NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|40018633|ref|NP_004499|]
View 

isopentenyl-diphosphate Delta-isomerase 1 isoform a [Homo sapiens]

Protein Classification

NUDIX hydrolase( domain architecture ID 225)

NUDIX hydrolase catalyzes the hydrolysis of nucleoside diphosphates linked to other moieties (X); it requires a divalent cation, such as Mg2+ or Mn2+ for its activity

CATH:  3.90.79.10
EC:  3.6.1.-
Gene Ontology:  GO:0016817|GO:0009132|GO:0046872
PubMed:  15581572|16378245|27936487
SCOP:  3000098

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NUDIX_Hydrolase super family cl00447
NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three ...
 78-284 7.54e-93

NUDIX hydrolase superfamily; 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.


The actual alignment was detected with superfamily member PLN02552:

Pssm-ID: 469772 [Multi-domain]  Cd Length: 247  Bit Score: 274.69  E-value: 7.54e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633   78 CILIDENDNKIGAETKKNCHLNENIEK-GLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPL--------S 148
Cdd:PLN02552  25 CILVDENDNVVGHDSKYNCHLFEKIEPrGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLygqdpnevD 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  149 NPAELEESDALGVRRAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSD------GIWGEHEIDYILLVRKN--VTLNP 220
Cdd:PLN02552 105 RESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDvthgpdGKWGEHELDYLLFIRPVrdVKVNP 184

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 40018633  221 DPNEIKSYCYVSkeELKELLKKAASGEIKITPWFKIIAATFLFKWWDNLNHLNQFVDHEKIYRM 284
Cdd:PLN02552 185 NPDEVADVKYVN--REELKEMMRKESGLKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
 
Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 78-284 7.54e-93

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 274.69  E-value: 7.54e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633   78 CILIDENDNKIGAETKKNCHLNENIEK-GLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPL--------S 148
Cdd:PLN02552  25 CILVDENDNVVGHDSKYNCHLFEKIEPrGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLygqdpnevD 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  149 NPAELEESDALGVRRAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSD------GIWGEHEIDYILLVRKN--VTLNP 220
Cdd:PLN02552 105 RESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDvthgpdGKWGEHELDYLLFIRPVrdVKVNP 184

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 40018633  221 DPNEIKSYCYVSkeELKELLKKAASGEIKITPWFKIIAATFLFKWWDNLNHLNQFVDHEKIYRM 284
Cdd:PLN02552 185 NPDEVADVKYVN--REELKEMMRKESGLKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 77-259 4.70e-78

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: 233.93  E-value: 4.70e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  77 MCILIDENDNKIGAETKKNCHLNEniekGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLsnPAElees 156
Cdd:cd02885   1 EVILVDEDDNPIGTAEKLEAHRKG----TLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPL--PGE---- 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633 157 dalGVRRAAQRRLKAELGIpleevPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeL 236
Cdd:cd02885  71 ---GVEDAAQRRLREELGI-----PVCDLEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVS---L 139

                       170       180
                ....*....|....*....|...
gi 40018633 237 KELLKKAASGEIKITPWFKIIAA 259
Cdd:cd02885 140 EELRELLAATPEAFTPWFRLILE 162
IPP_isom_1 TIGR02150
isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two ...
 78-258 2.81e-75

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: 226.84  E-value: 2.81e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633    78 CILIDENDNKIGAETKKNCHLNENIekglLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSnpaeleesd 157
Cdd:TIGR02150   1 VILVDENDNPIGTASKAEVHLQETP----LHRAFSVFLFNEEGELLLQRRASSKITWPGVWTNSCCSHPLP--------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633   158 alGVRRAAQRRLKAELGIPLEEVPpeeINYLTRIHYKAQsDGIWGEHEIDYILLVRKNVTLNPDPnEIKSYCYVSKEELK 237
Cdd:TIGR02150  68 --GELEAAIRRLRHELGIPADDVP---LTVLPRFSYRAR-DDAWGEHELCPVFFARANVDLNPNP-EVAEYRWVSLEELK 140

                         170       180
                  ....*....|....*....|.
gi 40018633   238 ELLKKAASGeikITPWFKIIA 258
Cdd:TIGR02150 141 EILAKPWAG---FSPWFRIQA 158
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 79-257 7.67e-47

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: 154.20  E-value: 7.67e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  79 ILIDENDNKIGAETKKNCHlneniEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaeleESda 158
Cdd:COG1443   5 DLVDEDGRPIGTAERAEVH-----RKGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPRAG-----ET-- 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633 159 lgVRRAAQRRLKAELGIpleeVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeLKE 238
Cdd:COG1443  73 --YEEAAVRELEEELGI----TVDDDLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVT---LEE 143

                       170
                ....*....|....*....
gi 40018633 239 LLKKAASGEIKITPWFKII 257
Cdd:COG1443 144 LLALLEAGPEAFTPWFRLY 162
NUDIX pfam00293
NUDIX domain;
106-254 1.54e-15

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 71.75  E-value: 1.54e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633   106 LLHRAFSVFLFNTENKLLLQQRSdaKITFPGCFtntccshplSNPA-ELEESDAlgVRRAAQRRLKAELGIpleevPPEE 184
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRS--KKPFPGWW---------SLPGgKVEPGET--PEEAARRELEEETGL-----EPEL 62

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 40018633   185 INYLTRIHYKAQSDGIWG-EHEIDYILLVRKNVTLNPDPN-EIKSYCYVSkeELKELLKKAASGEIKITPWF 254
Cdd:pfam00293  63 LELLGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDgEVEEVRWVP--LEELLLLKLAPGDRKLLPWL 132
 
Name Accession Description Interval E-value
PLN02552 PLN02552
isopentenyl-diphosphate delta-isomerase
 78-284 7.54e-93

isopentenyl-diphosphate delta-isomerase


Pssm-ID: 215303 [Multi-domain]  Cd Length: 247  Bit Score: 274.69  E-value: 7.54e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633   78 CILIDENDNKIGAETKKNCHLNENIEK-GLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPL--------S 148
Cdd:PLN02552  25 CILVDENDNVVGHDSKYNCHLFEKIEPrGLLHRAFSVFLFNSKYELLLQQRAATKVTFPLVWTNTCCSHPLygqdpnevD 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  149 NPAELEESDALGVRRAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSD------GIWGEHEIDYILLVRKN--VTLNP 220
Cdd:PLN02552 105 RESELIDGNVLGVKNAAQRKLLHELGIPAEDVPVDQFTFLTRLHYKAADDvthgpdGKWGEHELDYLLFIRPVrdVKVNP 184

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 40018633  221 DPNEIKSYCYVSkeELKELLKKAASGEIKITPWFKIIAATFLFKWWDNLNHLNQFVDHEKIYRM 284
Cdd:PLN02552 185 NPDEVADVKYVN--REELKEMMRKESGLKLSPWFRLIVDNFLMKWWDDLEKGTEAVDMKTIHKL 246
NUDIX_IPP_Isomerase cd02885
Isopentenyl diphosphate isomerase; Isopentenyl diphosphate (IPP) isomerase, a member of the ...
 77-259 4.70e-78

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: 233.93  E-value: 4.70e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  77 MCILIDENDNKIGAETKKNCHLNEniekGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLsnPAElees 156
Cdd:cd02885   1 EVILVDEDDNPIGTAEKLEAHRKG----TLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPL--PGE---- 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633 157 dalGVRRAAQRRLKAELGIpleevPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeL 236
Cdd:cd02885  71 ---GVEDAAQRRLREELGI-----PVCDLEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVS---L 139

                       170       180
                ....*....|....*....|...
gi 40018633 237 KELLKKAASGEIKITPWFKIIAA 259
Cdd:cd02885 140 EELRELLAATPEAFTPWFRLILE 162
IPP_isom_1 TIGR02150
isopentenyl-diphosphate delta-isomerase, type 1; This model represents type 1 of two ...
 78-258 2.81e-75

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: 226.84  E-value: 2.81e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633    78 CILIDENDNKIGAETKKNCHLNENIekglLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSnpaeleesd 157
Cdd:TIGR02150   1 VILVDENDNPIGTASKAEVHLQETP----LHRAFSVFLFNEEGELLLQRRASSKITWPGVWTNSCCSHPLP--------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633   158 alGVRRAAQRRLKAELGIPLEEVPpeeINYLTRIHYKAQsDGIWGEHEIDYILLVRKNVTLNPDPnEIKSYCYVSKEELK 237
Cdd:TIGR02150  68 --GELEAAIRRLRHELGIPADDVP---LTVLPRFSYRAR-DDAWGEHELCPVFFARANVDLNPNP-EVAEYRWVSLEELK 140

                         170       180
                  ....*....|....*....|.
gi 40018633   238 ELLKKAASGeikITPWFKIIA 258
Cdd:TIGR02150 141 EILAKPWAG---FSPWFRIQA 158
Idi COG1443
Isopentenyldiphosphate isomerase [Lipid transport and metabolism]; Isopentenyldiphosphate ...
 79-257 7.67e-47

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: 154.20  E-value: 7.67e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  79 ILIDENDNKIGAETKKNCHlneniEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaeleESda 158
Cdd:COG1443   5 DLVDEDGRPIGTAERAEVH-----RKGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPRAG-----ET-- 72

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633 159 lgVRRAAQRRLKAELGIpleeVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeLKE 238
Cdd:COG1443  73 --YEEAAVRELEEELGI----TVDDDLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVT---LEE 143

                       170
                ....*....|....*....
gi 40018633 239 LLKKAASGEIKITPWFKII 257
Cdd:COG1443 144 LLALLEAGPEAFTPWFRLY 162
PRK03759 PRK03759
isopentenyl-diphosphate Delta-isomerase;
75-254 1.55e-33

isopentenyl-diphosphate Delta-isomerase;


Pssm-ID: 235156 [Multi-domain]  Cd Length: 184  Bit Score: 120.84  E-value: 1.55e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633   75 AEMCILIDENDNKIGAETKKNCHLNEniekGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLsnPAEle 154
Cdd:PRK03759   5 TELVVLLDEQGVPTGTAEKAAAHTAD----TPLHLAFSCYLFDADGRLLVTRRALSKKTWPGVWTNSCCGHPQ--PGE-- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  155 esdalGVRRAAQRRLKAELGIPLEEVPPEeinyLTRIHYKA-QSDGIWgEHEIDYILLVRKNVTLNPDPNEIKSYCYVSk 233
Cdd:PRK03759  77 -----SLEDAVIRRCREELGVEITDLELV----LPDFRYRAtDPNGIV-ENEVCPVFAARVTSALQPNPDEVMDYQWVD- 145

                        170       180
                 ....*....|....*....|.
gi 40018633  234 eeLKELLKKAASGEIKITPWF 254
Cdd:PRK03759 146 --PADLLRAVDATPWAFSPWM 164
NUDIX_Hydrolase cd04692
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 82-225 1.11e-21

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: 88.38  E-value: 1.11e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  82 DENDNKIGAETKKNCHlneniEKGLLHRAFSVFLFNTEN-KLLLQQRSDAKITFPGCFTNTCCSHPLSNpaeleESdalg 160
Cdd:cd04692   5 DEDGRPIGVATRSEVH-----RQGLWHRTVHVWLVNPEEgRLLLQKRSANKDDFPGLWDISAAGHIDAG-----ET---- 70

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 40018633 161 VRRAAQRRLKAELGIpleEVPPEEINYLTRIHYKAQSDGIWGeHEIDYILLVRKNVTLN---PDPNEI 225
Cdd:cd04692  71 YEEAAVRELEEELGL---TVSPEDLIFLGVIREEVIGGDFID-NEFVHVYLYETDRPLEefkLQPEEV 134
NUDIX_Hydrolase cd04693
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 82-232 3.32e-17

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: 76.80  E-value: 3.32e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  82 DENDNKIGaETKKNchlNENIEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaelEESdalgv 161
Cdd:cd04693   7 DENRNKTG-RTHRR---GEPLPEGEYHLVVHVWIFNSDGEILIQQRSPDKKGFPGMWEASTGGSVLAG----ETS----- 73

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 40018633 162 RRAAQRRLKAELGIpleEVPPEEINYLTRIHYkaqsdgiwgEHEIDYILLVRKNVTLN---PDPNEIKSYCYVS 232
Cdd:cd04693  74 LEAAIRELKEELGI---DLDADELRPILTIRF---------DNGFDDIYLFRKDVDIEdltLQKEEVQDVKWVT 135
NUDIX pfam00293
NUDIX domain;
106-254 1.54e-15

NUDIX domain;


Pssm-ID: 395229 [Multi-domain]  Cd Length: 132  Bit Score: 71.75  E-value: 1.54e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633   106 LLHRAFSVFLFNTENKLLLQQRSdaKITFPGCFtntccshplSNPA-ELEESDAlgVRRAAQRRLKAELGIpleevPPEE 184
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRS--KKPFPGWW---------SLPGgKVEPGET--PEEAARRELEEETGL-----EPEL 62

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 40018633   185 INYLTRIHYKAQSDGIWG-EHEIDYILLVRKNVTLNPDPN-EIKSYCYVSkeELKELLKKAASGEIKITPWF 254
Cdd:pfam00293  63 LELLGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDgEVEEVRWVP--LEELLLLKLAPGDRKLLPWL 132
NUDIX_Hydrolase cd04697
uncharacterized NUDIX hydrolase subfamily; NUDIX hydrolase is a superfamily of enzymes found ...
 78-232 4.12e-12

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: 62.64  E-value: 4.12e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  78 CILIDENDNKIGAETKKnchlnENIEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGcFTNTCCShplsnpaeleesd 157
Cdd:cd04697   1 VDIVDENNEVVGAATRA-----EMRRQKLIHRATYIVVRNAAGRLLVQKRTMDKDYCPG-YLDPATG------------- 61

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633 158 alGV-------RRAAQRRLKAELGIplEEVPPEeinYLTRIHYKAQSDGIWGE-HEIDYillvRKNVTlnPDPNEIKSYC 229
Cdd:cd04697  62 --GVvgagesyEENARRELEEELGI--DGVPLR---PLFTFYYEDDRSRVWGAlFECVY----DGPLK--LQPEEVAEVD 128


                ...
gi 40018633 230 YVS 232
Cdd:cd04697 129 WMS 131
NUDIX_DR0079 cd24154
NUDIX domain family found in Deinococcus radiodurans, and similar proteins; Deinococcus ...
 109-189 1.20e-04

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: 40.66  E-value: 1.20e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633 109 RAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaelEESDAlgvrrAAQRRLKAELGIPLEEVPPEEINYL 188
Cdd:cd24154   3 RVVNAFLINSQGQLWIPRRTADKRIFPLALDMSVGGHVSSG----ETYEQ-----AFVRELQEELNLDLDQLSYRVLGKL 73


                .
gi 40018633 189 T 189
Cdd:cd24154  74 T 74
PLN02791 PLN02791
Nudix hydrolase homolog
 105-224 4.64e-04

Nudix hydrolase homolog


Pssm-ID: 215425 [Multi-domain]  Cd Length: 770  Bit Score: 41.34  E-value: 4.64e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633  105 GLLHRAFSVFLF-NTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNPAELeesdalgvrRAAQRRLKAELGIPLEEVPPE 183
Cdd:PLN02791  29 GDYHRAVHVWIYsESTQELLLQRRADCKDSWPGQWDISSAGHISAGDTSL---------LSAQRELEEELGIILPKDAFE 99

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 40018633  184 EI-NYLTRIhykAQSDGIWGEHEIDYILLVrknVTLNPDPNE 224
Cdd:PLN02791 100 LLfVFLQEC---VINDGKFINNEYNDVYLV---TTLDPIPLE 135
NUDIX_Hydrolase cd02883
NUDIX hydrolase superfamily; NUDIX hydrolase is a superfamily of enzymes found in all three ...
 112-232 8.73e-03

NUDIX hydrolase superfamily; 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: 467528 [Multi-domain]  Cd Length: 106  Bit Score: 35.07  E-value: 8.73e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40018633 112 SVFLFNTENKLLLQQRSDA----KITFPGCFtntccshplsnpAELEESdalgVRRAAQRRLKAELGIPLEEVPPEEINY 187
Cdd:cd02883   4 GAVVFDDEGRVLLVRRSDGpgpgGWELPGGG------------VEPGET----PEEAAVREVREETGLDVEVLRLLGVYE 67

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 40018633 188 LTRIHYKAQSDGIWgeheidYILLVRKNVTLNPDPNEIKSYCYVS 232
Cdd:cd02883  68 FPDPDEGRHVVVLV------FLARVVGGEPPPLDDEEISEVRWVP 106
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH