Entry
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
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
Orthology
K21510 Escherichia phage 5'-deoxynucleotidase
Genes
PLEU : 114692535(Hddc2) 114695970
PLOP : 125357255(Hddc2) 125360109
TUP : 102472784(HDDC2) 102483093
PKL : 118705881(HDDC2) 118730742
SANH : 107675094 107676251
CCAR : 109044938 109061442 109084535
CAUA : 113051146 113075685 113120447
CGIB : 127938245 127984254
AOCE : 111574587 111580639
ARUT : 117402809 117411072
DME : Dmel_CG11050(CG11050)
DSI : Dsimw501_GD23421(Dsim_GD23421)
AGA : AgaP_AGAP010140 AgaP_AGAP012582
AALB : 109404738 109414417
AGIF : 122851358 122851360
APLN : 108738763 112905871
BMAN : 114251361 114251362
SGRE : 126323885 126362190
PCLA : 123749904 123757555
PPOI : 119096294 119096581
CEL : CELE_F45F2.9(F45F2.9)
CSAT : 104702904 104713826 104741240 104752013 104756926 104776673
EUS : EUTSA_v10000291mg EUTSA_v10008520mg
BRP : 103835474 103842395 103864500
BNA : 106361849 106361916 106411766 106446609 111215051
BOE : 106309631 106329176 106336814
RSZ : 108809058 108819422 108852023
THJ : 104800067 104803526 104808481
CPAP : 110812651 110824269
CIC : CICLE_v10009257mg CICLE_v10032423mg
MINC : 123194280 123200055 123215622
GHI : 107899688 107920365 107925439 107957134
DZI : 111285710 111288326 111304251
GMX : 100784513 100789619 100798792 100819398
GSJ : 114388344 114392310 114394853 114414361
PVU : PHAVU_003G023900g PHAVU_003G152400g
VAR : 108321554 108335155 108335965
CCAJ : 109790208 109811840
APRC : 113846785 113868855
MTR : 25480606 25494275 25494276
TPRA : 123904340 123911635
LJA : Lj2g3v1193030.1(Lj2g3v1193030.1) Lj6g3v1048960.1(Lj6g3v1048960.1)
AHF : 112699302 112723484 112750494 112802717
LANG : 109336974 109339438 109355754
PCIN : 129310028 129321384
FVE : 101293363 101293585 105351760
PMUM : 103323362 103341396
PAVI : 110757764 110760825
PDUL : 117627404 117637391
MDM : 103416471 103425506 103452297
MSYL : 126594899 126597725 126607502
PXB : 103946814 103947379 103964530 103964532
MNT : 112090648 112094974 21405778
MCHA : 111015177 111020874
CMAX : 111468637 111468905 111487961 111494015
CMOS : 111435665 111443961 111446937 111450859
CPEP : 111784878 111784879 111786025 111798110 111805232 111806190 111809402
HBR : 110642642 110650738 110660702
MESC : 110618037 110630785
PEU : 105115357 105115417 105123176
PALZ : 118040004 118058222
CILL : 122313514 122316996
VVI : 100260381 100260974 100267908 104878955
VRI : 117924506 117925584 117932142 117932267
SPEN : 107018743 107024151
SSTN : 125869124 125876060
CANN : 107848338 107854258
NTA : 107762621 107800937 107814067 107817745 107832532
SIND : 105155626 105156442
SSPL : 121769361 121799397
APAN : 127260690 127265048
HAN : 110872137 110886115 110894556
ECAD : 122581683 122595756
CCAV : 112517235 112525137
CSIN : 114258973 114261680 114291298 114304980 114315526
CQI : 110685994 110698301 110720553 110721915
NNU : 104603098 104605368 104612321
MING : 122077968 122079245
PSOM : 113277784 113298470 113302971 113355977
DOSA : Os01t0641100-01(Os01g0641100) Os02t0179100-01(Os02g0179100)
TDC : 119268477 119276367 119316288 119323540
TAES : 123061576 123070209 123078647 123132495 123136566 123144073
TUA : 125517145 125517155 125544226
LPER : 127308072 127343088
SITA : 101762598 101779620
PVIR : 120654835 120671513 120676850 120681125 120709954
PHAI : 112879103 112893835
ZOF : 121971105 121976559 122027049 122028784 122032241 122033587
NCOL : 116245986 116259947
SMO : SELMODRAFT_124866 SELMODRAFT_91657
SCE : YBR242W YGL101W(YGK1)
SEUB : DI49_1266 DI49_1871
SPAO : SPAR_B03380 SPAR_G01440
CGR : CAGL0C01749g CAGL0J10362g
NCS : NCAS_0D03470(NCAS0D03470) NCAS_0H01220(NCAS0H01220)
NDI : NDAI_0F02070(NDAI0F02070) NDAI_0I01370(NDAI0I01370)
TPF : TPHA_0J02040(TPHA0J02040)
TBL : TBLA_0A01800(TBLA0A01800)
TDL : TDEL_0B03970(TDEL0B03970)
KAF : KAFR_0A04430(KAFR0A04430) KAFR_0G03550(KAFR0G03550)
KNG : KNAG_0F02290(KNAG0F02290) KNAG_0M00590(KNAG0M00590)
CAL : CAALFM_CR03020CA(CaO19.2864)
NTE : NEUTE1DRAFT79310(NEUTE1DRAFT_79310)
SSCK : SPSK_03504 SPSK_05481
FGR : FGSG_05665 FGSG_08678
FPU : FPSE_06260 FPSE_11702
FVR : FVEG_01985 FVEG_06820
FOX : FOXG_03122 FOXG_09219 FOXG_14280
NHE : NECHADRAFT_91944 NECHADRAFT_95415
PLJ : VFPFJ_01465 VFPFJ_11518
VAL : VDBG_01148 VDBG_01891
PFY : PFICI_04207 PFICI_05942 PFICI_05943
NFI : NFIA_086930 NFIA_094390
APUU : APUU_50161S APUU_51121S
PCS : Pc12g01760 Pc20g13770
TRG : TRUGW13939_04678 TRUGW13939_07607
ZTR : MYCGRDRAFT_51582 MYCGRDRAFT_93463
ABP : AGABI1DRAFT35589(AGABI1DRAFT_35589)
ABV : AGABI2DRAFT206438(AGABI2DRAFT_206438)
PCUB : JR316_0008412 JR316_0008454
PGR : PGTG_06099 PGTG_11011
EHI : EHI_175070(262.t00006)
ECO : b2291(yfbR) b2361(yfdR)
ECJ : JW2288(yfbR) JW2358(yfdR)
ECD : ECDH10B_2453(yfbR) ECDH10B_2524(yfdR)
EBW : BWG_2065(yfbR) BWG_2128(yfdR)
ECF : ECH74115_3430(yfbR) ECH74115_5538
ETW : ECSP_3165(yfbR) ECSP_5134
EOI : ECO111_3039(yfbR) ECO111_4879
EOJ : ECO26_3279(yfbR) ECO26_3710
EOH : ECO103_0512 ECO103_2755(yfbR)
ECOO : ECRM13514_3047(yfbR) ECRM13514_5192
ECOH : ECRM13516_2820 ECRM13516_2991(yfbR) ECRM13516_5353
EOK : G2583_2828(yfbR) G2583_5180(yfdR)
ELH : ETEC_0271 ETEC_2426 ETEC_4312 ETEC_4679
ECW : EcE24377A_2584(yfbR)
EUN : UMNK88_282 UMNK88_2841
ECV : APECO1_2048(yfdR) APECO1_3868(yfdR) APECO1_4273(yfbR)
ECOA : APECO78_03040 APECO78_04665 APECO78_06200 APECO78_14760 APECO78_15270
ECQ : ECED1_2128(yfdR) ECED1_2755(yfbR)
EUM : ECUMN_0861(yfdR) ECUMN_2630(yfbR)
ECT : ECIAI39_2438(yfbR) ECIAI39_4850(yfdR)
EOC : CE10_2673(yfbR) CE10_5126(yfdR)
ECI : UTI89_C2573(yfbR) UTI89_C3007(yfdR1) UTI89_C5091(yfdR2)
EIH : ECOK1_0518 ECOK1_2524(yfbR) ECOK1_3018 ECOK1_4890
ECZ : ECS88_0535(yfdR) ECS88_2438(yfbR) ECS88_2913(yfdR) ECS88_5000(yfdR)
ECC : c2832(yfbR) c3202(yfdR)
EDH : EcDH1_1297 EcDH1_1365
EDJ : ECDH1ME8569_2228(yfbR) ECDH1ME8569_2298(yfdR)
ELU : UM146_03330 UM146_05360
ECOI : ECOPMV1_00523 ECOPMV1_02450(yfbR) ECOPMV1_04437
ECOJ : P423_12790 P423_14545
EFE : EFER_0575(yfdR) EFER_0878(yfbR) EFER_4418(yfdR)
EAL : EAKF1_ch1465 EAKF1_ch1783 EAKF1_ch3688c(yfbR)
SEO : STM14_2477 STM14_2875
SEV : STMMW_20271 STMMW_23541
SEY : SL1344_1970 SL1344_2301
SEJ : STMUK_2023 STMUK_2362
SEB : STM474_2075 STM474_2429(yfbR)
SEF : UMN798_2154 UMN798_2517
SETC : CFSAN001921_05135 CFSAN001921_06830
SENR : STMDT2_19671 STMDT2_23011
SEND : DT104_20561 DT104_23881
SENI : CY43_10765 CY43_12485
SEEN : SE451236_16160 SE451236_17855
SEW : SeSA_A2560 SeSA_A4441
ECLE : ECNIH2_02220 ECNIH2_16030
ECLX : LI66_15370 LI66_17125
EHM : AB284_10050 AB284_23795
ELG : BH714_08520 BH714_11865
ERN : BFV67_15055 BFV67_15360
ENF : AKI40_1170 AKI40_1570
EHU : D5067_0005570 D5067_0007260
KOC : AB185_13960 AB185_15705
KLL : BJF97_11900 BJF97_20585 BJF97_22285
RTG : NCTC13098_01980(yfbR)
REE : electrica_01466(yfbR)
CFD : CFNIH1_22515 CFNIH1_23000
CWE : CO701_06460 CO701_12450
CFQ : C2U38_16950 C2U38_24145
CAMA : F384_12230 F384_15560
CAF : AL524_07455 AL524_10665
CFAR : CI104_17565 CI104_20605
CIR : C2U53_14405 C2U53_27415 C2U53_28040
CIE : AN232_12360 AN232_15015
CTEL : GBC03_09225 GBC03_12895
CLAP : NCTC11466_01302(yfbR)
KOO : O9K67_05790 O9K67_07765(yfbR)
KIE : NCTC12125_00385(yfbR) NCTC12125_00754
LEY : DVA43_01680 DVA43_24030
BFT : MNO13_06895(yfbR) MNO13_15255
AHN : NCTC12129_01522(yfbR) NCTC12129_02197(yfdR)
SGOE : A8O29_005480 A8O29_007055(yfbR)
PSHI : SAMEA2665130_2010(yfbR)
TOE : QMG90_07575(yfbR) QMG90_07895
EBC : C2U52_06300 C2U52_17455
YPG : YpAngola_A1820(yfbR)
YPI : YpsIP31758_1449(yfbR)
YEL : LC20_00463 LC20_03700 LC20_03939
YEW : CH47_3887 CH47_759(yfbR)
YEE : YE5303_00311 YE5303_11301 YE5303_12211
YSI : BF17_14265 BF17_22405
YRB : UGYR_04550 UGYR_04820
YMA : DA391_09590 DA391_15350
YHI : D5F51_03300 D5F51_05200
YCA : F0T03_06495 F0T03_07635 F0T03_12825
SMAC : SMDB11_2632 SMDB11_2703
SMW : SMWW4_v1c34200(yfbR)
SRR : SerAS9_3443 SerAS9_3509
SRS : SerAS12_3444 SerAS12_3510
SRA : SerAS13_3445 SerAS13_3511
SERM : CLM71_08585 CLM71_16395
SFJ : SAMEA4384070_3427(yfbR)
SOF : NCTC11214_03366(yfbR)
SRHZ : FO014_00480 FO014_17835
RACE : JHW33_00800(yfbR) JHW33_03165
EAME : GXP68_05855 GXP68_06675(yfbR)
PAQU : DMB82_0007410(yfbR)
BNG : EH206_06975 EH206_09700
SLIG : GTU79_19140(yfbR) GTU79_21340
EPY : EpC_12570(yfbR) EpC_20810(yfdR)
EPR : EPYR_01340(yfbR) EPYR_02237(yfdR)
PAQ : PAGR_g1389 PAGR_g1809
PAO : Pat9b_2156 Pat9b_2735
PSTW : DSJ_15645 DSJ_17090
TPTY : NCTC11468_01548 NCTC11468_02511(yfbR)
PVG : CRN77_10075 CRN77_14475 CRN77_14705
PROT : BTA34_05620 BTA34_10485
PCOL : F1325_11595 F1325_12430
PCIB : F9282_06585 F9282_07710 F9282_12505
PPEE : I6G31_02450 I6G31_13680 I6G31_16040(yfbR)
XHO : A9255_01745 A9255_18570
PRG : RB151_026750(yfbR_2)
PHEI : NCTC12003_01552(yfbR_2)
PRJ : NCTC6933_02344(yfbR_2)
MWI : MNY66_09885(yfbR) MNY66_16305
LRI : NCTC12151_01240(yfbR)
HPIT : NCTC13334_01255(yfbR)
PMV : PMCN06_0811(yfbR) PMCN06_1384
PDAG : 4362423_00968(yfbR)
AACN : AANUM_1872 AANUM_1967
ASEG : NCTC10977_01568(yfbR)
AVT : NCTC3438_01704(yfbR)
RPNE : NCTC8284_02661(yfbR_1)
PAET : NCTC13378_00526(yfbR)
VPL : SA104470976_01683(yfbR)
PFX : A7318_12585 A7318_15765
AMC : MADE_1011590 MADE_1013415
AMH : I633_12015 I633_12095 I633_12465
AMAA : amad1_11655 amad1_11710 amad1_12055
AMAL : I607_10980 I607_11035 I607_11375
AMAE : I876_11350 I876_11405 I876_11750
AMAO : I634_11205 I634_11260 I634_11605
AMAD : I636_11235 I636_11290 I636_11630
AMAI : I635_11640 I635_11695 I635_12035
AMAG : I533_10985 I533_11045 I533_11390
ALT : ambt_05925 ambt_09260
ASP : AOR13_1182 AOR13_1718
ASQ : AVL57_07345 AVL57_12755
AAW : AVL56_06225 AVL56_11880
ALR : DS731_08895 DS731_11805
ALE : AV939_06355 AV939_11595
ALZ : AV940_06200 AV940_11360
APEL : CA267_000790(yfbR) CA267_016890(yfbR)
SALK : FBQ74_06760 FBQ74_09460
PAT : Patl_2017 Patl_2032 Patl_2033
SALH : HMF8227_01578(yfbR) HMF8227_02333
FES : HER31_04135(yfbR) HER31_11835(yfbR)
METL : U737_03135 U737_23360
MRP : NM686_007005(yfbR) NM686_015865(yfbR)
AEL : NCTC12917_01897(yfbR)
CDIZ : CEDIAZO_01289(yfbR)
GPB : HDN1F_31930 HDN1F_31970
CVC : BKX93_02095 BKX93_12485
CHRO : CXB49_10445 CXB49_22595
ACIP : CBP36_20990 CBP36_21610
BBAG : E1O_01390 E1O_04830 E1O_11910
MCI : Mesci_3897 Mesci_4806
NKI : KW403_12410 KW403_15070
KMN : HW532_04830 HW532_21475
SMQ : SinmeB_0727 SinmeB_5290
SINO : SS05631_c08340 SS05631_c15120
ENU : PYH37_002132 PYH37_003344
ARUI : G6M88_12590 G6M88_23930
RIR : BN877_I1039 BN877_I1826
RHV : BA939_00150 BA939_14380
RHK : Kim5_CH01541 Kim5_PA00010
OIN : IAR37_06445 IAR37_16645
MAQU : Maq22A_3p50055 Maq22A_c16810
MTUN : MTUNDRAET4_0049.2 MTUNDRAET4_0719
CHEL : AL346_00275 AL346_13440
DNP : N8A98_04200 N8A98_06685
MTW : CQW49_07480 CQW49_10245
CMET : K6K41_04655 K6K41_22795
LABT : FIU93_00230 FIU93_22560
SEDI : EBB79_07235 EBB79_20810
POQ : KZX46_03735 KZX46_21980
SHUM : STHU_09200 STHU_09730
HJO : AY555_02045 AY555_02910
THAC : CSC3H3_01145 CSC3H3_12840 CSC3H3_20640
VRM : 44547418_00296(yfbR)
VDN : NCTC11831_00268(yfbR)
MANA : MAMMFC1_01844(yfbR)
AHEL : Q31a_11680 Q31a_17560
» show all
Taxonomy
Reference
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
Sequence
Reference
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
Sequence
Other DBs
ExplorEnz - The Enzyme Database: 3.1.3.89
ExPASy - ENZYME nomenclature database: 3.1.3.89