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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456998   8 HLSNRLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLsnPAEleesdalGVRRAAQRRLKAELGIpleev 87
Cdd:cd02885    21 HRKGTLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPL--PGE-------GVEDAAQRRLREELGI----- 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370456998  88 PPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeLKELLKKAASGEIKITPWFKIIAA 166
Cdd:cd02885    87 PVCDLEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVS---LEELRELLAATPEAFTPWFRLILE 162

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456998  11 NRLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaeleESdalgVRRAAQRRLKAELGIpleeVPPE 90
Cdd:COG1443    25 KGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPRAG-----ET----YEEAAVRELEEELGI----TVDD 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1370456998  91 EINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeLKELLKKAASGEIKITPWFKII 164
Cdd:COG1443    92 DLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVT---LEELLALLEAGPEAFTPWFRLY 162

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456998   8 HLSNRLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLsnPAEleesdalGVRRAAQRRLKAELGIpleev 87
Cdd:cd02885    21 HRKGTLLHRAFSVFLFNSKGELLLQRRALSKYTWPGLWTNTCCSHPL--PGE-------GVEDAAQRRLREELGI----- 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1370456998  88 PPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeLKELLKKAASGEIKITPWFKIIAA 166
Cdd:cd02885    87 PVCDLEELPRFRYRATDDNGLVEHEIDHVFVGRADGDPVPNPEEVSDYRWVS---LEELRELLAATPEAFTPWFRLILE 162

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456998  11 NRLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaeleESdalgVRRAAQRRLKAELGIpleeVPPE 90
Cdd:COG1443    25 KGLLHRAFSVFVFNSDGRLLLQRRALTKDHWPGLWDNTVCGHPRAG-----ET----YEEAAVRELEEELGI----TVDD 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1370456998  91 EINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSkeeLKELLKKAASGEIKITPWFKII 164
Cdd:COG1443    92 DLRPLGTFRYRAVDANGLVENEFCHVFVARLDGPLTPQPEEVAEVRWVT---LEELLALLEAGPEAFTPWFRLY 162

NUDIX domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456998  13 LLHRAFSVFLFNTENKLLLQQRSdaKITFPGCFtntccshplSNPA-ELEESDAlgVRRAAQRRLKAELGIpleevPPEE 91
Cdd:pfam00293   1 KRRVAVGVVLLNEKGRVLLVRRS--KKPFPGWW---------SLPGgKVEPGET--PEEAARRELEEETGL-----EPEL 62

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1370456998  92 INYLTRIHYKAQSDGIWG-EHEIDYILLVRKNVTLNPDPN-EIKSYCYVSkeELKELLKKAASGEIKITPWF 161
Cdd:pfam00293  63 LELLGSLHYLAPFDGRFPdEHEILYVFLAEVEGELEPDPDgEVEEVRWVP--LEELLLLKLAPGDRKLLPWL 132

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456998   8 HLSNRLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaelEESdalgvRRAAQRRLKAELGIpleEV 87
Cdd:cd04693    22 PLPEGEYHLVVHVWIFNSDGEILIQQRSPDKKGFPGMWEASTGGSVLAG----ETS-----LEAAIRELKEELGI---DL 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1370456998  88 PPEEINYLTRIHYkaqsdgiwgEHEIDYILLVRKNVTLN---PDPNEIKSYCYVS 139
Cdd:cd04693    90 DADELRPILTIRF---------DNGFDDIYLFRKDVDIEdltLQKEEVQDVKWVT 135

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456998  16 RAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNpaelEESDAlgvrrAAQRRLKAELGIPLEEVPPEEINYL 95
Cdd:cd24154     3 RVVNAFLINSQGQLWIPRRTADKRIFPLALDMSVGGHVSSG----ETYEQ-----AFVRELQEELNLDLDQLSYRVLGKL 73

                  .
gi 1370456998  96 T 96
Cdd:cd24154    74 T 74

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370456998  19 SVFLFNTENKLLLQQRSDA----KITFPGCFtntccshplsnpAELEESdalgVRRAAQRRLKAELGIPLEEVPPEEINY 94
Cdd:cd02883     4 GAVVFDDEGRVLLVRRSDGpgpgGWELPGGG------------VEPGET----PEEAAVREVREETGLDVEVLRLLGVYE 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1370456998  95 LTRIHYKAQSDGIWgeheidYILLVRKNVTLNPDPNEIKSYCYVS 139
Cdd:cd02883    68 FPDPDEGRHVVVLV------FLARVVGGEPPPLDDEEISEVRWVP 106