752
Pathway
Operon: Cytidyl Pyrophosphate Biosynthesis of Isoprenoids
The ispDF operon in E. coli contains two genes that encode proteins that are used to form building blocks for isoprenoid compounds. There is currently no information on the regulation of this operon.
The first gene in the operon, ispD, also known as ygbP, encodes the protein 2-C-methyl-D-erythritol 4-phosphate (MEP) cytidylyltransferase. This protein catalyzes the reaction of MEP, a hydrogen ion and cytidine triphosphate, which form a pyrophosphate molecule and 4-CDP-2-C-methyl-D-erythritol.
The second gene, ispF, also known as ygbB or mecS, encodes for the protein 2-C-D-erythritol 2,4-cyclodiphosphate synthase. This protein is involved in the formation of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are building blocks in the biosynthesis of isoprenoids, also known as terpenoids.
Signaling
PW000988
Center
PathwayVisualizationContext1275
1185
2040
#000099
PathwayVisualization736
752
Operon: Cytidyl Pyrophosphate Biosynthesis of Isoprenoids
The ispDF operon in E. coli contains two genes that encode proteins that are used to form building blocks for isoprenoid compounds. There is currently no information on the regulation of this operon.
The first gene in the operon, ispD, also known as ygbP, encodes the protein 2-C-methyl-D-erythritol 4-phosphate (MEP) cytidylyltransferase. This protein catalyzes the reaction of MEP, a hydrogen ion and cytidine triphosphate, which form a pyrophosphate molecule and 4-CDP-2-C-methyl-D-erythritol.
The second gene, ispF, also known as ygbB or mecS, encodes for the protein 2-C-D-erythritol 2,4-cyclodiphosphate synthase. This protein is involved in the formation of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are building blocks in the biosynthesis of isoprenoids, also known as terpenoids.
Signaling
3
2288
10518523
Rohdich F, Wungsintaweekul J, Fellermeier M, Sagner S, Herz S, Kis K, Eisenreich W, Bacher A, Zenk MH: Cytidine 5'-triphosphate-dependent biosynthesis of isoprenoids: YgbP protein of Escherichia coli catalyzes the formation of 4-diphosphocytidyl-2-C-methylerythritol. Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):11758-63.
752
Pathway
280371
30025762
Englund E, Shabestary K, Hudson EP, Lindberg P: Systematic overexpression study to find target enzymes enhancing production of terpenes in Synechocystis PCC 6803, using isoprene as a model compound. Metab Eng. 2018 Sep;49:164-177. doi: 10.1016/j.ymben.2018.07.004. Epub 2018 Jul 17.
752
Pathway
1
Cell
CL:0000000
2
Platelet
CL:0000233
5
Hepatocyte
CL:0000182
3
Neuron
CL:0000540
4
Cardiomyocyte
CL:0000746
1
Homo sapiens
9606
Eukaryote
Human
3
Escherichia coli
562
Prokaryote
17
Rattus norvegicus
10116
Eukaryote
Rat
12
Mus musculus
10090
Eukaryote
Mouse
24
Solanum lycopersicum
4081
Eukaryote
Tomato
18
Saccharomyces cerevisiae
4932
Eukaryote
Yeast
21
Xenopus laevis
8355
Eukaryote
African clawed frog
4
Arabidopsis thaliana
3702
Eukaryote
Thale cress
51
Picea sitchensis
3332
Eukaryote
Sitka spruce
60
Nitzschia sp.
0001
Eukaryote
Nitzschia4
5
Bos taurus
9913
Eukaryote
Cattle
10
Drosophila melanogaster
7227
Eukaryote
Fruit fly
6
Caenorhabditis elegans
6239
Eukaryote
Roundworm
49
Bathymodiolus platifrons
220390
Eukaryote
Deep sea mussel
2
Bacteria
2
Prokaryote
Bacteria
3
Mitochondrial Matrix
GO:0005759
5
Cytoplasm
GO:0005737
7
Endoplasmic Reticulum Membrane
GO:0005789
25
Golgi apparatus
GO:0005794
1
Cytosol
GO:0005829
2
Mitochondrion
GO:0005739
10
Cell Membrane
GO:0005886
35
Chloroplast
GO:0009507
13
Endoplasmic Reticulum
GO:0005783
11
Extracellular Space
GO:0005615
4
Peroxisome
GO:0005777
14
Mitochondrial Outer Membrane
GO:0005741
27
Peroxisome Membrane
GO:0005778
15
Nucleus
GO:0005634
26
Golgi apparatus membrane
GO:0000139
12
Mitochondrial Inner Membrane
GO:0005743
2
Endothelium
BTO:0000393
1
Liver
BTO:0000759
72
9
7
Nervous System
BTO:0001484
5
cardiocyte
BTO:0001539
8
Blood Vessel
BTO:0001102
74
11
4
3
1
1
PW_BS000004
8
5
1
1
PW_BS000008
49
7
1
1
PW_BS000049
43
25
1
1
PW_BS000043
2
1
1
1
PW_BS000002
3
2
1
1
PW_BS000003
14
10
1
PW_BS000014
103
3
3
1
PW_BS000103
120
3
17
1
PW_BS000120
133
3
12
1
PW_BS000133
155
3
24
1
PW_BS000155
161
3
18
1
PW_BS000161
178
3
21
1
PW_BS000178
160
1
18
1
PW_BS000160
222
3
4
1
PW_BS000024
198
5
18
1
PW_BS000024
225
35
4
1
PW_BS000024
164
4
PW_BS000164
249
13
4
1
PW_BS000024
151
1
4
1
PW_BS000151
306
35
51
1
PW_BS000024
294
11
4
1
PW_BS000024
111
5
12
1
PW_BS000111
132
1
12
1
PW_BS000132
112
2
12
1
PW_BS000112
356
25
12
1
PW_BS000028
115
10
12
PW_BS000115
331
7
12
1
PW_BS000028
293
4
1
PW_BS000024
368
3
60
1
PW_BS000028
406
3
5
1
PW_BS000115
122
5
5
1
PW_BS000122
124
1
5
1
PW_BS000124
407
2
5
1
PW_BS000115
383
7
5
1
PW_BS000100
419
25
5
1
PW_BS000115
405
10
5
PW_BS000115
135
5
17
1
PW_BS000135
118
1
17
1
PW_BS000118
119
2
17
1
PW_BS000119
398
7
17
1
PW_BS000113
455
25
17
1
PW_BS000115
376
10
17
PW_BS000053
479
3
10
1
PW_BS000115
495
7
10
1
PW_BS000115
490
25
10
1
PW_BS000115
297
5
10
1
PW_BS000024
299
1
10
1
PW_BS000024
481
2
10
1
PW_BS000115
478
10
10
PW_BS000115
501
3
6
1
PW_BS000115
390
7
6
1
PW_BS000112
507
25
6
1
PW_BS000115
205
5
6
1
PW_BS000024
388
1
6
1
PW_BS000112
206
2
6
1
PW_BS000024
209
10
6
PW_BS000024
16
2
1
2
PW_BS000016
26
1
1
1
5
PW_BS000026
5
4
1
1
PW_BS000005
18
13
1
1
PW_BS000018
22
14
1
1
PW_BS000022
39
7
1
1
3
PW_BS000039
21
5
1
1
4
PW_BS000021
46
1
1
4
PW_BS000046
10
1
7
1
1
PW_BS000010
59
27
1
1
PW_BS000059
23
15
1
1
PW_BS000023
29
1
1
1
PW_BS000029
7
1
1
PW_BS000007
31
1
5
1
1
PW_BS000031
91
8
5
1
1
PW_BS000091
54
1
3
1
5
PW_BS000054
56
26
1
1
PW_BS000056
104
14
3
1
PW_BS000104
147
1
24
1
PW_BS000147
166
1
1
PW_BS000166
199
14
18
1
PW_BS000024
213
7
18
1
PW_BS000024
211
10
18
PW_BS000024
214
25
18
1
PW_BS000024
216
4
18
1
PW_BS000024
210
13
18
1
PW_BS000024
288
14
4
1
PW_BS000024
226
4
4
1
PW_BS000024
290
5
49
1
PW_BS000024
285
10
4
1
PW_BS000024
308
10
1
1
PW_BS000024
329
14
12
1
PW_BS000028
336
1
12
1
PW_BS000028
334
4
12
1
PW_BS000028
335
27
12
1
PW_BS000028
130
13
12
1
PW_BS000130
184
1
2
1
PW_BS000024
372
10
2
PW_BS000028
15
11
1
PW_BS000015
253
5
4
1
PW_BS000024
51
8
1
PW_BS000051
27
15
1
PW_BS000027
223
12
4
1
PW_BS000024
382
14
5
1
PW_BS000100
408
4
5
1
PW_BS000115
429
1
5
1
PW_BS000115
125
13
5
1
PW_BS000125
422
27
5
1
PW_BS000115
399
14
17
1
PW_BS000113
374
4
17
1
PW_BS000053
464
1
17
1
PW_BS000115
136
13
17
1
PW_BS000136
375
27
17
1
PW_BS000053
484
14
10
1
PW_BS000115
482
4
10
1
PW_BS000115
491
27
10
1
PW_BS000115
300
13
10
1
PW_BS000024
389
14
6
1
PW_BS000112
502
4
6
1
PW_BS000115
508
27
6
1
PW_BS000115
395
13
6
1
PW_BS000113
117
1
3
1
PW_BS000117
94
3
PW_BS000094
100
5
2
1
PW_BS000100
89
2
PW_BS000089
1027
Manganese
HMDB0001333
Manganese is an essential trace nutrient in all forms of life. Physiologically, it. exists as an ion in the body. It is concentrated in cell mitochondria, mostly in the pituitary gland, liver, pancreas, kidney, and bone, influences the synthesis of mucopolysaccharides, stimulates hepatic synthesis of cholesterol and fatty acids, and is a cofactor in many enzymes, including arginase and alkaline phosphatase in the liver.
16397-91-4
C19610
27854
29035
MN%2b3
25916
[Mn++]
Mn
InChI=1S/Mn/q+2
WAEMQWOKJMHJLA-UHFFFAOYSA-N
manganese(2+) ion
54.938
54.938049636
0
manganese(2+) ion
2
2
FDB003636
Manganese;Manganese (ii) ion;Manganese(ii);Manganese, ion (mn2+);Manganous ion;Mn(2+);Mn2+
PW_C001027
Mn2+
27
4
473
8
1486
49
1553
43
2271
2
2394
3
2513
14
5394
103
5450
120
5576
133
6052
155
6113
161
6497
178
6926
160
7485
222
11880
198
11939
225
11958
164
12471
249
13360
151
15221
306
77050
294
77494
111
77832
132
77961
112
78267
356
78490
115
78524
331
79247
293
80032
368
119996
406
120401
122
121058
124
121211
407
121295
383
121378
419
122488
405
123044
135
123622
118
123781
119
123865
398
123937
455
125054
376
125375
479
125976
495
126051
490
126060
297
126158
299
126543
481
126642
478
126917
501
127429
390
127503
507
127512
205
127765
388
128116
206
128218
209
423
Magnesium
HMDB0000547
Magnesium salts are essential in nutrition, being required for the activity of many enzymes, especially those concerned with oxidative phosphorylation. Physiologically, it exists as an ion in the body. It is a component of both intra- and extracellular fluids and is excreted in the urine and feces. Deficiency causes irritability of the nervous system with tetany, vasodilatation, convulsions, tremors, depression, and psychotic behavior. Magnesium ion in large amounts is an ionic laxative, and magnesium sulfate (Epsom salts) is sometimes used for this purpose. So-called "milk of magnesia" is a water suspension of one of the few insoluble magnesium compounds, magnesium hydroxide; the undissolved particles give rise to its appearance and name. Milk of magnesia is a mild base, and is commonly used as an antacid.
22537-22-0
C00305
888
18420
13-HYDROXY-MAGNESIUM-PROTOPORP
865
DB01378
[Mg++]
Mg
InChI=1S/Mg/q+2
JLVVSXFLKOJNIY-UHFFFAOYSA-N
magnesium(2+) ion
24.305
23.985041898
0
magnesium(2+) ion
2
2
FDB003518
Magnesium;Magnesium ions;Magnesium ion;Magnesium, doubly charged positive ion;Magnesium, ion (mg(2+));Mg(2+);Mg2+
PW_C000423
Mg2+
86
8
227
4
268
16
476
2
727
26
811
5
819
18
883
22
936
39
983
3
992
21
1167
46
1483
49
1529
43
1764
14
2124
10
2411
59
2942
23
3126
29
3373
7
4540
31
4774
91
4869
54
4974
56
5253
104
5329
111
5356
112
5376
103
5906
147
5934
151
6038
155
6094
161
6250
166
6484
178
6594
164
6881
160
6979
199
7170
205
7194
206
7227
213
7233
211
7250
214
7310
216
7313
198
7473
222
11763
132
11843
210
12312
225
12324
249
12513
288
12581
226
12729
290
15275
285
15337
308
77137
133
77236
329
77937
336
78393
334
78417
335
78489
115
78522
331
78536
356
78574
130
80020
368
80045
184
80048
372
80623
118
80654
135
80865
15
80965
253
81841
51
93832
383
94900
27
108596
223
110559
390
115687
398
119974
406
120070
122
120247
382
120702
407
120981
408
121181
124
121265
429
121319
419
121924
125
122086
405
122408
422
122759
120
122921
399
123307
119
123546
374
123835
464
123889
455
124477
136
124637
376
124978
375
125447
297
125598
484
125669
479
125777
481
125921
482
125947
299
125973
495
126000
490
126243
478
126553
491
126753
300
127125
389
127164
501
127380
502
127407
388
127451
507
127804
209
128125
508
128347
395
58
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
DNA
PW_NA000058
IspF, ygbB
2CMDE24
137109
117
57
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
DNA
PW_NA000057
ispD,ygbP
2CMDE4P
137112
117
47
Promoter
DNA
PW_NA000047
P
134701
94
137104
117
143
terminator
DNA
PW_NA000143
Termina
137114
117
6674
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
P62617
Involved in 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity. Converts 4-diphosphocytidyl-2-C-methyl-D-erythritol 2- phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) and CMP. Also converts 4-diphosphocytidyl-2-C-methyl-D- erythritol into 2-C-methyl-D-erythritol 3,4-cyclophosphate and CMP.
ispF
b2746
AB038256
3
4.6.1.12
135521
100
135528
89
137110
117
6818
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Q46893
Involved in catalytic activity. Catalyzes the formation of 4-diphosphocytidyl-2-C- methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4- phosphate (MEP).
ispD
b2747
AB037143
3
2.7.7.60
135526
89
137113
117
3812
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
3
PW_P003812
10743
6674
3
562
1027
13577
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferas
3
PW_P013577
23449
6818
2
1281
423
137111
117
180443
PW_R180443
Right
681332
58
1
NucleicAcid
false
681333
3812
1
ProteinComplex
false
180444
PW_R180444
Right
681334
57
1
NucleicAcid
false
681335
13577
1
ProteinComplex
false
180445
PW_R180445
Right
681336
47
1
NucleicAcid
false
681337
57
1
NucleicAcid
false
180446
PW_R180446
Unknown
681338
58
1
NucleicAcid
false
681339
143
1
NucleicAcid
false
2686930
1027
117
9
false
840
632
10
regular
100
25
2686931
423
117
9
false
590
630
10
regular
100
25
3874
58
226
117
false
770
440
14
242
gene
regular
150
30
3875
57
225
117
false
505
442
14
268
gene
regular
150
30
3876
47
227
117
false
355
442
14
150
nucleic_acid
regular
150
30
3877
143
229
117
false
1012
440
14
150
nucleic_acid
regular
150
30
951958
6674
117
16
false
805
647
8
subunit
regular
170
90
951959
6818
117
6
false
560
645
8
subunit
regular
160
80
805958
3812
736
117
947726
951958
36960
2686930
3674295
Cofactor
805959
13577
736
117
947727
951959
36961
2686931
3674298
Cofactor
3674294
M891 470 C891 500 155 232.5 155 262.5
5
true
18
3674295
M100 332.5 L100 382.5 L150 332.5 z
10
true
18
3674296
M890 647 C890 617 891 500 891 470
5
false
18
true
M 624.9468550441649 89.26155629629604 L 610 88 L 616.3808877211858 101.57513432307834
false
3674297
M639 472 C639 502 230 225 230 255
5
true
18
3674298
M175 325 L175 375 L225 325 z
10
true
18
3674299
M640 645 C640 615 639 502 639 472
5
false
18
true
M 704.9468550441649 89.26155629629604 L 690 88 L 696.3808877211858 101.57513432307834
false
3674300
M505 457 C535 457 489.5 747 519.5 747
5
true
18
3674301
M505 457 C475 457 549.5 747 519.5 747
5
true
18
true
M 704.9468550441649 89.26155629629604 L 690 88 L 696.3808877211858 101.57513432307834
false
3674302
M1012 455 C1042 455 1094 745 1124 745
5
true
18
3674303
M1012 455 C982 455 1154 745 1124 745
5
true
18
800066
736
180443
117
1783
3874
3674294
Left
18928
805958
3674296
Right
800067
736
180444
117
1784
3875
3674297
Left
18929
805959
3674299
Right
800068
736
180445
117
1785
3876
3674300
Left
1786
3875
3674301
Right
800069
736
180446
117
1787
3874
3674302
Left
1788
3877
3674303
Right
187156
1196
344
1.0
1.0
0
2
92
479
481
1411
M279 382.33333333333326 C279 332.33333333333326 329 282.33333333333326 379 282.33333333333326 C763 282.33333333333326 1263 282.33333333333326 1647 282.33333333333326 C1697 282.33333333333326 1747 332.33333333333326 1747 382.33333333333326 C1747 509.33333333333326 1747 673.3333333333333 1747 800.3333333333333 C1747 850.3333333333333 1697 900.3333333333333 1647 900.3333333333333 C1263 900.3333333333333 763 900.3333333333333 379 900.3333333333333 C329 900.3333333333333 279 850.3333333333333 279 800.3333333333333 C279 673.3333333333333 279 509.33333333333326 279 382.33333333333326
1
true
6
0.0
0.0
1412
M123 226 C123 176 173 126 223 126 C701 126 1321 126 1799 126 C1849 126 1899 176 1899 226 C1899 444 1899 726 1899 944 C1899 994 1849 1044 1799 1044 C1321 1044 701 1044 223 1044 C173 1044 123 994 123 944 C123 726 123 444 123 226
1
true
6
1776.0
918.0