KEGG   ENZYME: 3.1.3.89Help
Entry
EC 3.1.3.89                 Enzyme                                 

Name
5'-deoxynucleotidase;
yfbR (gene name)
Class
Hydrolases;
Acting on ester bonds;
Phosphoric-monoester hydrolases
BRITE hierarchy
Sysname
2'-deoxyribonucleoside 5'-monophosphate phosphohydrolase
Reaction(IUBMB)
a 2'-deoxyribonucleoside 5'-monophosphate + H2O = a 2'-deoxyribonucleoside + phosphate [RN:R10776]
Reaction(KEGG)
Substrate
2'-deoxyribonucleoside 5'-monophosphate [CPD:C00676];
H2O [CPD:C00001]
Product
2'-deoxyribonucleoside [CPD:C02269];
phosphate [CPD:C00009]
Comment
The enzyme, characterized from the bacterium Escherichia coli, shows strict specificity towards deoxyribonucleoside 5'-monophosphates and does not dephosphorylate 5'-ribonucleotides or ribonucleoside 3'-monophosphates. A divalent metal cation is required for activity, with cobalt providing the highest activity.
History
EC 3.1.3.89 created 2013
Pathway
ec00240  Pyrimidine metabolism
ec01100  Metabolic pathways
Orthology
K08722  5'-deoxynucleotidase
K21510  5'-deoxynucleotidase
Genes
ECO: b2291(yfbR)
ECJ: JW2288(yfbR)
ECD: ECDH10B_2453(yfbR)
EBW: BWG_2065(yfbR)
ECOK: ECMDS42_1862(yfbR)
ECE: Z3552
ECS: ECs3175
ECF: ECH74115_3430(yfbR)
ETW: ECSP_3165(yfbR)
ELX: CDCO157_2939
EOJ: ECO26_3279(yfbR)
EOI: ECO111_3039(yfbR)
EOH: ECO103_2755(yfbR)
ECG: E2348C_2431(yfbR)
EOK: G2583_2828(yfbR)
ECC: c2832(yfbR)
ECP: ECP_2330
ECI: UTI89_C2573(yfbR)
ECV: APECO1_4273(yfbR)
ECX: EcHS_A2440(yfbR)
ECW: EcE24377A_2584(yfbR)
ECM: EcSMS35_2446(yfbR)
ECY: ECSE_2548
ECR: ECIAI1_2365(yfbR)
ECQ: ECED1_2755(yfbR)
ECK: EC55989_2535(yfbR)
ECT: ECIAI39_2438(yfbR)
EOC: CE10_2673(yfbR)
EUM: ECUMN_2630(yfbR)
ECZ: ECS88_2438(yfbR)
ELH: ETEC_2426
ESE: ECSF_2168
ESO: O3O_17590
ESM: O3M_07995
ESL: O3K_08045
EBR: ECB_02216(yfbR)
EBD: ECBD_1368
EKF: KO11_11245(yfbR)
EAB: ECABU_c26230(yfbR)
EDJ: ECDH1ME8569_2228(yfbR)
EIH: ECOK1_2524(yfbR)
ENA: ECNA114_2381(yfbR)
ELW: ECW_m2480(yfbR)
ELL: WFL_12135(yfbR)
ELC: i14_2631(yfbR)
ELD: i02_2631(yfbR)
ELP: P12B_c2385(yfbR)
EBL: ECD_02216(yfbR)
EBE: B21_02176(yfbR)
ELF: LF82_3053(yfbR)
ECOI: ECOPMV1_02450(yfbR)
ECOJ: P423_12790
ECOO: ECRM13514_3047(yfbR)
ECOH: ECRM13516_2991(yfbR)
ECOS: EC958_2626(yfbR)
EFE: EFER_0878(yfbR)
EAL: EAKF1_ch3688c(yfbR)
STY: STY2562
STT: t0532
STM: STM2332
SEB: STM474_2429(yfbR)
SENI: CY43_12485
SPT: SPA0532
SEK: SSPA0496
SEI: SPC_1376
SEC: SCH_2333(yfbR)
SHB: SU5_02925
SENS: Q786_11505
SED: SeD_A2680
SEG: SG2361
SEL: SPUL_0556
SET: SEN2314
SENA: AU38_11700
SENO: AU37_11710
SENV: AU39_11710
SENQ: AU40_13110
SENL: IY59_12030
SEEP: I137_02565
SENB: BN855_24140(yfbR)
SENE: IA1_11620
SBG: SBG_2118
SBZ: A464_2447
SFL: SF2367
SFX: S2502
SFV: SFV_2358
SFE: SFxv_2612(yfbR)
SFN: SFy_3366
SFS: SFyv_3441
SFT: NCTC1_02602(yfbR)
SSN: SSON_2348
SBC: SbBS512_E2667(yfbR)
SDY: SDY_2487
ENC: ECL_03635
ECLO: ENC_39200
EEC: EcWSU1_03164(yfbR)
ECLX: LI66_15370
ECLY: LI62_16870
ECLZ: LI64_14805
ESA: ESA_00928
CSK: ES15_1183(yfbR)
CTU: CTU_29170
KPN: KPN_02681(yfbR)
KPU: KP1_3928
KPP: A79E_1420
KPT: VK055_4833(yfbR)
KPE: KPK_1466(yfbR)
KPR: KPR_2024
KPJ: N559_1571
KPX: PMK1_00179(yfbR)
KPNU: LI86_07665
KPNK: BN49_3899
KVA: Kvar_1372
KOX: KOX_26410
KOE: A225_4183
EAE: EAE_24445
CKO: CKO_00504
CRO: ROD_26931
CAMA: F384_12230
HDE: HDEF_1196
EBT: EBL_c12630(yfbR)
EBF: D782_1380
PSTS: E05_23260
YPE: YPO2559
YPK: y1627
YPA: YPA_2050
YPN: YPN_2153
YPM: YP_2370
YPG: YpAngola_A1820(yfbR)
YPZ: YPZ3_2262
YPD: YPD4_2453
YPX: YPD8_2148
YPH: YPC_1554(yfbR)
YPW: CH59_93
YPJ: CH55_52
YPV: BZ15_978
YPL: CH46_2556
YPS: YPTB2590
YPO: BZ17_4048
YPI: YpsIP31758_1449(yfbR)
YPY: YPK_1557
YPB: YPTS_2685
YPQ: DJ40_3953(yfbR)
YPU: BZ21_1886
YPR: BZ20_3619
YPC: BZ23_2170
YPF: BZ19_1951
YEN: YE1340
YEY: Y11_02121
YEW: CH47_759(yfbR)
YET: CH48_314
YAL: AT01_1187
YFR: AW19_1865(yfbR)
YIN: CH53_386
YKR: CH54_3921
YRO: CH64_1206
YRU: BD65_850
SPE: Spro_3311
SPLY: Q5A_017520(yfbR_1)
SMAF: D781_3101
SMW: SMWW4_v1c34200(yfbR)
SMAR: SM39_2905
SERF: L085_11580
RAA: Q7S_06040
ECA: ECA3034
PATR: EV46_14990
PATO: GZ59_30390
PCT: PC1_2775
PEC: W5S_1374
SGL: SG1603
SOD: Sant_1339(yfbR)
PES: SOPEG_2852(yfbR)
DDD: Dda3937_04026(yfbR)
DDQ: DDI_2714
ETA: ETA_12010(yfbR)
EPY: EpC_12570(yfbR)
EPR: EPYR_01340(yfbR)
EAM: EAMY_2377(yfbR)
EAY: EAM_2295(yfbR)
EBI: EbC_30820
ERJ: EJP617_34380(yfbR)
PAM: PANA_2639(yfbR)
PLF: PANA5342_1417(yfbR)
PAJ: PAJ_1927(yfbR)
PVA: Pvag_2109(yfbR)
PSTW: DSJ_17090
PLU: plu3092
PAY: PAU_01516(yfbR)
PMR: PMI1766
XBO: XBJ1_2930
XBV: XBW1_3154
XDO: XDD1_2599
XPO: XPG1_1227
PSI: S70_02420
PSX: DR96_3646(yfbR)
PRG: RB151_017760(yfbR_1) RB151_026750(yfbR_2)
MMK: MU9_2561
ETR: ETAE_2392
ETD: ETAF_2163(yfbR)
ETE: ETEE_0416(yfbR) ETEE_p1108(yfbR)
PSHI: SAMEA2665130_2010(yfbR)
PMU: PM0747
PMV: PMCN06_0811(yfbR)
PMP: Pmu_08190
PMUL: DR93_1579(yfbR)
AAT: D11S_1106
AAN: D7S_00235
AACN: AANUM_1967
VCH: VC1978
VCI: O3Y_09555
VCS: MS6_1735
VVY: VV1113
VPA: VP0926
VPB: VPBB_0884
VAG: N646_3076
VSP: VS_2195
VNI: VIBNI_A2417(yfbR)
VAN: VAA_3320
VSC: VSVS12_01282(yfbR)
VTA: A1990(yfbR)
PPR: PBPRA2627(SF2367)
SON: SO_2484(yfbR)
SDN: Sden_1994
SFR: Sfri_1906
SAZ: Sama_1696
SLO: Shew_1913
SSE: Ssed_2345
SPL: Spea_2047
SHL: Shal_2247
SWD: Swoo_2265
SWP: swp_2620
SVO: SVI_2028
SPSW: Sps_00776
CPS: CPS_3233
MAQ: Maqu_0157
MHC: MARHY0154
MAD: HP15_3866
MBS: MRBBS_0180(yfbR)
AMAC: MASE_10685
AAUS: EP12_11690
GNI: GNIT_1742
GPS: C427_2818
MVS: MVIS_3399
SAGA: M5M_17085
MCA: MCA0827
HCH: HCH_03679
AHA: AHA_2008
ASA: ASA_1886
AVR: B565_2221
AMED: B224_2575
ACAV: VI35_09890
TAU: Tola_2690
OCE: GU3_12345
PSPI: PS2015_854
GLO: Glov_1584
PPD: Ppro_1070
KVL: KVU_1601
PMW: B2K_08170
PRI: PRIO_2355
PSWU: SY83_21530
CTH: Cthe_2359
CCE: Ccel_1803
CSD: Clst_0355
CCEL: CCDG5_0105
RBR: RBR_11050
FPR: FP2_09550
FPA: FPR_16530
HSC: HVS_02535(yfbR)
BPB: bpr_I2014
BHU: bhn_I1826
CPY: Cphy_0261
HSD: SD1D_2073
OVA: OBV_39970
VPR: Vpar_0282
VRM: 44547418_00296(yfbR)
APV: Apar_0292
OLS: Olsu_0364
 » show all
Taxonomy
Reference
1  [PMID:15489502]
  Authors
Proudfoot M, Kuznetsova E, Brown G, Rao NN, Kitagawa M, Mori H, Savchenko A, Yakunin AF
  Title
General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG.
  Journal
J Biol Chem 279:54687-94 (2004)
DOI:10.1074/jbc.M411023200
  Sequence
[eco:b2291]
Reference
2  [PMID:18353368]
  Authors
Zimmerman MD, Proudfoot M, Yakunin A, Minor W
  Title
Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli.
  Journal
J Mol Biol 378:215-26 (2008)
DOI:10.1016/j.jmb.2008.02.036
  Sequence
[eco:b2291]
Other DBs
ExplorEnz - The Enzyme Database: 3.1.3.89
IUBMB Enzyme Nomenclature: 3.1.3.89
ExPASy - ENZYME nomenclature database: 3.1.3.89
BRENDA, the Enzyme Database: 3.1.3.89

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