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Conserved domains on  [gi|1002284995|ref|XP_015646798|]
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isopentenyl-diphosphate Delta-isomerase I [Oryza sativa Japonica Group]

Protein Classification

isopentenyl-diphosphate delta-isomerase( domain architecture ID 10791402)

isopentenyl-diphosphate delta-isomerase catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), a key step in the isoprenoid biosynthesis

CATH:  3.90.79.10
EC:  5.3.3.2
Gene Ontology:  GO:0046872
PubMed:  9418296|15581572|16378245
SCOP:  3000098

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 8-238 3.13e-162

isopentenyl-diphosphate delta-isomerase


:

Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 448.41  E-value: 3.13e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995   8 VEDAGMDEVQKRLMFDDECILVDEQDNVVGHESKYNCHLMEKIESENLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVW 87
Cdd:PLN02552    7 ATWAGMDAVQRRLMFEDECILVDENDNVVGHDSKYNCHLFEKIEPRGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVW 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  88 TNTCCSHPLY--------RESELIQENYLGVRNAAQRKLLDELGIPAEDVPVDQFTPLGRMLYKAPSD------GKWGEH 153
Cdd:PLN02552   87 TNTCCSHPLYgqdpnevdRESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDvthgpdGKWGEH 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 154 ELDYLLFI--VRDVKVVPNPDEVADVKYVSREQLKELIRKadagEEGLKLSPWFRLVVDNFLMGWWDHVEKGTlnEAVDM 231
Cdd:PLN02552  167 ELDYLLFIrpVRDVKVNPNPDEVADVKYVNREELKEMMRK----ESGLKLSPWFRLIVDNFLMKWWDDLEKGT--EAVDM 240


                  ....*..
gi 1002284995 232 ETIHKLK 238
Cdd:PLN02552  241 KTIHKLM 247
 
Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 8-238 3.13e-162

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 448.41  E-value: 3.13e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995   8 VEDAGMDEVQKRLMFDDECILVDEQDNVVGHESKYNCHLMEKIESENLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVW 87
Cdd:PLN02552    7 ATWAGMDAVQRRLMFEDECILVDENDNVVGHDSKYNCHLFEKIEPRGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVW 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  88 TNTCCSHPLY--------RESELIQENYLGVRNAAQRKLLDELGIPAEDVPVDQFTPLGRMLYKAPSD------GKWGEH 153
Cdd:PLN02552   87 TNTCCSHPLYgqdpnevdRESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDvthgpdGKWGEH 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 154 ELDYLLFI--VRDVKVVPNPDEVADVKYVSREQLKELIRKadagEEGLKLSPWFRLVVDNFLMGWWDHVEKGTlnEAVDM 231
Cdd:PLN02552  167 ELDYLLFIrpVRDVKVNPNPDEVADVKYVNREELKEMMRK----ESGLKLSPWFRLIVDNFLMKWWDDLEKGT--EAVDM 240


                  ....*..
gi 1002284995 232 ETIHKLK 238
Cdd:PLN02552  241 KTIHKLM 247
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 25-210 2.61e-84

Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the NUDIX hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mammals and plants. Despite sequence variations (mainly at the N-terminus), the core structure is highly conserved.


Pssm-ID: 467529 [Multi-domain]  Cd Length: 162  Bit Score: 247.79  E-value: 2.61e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  25 ECILVDEQDNVVGHESKYNCHLMEkieseNLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVWTNTCCSHPLYREseliq 104
Cdd:cd02885     1 EVILVDEDDNPIGTAEKLEAHRKG-----TLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPLPGE----- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 105 enylGVRNAAQRKLLDELGIPAEDvpvdqFTPLGRMLYKAPSDGKWGEHELDYLLFIVRDVKVVPNPDEVADVKYVSREQ 184
Cdd:cd02885    71 ----GVEDAAQRRLREELGIPVCD-----LEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVSLEE 141

                         170       180
                  ....*....|....*....|....*.
gi 1002284995 185 LKELIRkadagEEGLKLSPWFRLVVD 210
Cdd:cd02885   142 LRELLA-----ATPEAFTPWFRLILE 162
IPP_isom_1 TIGR02150
isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two ...
 26-209 2.43e-73

isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 273998 [Multi-domain]  Cd Length: 158  Bit Score: 219.91  E-value: 2.43e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  26 CILVDEQDNVVGHESKYNCHLMEkieseNLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVWTNTCCSHPLYreseliqe 105
Cdd:TIGR02150   1 VILVDENDNPIGTASKAEVHLQE-----TPLHRAFSVFLFNEEGELLLQRRASSKITWPGVWTNSCCSHPLP-------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 106 nylGVRNAAQRKLLDELGIPAEDVPvdqFTPLGRMLYKAPSDGkWGEHELDYLLFIVRDVKVVPNPdEVADVKYVSREQL 185
Cdd:TIGR02150  68 ---GELEAAIRRLRHELGIPADDVP---LTVLPRFSYRARDDA-WGEHELCPVFFARANVDLNPNP-EVAEYRWVSLEEL 139

                         170       180
                  ....*....|....*....|....
gi 1002284995 186 KELIRKADAGeeglkLSPWFRLVV 209
Cdd:TIGR02150 140 KEILAKPWAG-----FSPWFRIQA 158
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 27-208 4.43e-54

Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 441052 [Multi-domain]  Cd Length: 162  Bit Score: 171.15  E-value: 4.43e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  27 ILVDEQDNVVGHESKYNCHlmekieSENLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVWTNTCCSHPLYRESeliqen 106
Cdd:COG1443     5 DLVDEDGRPIGTAERAEVH------RKGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPRAGET------ 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 107 ylgVRNAAQRKLLDELGIpaedVPVDQFTPLGRMLYKAPSDGKWGEHELDYLLFIVRDVKVVPNPDEVADVKYVSREQLK 186
Cdd:COG1443    73 ---YEEAAVRELEEELGI----TVDDDLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVTLEELL 145

                         170       180
                  ....*....|....*....|..
gi 1002284995 187 ELIRkadagEEGLKLSPWFRLV 208
Cdd:COG1443   146 ALLE-----AGPEAFTPWFRLY 162
NUDIX pfam00293
NUDIX domain;
55-205 1.21e-13

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 65.58  E-value: 1.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  55 LLHRAFSVFLFNSKYELLLQQRSATKvtfPLVWTNTCCSHPLYRESeliqenylgVRNAAQRKLLDELGIPAEDVPVdqf 134
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRSKKP---FPGWWSLPGGKVEPGET---------PEEAARRELEEETGLEPELLEL--- 65

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002284995 135 tpLGRMLYKAPSDGKWG-EHELDYLLFIVRDVKVVPNPD-EVADVKYVSREQLKelirKADAGEEGLKLSPWF 205
Cdd:pfam00293  66 --LGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDgEVEEVRWVPLEELL----LLKLAPGDRKLLPWL 132
 
Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 8-238 3.13e-162

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 448.41  E-value: 3.13e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995   8 VEDAGMDEVQKRLMFDDECILVDEQDNVVGHESKYNCHLMEKIESENLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVW 87
Cdd:PLN02552    7 ATWAGMDAVQRRLMFEDECILVDENDNVVGHDSKYNCHLFEKIEPRGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVW 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  88 TNTCCSHPLY--------RESELIQENYLGVRNAAQRKLLDELGIPAEDVPVDQFTPLGRMLYKAPSD------GKWGEH 153
Cdd:PLN02552   87 TNTCCSHPLYgqdpnevdRESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDvthgpdGKWGEH 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 154 ELDYLLFI--VRDVKVVPNPDEVADVKYVSREQLKELIRKadagEEGLKLSPWFRLVVDNFLMGWWDHVEKGTlnEAVDM 231
Cdd:PLN02552  167 ELDYLLFIrpVRDVKVNPNPDEVADVKYVNREELKEMMRK----ESGLKLSPWFRLIVDNFLMKWWDDLEKGT--EAVDM 240


                  ....*..
gi 1002284995 232 ETIHKLK 238
Cdd:PLN02552  241 KTIHKLM 247
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 25-210 2.61e-84

Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the NUDIX hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mammals and plants. Despite sequence variations (mainly at the N-terminus), the core structure is highly conserved.


Pssm-ID: 467529 [Multi-domain]  Cd Length: 162  Bit Score: 247.79  E-value: 2.61e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  25 ECILVDEQDNVVGHESKYNCHLMEkieseNLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVWTNTCCSHPLYREseliq 104
Cdd:cd02885     1 EVILVDEDDNPIGTAEKLEAHRKG-----TLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPLPGE----- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 105 enylGVRNAAQRKLLDELGIPAEDvpvdqFTPLGRMLYKAPSDGKWGEHELDYLLFIVRDVKVVPNPDEVADVKYVSREQ 184
Cdd:cd02885    71 ----GVEDAAQRRLREELGIPVCD-----LEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVSLEE 141

                         170       180
                  ....*....|....*....|....*.
gi 1002284995 185 LKELIRkadagEEGLKLSPWFRLVVD 210
Cdd:cd02885   142 LRELLA-----ATPEAFTPWFRLILE 162
IPP_isom_1 TIGR02150
isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two ...
 26-209 2.43e-73

isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 273998 [Multi-domain]  Cd Length: 158  Bit Score: 219.91  E-value: 2.43e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  26 CILVDEQDNVVGHESKYNCHLMEkieseNLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVWTNTCCSHPLYreseliqe 105
Cdd:TIGR02150   1 VILVDENDNPIGTASKAEVHLQE-----TPLHRAFSVFLFNEEGELLLQRRASSKITWPGVWTNSCCSHPLP-------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 106 nylGVRNAAQRKLLDELGIPAEDVPvdqFTPLGRMLYKAPSDGkWGEHELDYLLFIVRDVKVVPNPdEVADVKYVSREQL 185
Cdd:TIGR02150  68 ---GELEAAIRRLRHELGIPADDVP---LTVLPRFSYRARDDA-WGEHELCPVFFARANVDLNPNP-EVAEYRWVSLEEL 139

                         170       180
                  ....*....|....*....|....
gi 1002284995 186 KELIRKADAGeeglkLSPWFRLVV 209
Cdd:TIGR02150 140 KEILAKPWAG-----FSPWFRIQA 158
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 27-208 4.43e-54

Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 441052 [Multi-domain]  Cd Length: 162  Bit Score: 171.15  E-value: 4.43e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  27 ILVDEQDNVVGHESKYNCHlmekieSENLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVWTNTCCSHPLYRESeliqen 106
Cdd:COG1443     5 DLVDEDGRPIGTAERAEVH------RKGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPRAGET------ 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 107 ylgVRNAAQRKLLDELGIpaedVPVDQFTPLGRMLYKAPSDGKWGEHELDYLLFIVRDVKVVPNPDEVADVKYVSREQLK 186
Cdd:COG1443    73 ---YEEAAVRELEEELGI----TVDDDLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVTLEELL 145

                         170       180
                  ....*....|....*....|..
gi 1002284995 187 ELIRkadagEEGLKLSPWFRLV 208
Cdd:COG1443   146 ALLE-----AGPEAFTPWFRLY 162
PRK03759 PRK03759
isopentenyl-diphosphate Delta-isomerase;
21-212 2.19e-40

isopentenyl-diphosphate Delta-isomerase;


Pssm-ID: 235156 [Multi-domain]  Cd Length: 184  Bit Score: 137.02  E-value: 2.19e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  21 MFDDECILVDEQDNVVGHESKYNCHlmekiESENLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVWTNTCCSHPLYRES 100
Cdd:PRK03759    3 METELVVLLDEQGVPTGTAEKAAAH-----TADTPLHLAFSCYLFDADGRLLVTRRALSKKTWPGVWTNSCCGHPQPGES 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 101 eliqenylgVRNAAQRKLLDELGIPAEDV-PVdqftpLGRMLYKAPSDGKWGEHELDYLLFIVRDVKVVPNPDEVADVKY 179
Cdd:PRK03759   78 ---------LEDAVIRRCREELGVEITDLeLV-----LPDFRYRATDPNGIVENEVCPVFAARVTSALQPNPDEVMDYQW 143

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1002284995 180 VSreqLKELIRKADAGeeGLKLSPWFRLVVDNF 212
Cdd:PRK03759  144 VD---PADLLRAVDAT--PWAFSPWMVLQAANL 171
NUDIX_Hydrolase cd04692
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 29-181 2.85e-19

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467574 [Multi-domain]  Cd Length: 142  Bit Score: 80.68  E-value: 2.85e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  29 VDEQDNVVGHESKynchlmEKIESENLLHRAFSVFLFNSK-YELLLQQRSATKVTFPLVWTNTCCSHPLYRESeliqeny 107
Cdd:cd04692     4 VDEDGRPIGVATR------SEVHRQGLWHRTVHVWLVNPEeGRLLLQKRSANKDDFPGLWDISAAGHIDAGET------- 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002284995 108 lgVRNAAQRKLLDELGIpaeDVPVDQFTPLGRMLYKApSDGKWGEHELDYLLFIVRDVKV---VPNPDEVADVKYVS 181
Cdd:cd04692    71 --YEEAAVRELEEELGL---TVSPEDLIFLGVIREEV-IGGDFIDNEFVHVYLYETDRPLeefKLQPEEVAGVVFVD 141
NUDIX_Hydrolase cd04693
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 53-191 2.83e-14

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467575 [Multi-domain]  Cd Length: 157  Bit Score: 67.94  E-value: 2.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  53 ENLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVWTNTCCSHPLYRESelIQEnylgvrnAAQRKLLDELGIpaeDVPVD 132
Cdd:cd04693    25 EGEYHLVVHVWIFNSDGEILIQQRSPDKKGFPGMWEASTGGSVLAGET--SLE-------AAIRELKEELGI---DLDAD 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1002284995 133 QFTPLGRMlykapsdgkWGEHELDYLLFIVRDV---KVVPNPDEVADVKYVSREQLKELIRK 191
Cdd:cd04693    93 ELRPILTI---------RFDNGFDDIYLFRKDVdieDLTLQKEEVQDVKWVTLEEILEMIES 145
NUDIX_Hydrolase cd04697
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 26-199 3.37e-14

uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and "house-cleaning" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase.


Pssm-ID: 467578 [Multi-domain]  Cd Length: 157  Bit Score: 67.64  E-value: 3.37e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  26 CILVDEQDNVVGHESKynchlmEKIESENLLHRAFSVFLFNSKYELLLQQRSATKVTFPLVWtnTCCSHPLYRESELIQE 105
Cdd:cd04697     1 VDIVDENNEVVGAATR------AEMRRQKLIHRATYIVVRNAAGRLLVQKRTMDKDYCPGYL--DPATGGVVGAGESYEE 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 106 NylgvrnaAQRKLLDELGIpaEDVPvdqFTPLGRMLYKAPSDGKWGE-HELDYllfivrDVKVVPNPDEVADVKYVSREQ 184
Cdd:cd04697    73 N-------ARRELEEELGI--DGVP---LRPLFTFYYEDDRSRVWGAlFECVY------DGPLKLQPEEVAEVDWMSEDE 134

                         170
                  ....*....|....*
gi 1002284995 185 LKELIRKADAGEEGL 199
Cdd:cd04697   135 ILQAARGEEFTPDGR 149
NUDIX pfam00293
NUDIX domain;
55-205 1.21e-13

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 65.58  E-value: 1.21e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  55 LLHRAFSVFLFNSKYELLLQQRSATKvtfPLVWTNTCCSHPLYRESeliqenylgVRNAAQRKLLDELGIPAEDVPVdqf 134
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRSKKP---FPGWWSLPGGKVEPGET---------PEEAARRELEEETGLEPELLEL--- 65

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002284995 135 tpLGRMLYKAPSDGKWG-EHELDYLLFIVRDVKVVPNPD-EVADVKYVSREQLKelirKADAGEEGLKLSPWF 205
Cdd:pfam00293  66 --LGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDgEVEEVRWVPLEELL----LLKLAPGDRKLLPWL 132
PLN02791 PLN02791
Nudix hydrolase homolog
 57-193 3.15e-09

Nudix hydrolase homolog


Pssm-ID: 215425 [Multi-domain]  Cd Length: 770  Bit Score: 56.75  E-value: 3.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  57 HRAFSVFLF-NSKYELLLQQRSATKVTFPLVWTNTCCSHPLYRESELIqenylgvrnAAQRKLLDELGIpaeDVPVDQFT 135
Cdd:PLN02791   32 HRAVHVWIYsESTQELLLQRRADCKDSWPGQWDISSAGHISAGDTSLL---------SAQRELEEELGI---ILPKDAFE 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002284995 136 PLGRMLYK-APSDGKWGEHELD--YLLFIVRDVKV---VPNPDEVADVKYVSREQLKELIRKAD 193
Cdd:PLN02791  100 LLFVFLQEcVINDGKFINNEYNdvYLVTTLDPIPLeafTLQESEVSAVKYMSIEEYKSALAKED 163
PRK15393 PRK15393
NUDIX hydrolase YfcD; Provisional
 28-204 6.87e-06

NUDIX hydrolase YfcD; Provisional


Pssm-ID: 185291 [Multi-domain]  Cd Length: 180  Bit Score: 45.18  E-value: 6.87e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995  28 LVDEQDNVVGHESKynchlmEKIESENLLHRAFSVFLFNSKYELLLQQRSATKVTFPlVWTNTCCSHPLyreseLIQENY 107
Cdd:PRK15393   14 IVNENNEVIAQASR------EQMRAQCLRHRATYIVVHDGMGKILVQRRTETKDFLP-GMLDATAGGVV-----QAGEQL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002284995 108 LgvrNAAQRKLLDELGIpaEDVPvdqFTPLGRMLYKAPSDGKWGEheldyLLFIVRDVKVVPNPDEVADVKYVSREQLKE 187
Cdd:PRK15393   82 L---ESARREAEEELGI--AGVP---FAEHGQFYFEDENCRVWGA-----LFSCVSHGPFALQEEEVSEVCWMTPEEITA 148

                         170
                  ....*....|....*...
gi 1002284995 188 liRKADAGEEGLK-LSPW 204
Cdd:PRK15393  149 --RCDEFTPDSLKaLALW 164
NUDIX_DR0079 cd24154
NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus ...
 58-85 8.58e-03

NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus radiodurans protein DR_0079 is one of 21 NUDIX hydrolases that it encodes, and it has been observed to have a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP), and for their corresponding deoxyribose nucleotides, dCDP and dCTP, to a lesser degree. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance _ "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required.


Pssm-ID: 467602 [Multi-domain]  Cd Length: 121  Bit Score: 35.27  E-value: 8.58e-03
                          10        20
                  ....*....|....*....|....*...
gi 1002284995  58 RAFSVFLFNSKYELLLQQRSATKVTFPL 85
Cdd:cd24154     3 RVVNAFLINSQGQLWIPRRTADKRIFPL 30
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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