS03_3203
BGO: BM43_213
BUK: MYA_1874
BUL: BW21_1528
BXE: Bxe_A1614
BXB: DR64_3772
BPH: Bphy_1402
BFN: OI25_2910
PNU: Pnuc_0850
PNE: Pnec_0989
PPNO: DA70_07075
PPNM: LV28_23605
PPUL: RO07_17925
PSPU: NA29_19280
PAPI: SG18_16670
HYF: DTO96_101453(roxA)
BPE: BP1567
BPC: BPTD_1549
BPER: BN118_2761
BPET: B1917_1490
BPEU: Q425_14310
BPA: BPP2264
BPAR: BN117_1419
BBR: BB1659
BPT: Bpet3471
BAV: BAV2591
BHO: D560_0099
BHM: D558_0096
BHZ: ACR54_01193(ycfD)
TEA: KUI_0588
TEG: KUK_0457
TAS: TASI_0635
TAT: KUM_0388
PUT: PT7_0175
AMIM: MIM_c12300
BPSI: IX83_05625
AFQ: AFA_04390
ODI: ODI_R3081
RFR: Rfer_2644
POL: Bpro_3175
PNA: Pnap_1191
AAV: Aave_1332
AJS: Ajs_1005
AAA: Acav_1349
ACRA: BSY15_2755
VEI: Veis_2658
DAC: Daci_5092
CTES: O987_06290
RTA: Rta_25740
LIM: L103DPR2_01426(ycfD)
LIH: L63ED372_01447(ycfD)
HYB: Q5W_05245
HPSE: HPF_09425(ycfD)
CBAA: SRAA_0408
CBAB: SMCB_0293
MPT: Mpe_A2568
HAR: HEAR2170
MMS: mma_1286
JAG: GJA_1368
CFU: CFU_1681 CFU_2177(yxbC)
LCH: Lcho_2642
TIN: Tint_0783
THI: THI_1023
RGE: RGE_34850
BBAG: E1O_21330
PBH: AAW51_1689(ycfD)
TBD: Tbd_0585
MMB: Mmol_1947
MEH: M301_2366
MEP: MPQ_1808
SLT: Slit_2286
GCA: Galf_2197
AZO: azo1099
AOA: dqs_1209
BPRC: D521_0856
SJP: SJA_C2-05350(jmjC)
SSY: SLG_14090
SPHB: EP837_03608(ycfD)
SPHR: BSY17_1256
SINB: SIDU_11030
SPHT: K426_22909
SFLA: SPHFLASMR4Y_00511(roxA)
BLAS: BSY18_437
ADO: A6F68_02914(ycfD)
SALS: SLNWT_7113
SLE: sle_66690(sle_66690)
SRU: SRU_0770
SRM: SRM_00949
RMR: Rmar_0038
 » show all
Taxonomy
Reference
1  [PMID:23103944]
  Authors
Ge W, Wolf A, Feng T, Ho CH, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TD, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen MM, McCullagh JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ
  Title
Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans.
  Journal
Nat Chem Biol 8:960-2 (2012)
DOI:10.1038/nchembio.1093
  Sequence
[eco:b1128]
Reference
2  [PMID:24530688]
  Authors
van Staalduinen LM, Novakowski SK, Jia Z
  Title
Structure and functional analysis of YcfD, a novel 2-oxoglutarate/Fe(2)(+)-dependent oxygenase involved in translational regulation  in Escherichia coli.
  Journal
J Mol Biol 426:1898-910 (2014)
DOI:10.1016/j.jmb.2014.02.008
  Sequence
[eco:b1128]
Other DBs
ExplorEnz - The Enzyme Database: 1.14.11.47
IUBMB Enzyme Nomenclature: 1.14.11.47
ExPASy - ENZYME nomenclature database: 1.14.11.47
BRENDA, the Enzyme Database: 1.14.11.47

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