superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis

Zrenner R, Stitt M, Sonnewald U, Boldt R. Pyrimidine and purine biosynthesis and degradation in plants. Annu Rev Plant Biol. 2006;57():805–36. doi: 10.1146/annurev.arplant.57.032905.105421. PMID: 16669783.

Metabolites

1,10-Phenanthroline

Formula: C12H8N2 (180.0687448)

CAS ID: 66-71-7

CO2

Formula: CO2 (43.98983)

CAS ID: 124-38-9

Diphosphate

Formula: H4P2O7 (177.9432294)

CAS ID: 2466-09-3

H+

Formula: H (1.0078246)

CAS ID: 12408-02-5

H2O

Formula: H2O (18.0105642)

CAS ID: 7732-18-5

HCO3-

Formula: HCO3 (60.9925696)

CAS ID: 71-52-3

Magnesium cation

Formula: Mg (23.98505)

CAS ID: 22537-22-0

Manganese(2+)

Formula: Mn (54.938046)

CAS ID: 7439-96-5

Mercaptoethanol

Formula: C2H6OS (78.0139346)

CAS ID: 60-24-2

Potassium cation

Formula: K (38.963708)

CAS ID: 24203-36-9

Sodium cation

Formula: Na (22.98977)

CAS ID: 17341-25-2

Zinc cation

Formula: Zn (63.929145)

CAS ID: 23713-49-7

Etoposide glucuronide

Formula: C35H40O19 (764.216369)

CAS ID: 100007-55-4

succinate(2-)

Formula: C4H4O4 (116.01095839999999)

CAS ID: 56-14-4

cyanate

Formula: CNO (41.997989)

CAS ID: 71000-82-3

NADPH(4-)

Formula: C21H26N7O17P3 (741.0598016)

CAS ID: 53-57-6

ATP(4-)

Formula: C10H12N5O13P3 (502.9644492)

CAS ID:

UDP(3-)

Formula: C9H11N2O12P2 (400.9787246)

CAS ID: 86527-70-0

ADP(3-)

Formula: C10H12N5O10P2 (424.0059412)

CAS ID:

dTDP(3-)

Formula: C10H13N2O11P2 (398.9994588)

CAS ID:

dTMP(2-)

Formula: C10H13N2O8P (320.0409508)

CAS ID: 14057-65-9

dUDP(3-)

Formula: C9H11N2O11P2 (384.9838096)

CAS ID:



Enzyme

EC Number name full name note
3.6.1.-
1.17.4.1 ribonucleoside-diphosphate reductase 2'-deoxyribonucleoside-5'-diphosphate:thioredoxin-disulfide 2'-oxidoreductase
1.3.5.2 dihydroorotate dehydrogenase (quinone) (S)-dihydroorotate:quinone oxidoreductase
2.1.1.45 thymidylate synthase 5,10-methylenetetrahydrofolate:dUMP C-methyltransferase
2.1.3.2 aspartate carbamoyltransferase carbamoyl-phosphate:L-aspartate carbamoyltransferase
2.4.2.10 orotate phosphoribosyltransferase orotidine-5'-phosphate:diphosphate phospho-alpha-D-ribosyl-transferase
2.7.13.3 histidine kinase ATP:protein-L-histidine N-phosphotransferase
2.7.4.14 UMP/CMP kinase ATP:CMP(UMP) phosphotransferase
2.7.4.22 UMP kinase ATP:UMP phosphotransferase
2.7.4.3 adenylate kinase ATP:AMP phosphotransferase
2.7.4.6 nucleoside-diphosphate kinase ATP:nucleoside-diphosphate phosphotransferase
2.7.4.9 dTMP kinase ATP:dTMP phosphotransferase
3.5.1.2 glutaminase L-glutamine amidohydrolase
3.5.2.3 dihydroorotase (S)-dihydroorotate amidohydrolase
3.6.1.12 dCTP diphosphatase dCTP nucleotidohydrolase
3.6.1.15 nucleoside-triphosphate phosphatase unspecific diphosphate phosphohydrolase
3.6.1.23 dUTP diphosphatase dUTP nucleotidohydrolase
3.6.1.9 nucleotide diphosphatase dinucleotide nucleotidohydrolase
4.1.1.23 orotidine-5'-phosphate decarboxylase orotidine-5'-phosphate carboxy-lyase (UMP-forming)
6.3.4.16 carbamoyl-phosphate synthase (ammonia) carbon-dioxide:ammonia ligase (ADP-forming, carbamate-phosphorylating)
6.3.4.2 CTP synthase (glutamine hydrolysing) UTP:ammonia ligase (ADP-forming)
6.3.5.5 carbamoyl-phosphate synthase (glutamine-hydrolysing) hydrogen-carbonate:L-glutamine amido-ligase (ADP-forming, carbamate-phosphorylating)


Proteins

Protein ID name full name
P00452 nrdA Ribonucleoside-diphosphate reductase 1 subunit alpha
P00572 CDC8 Thymidylate kinase
P00968 carB Carbamoyl phosphate synthase large chain
P05020 pyrC Dihydroorotase
P06968 dut Deoxyuridine 5'-triphosphate nucleotidohydrolase
P08244 pyrF Orotidine 5'-phosphate decarboxylase
P09938 RNR2 Ribonucleoside-diphosphate reductase small chain 1
P0A6F1 carA Carbamoyl phosphate synthase small chain
P0A720 tmk Thymidylate kinase
P0A763 ndk Nucleoside diphosphate kinase
P0A786 pyrB Aspartate carbamoyltransferase catalytic subunit
P0A7E1 pyrD Dihydroorotate dehydrogenase (quinone)
P0A7E3 pyrE Orotate phosphoribosyltransferase
P0A7E5 pyrG CTP synthase
P0A7E9 pyrH Uridylate kinase
P0A884 thyA Thymidylate synthase
P15700 URA6 Uridylate kinase
P21524 RNR1 Ribonucleoside-diphosphate reductase large chain 1
P36010 YNK1 Nucleoside diphosphate kinase
P49723 RNR4 Ribonucleoside-diphosphate reductase small chain 2
P52006 nudI Nucleoside triphosphatase NudI
P69441 adk Adenylate kinase
P69924 nrdB Ribonucleoside-diphosphate reductase 1 subunit beta