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Uridine 5'-diphosphate (YMDB00307)
| Identification | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| YMDB ID | YMDB00307 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Name | Uridine 5'-diphosphate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Species | Saccharomyces cerevisiae | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Strain | Baker's yeast | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Description | Uridine 5'-diphosphate, also known as 5'-UDP or uridine diphosphoric acid, belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. Uridine 5'-diphosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Uridine 5'-diphosphate exists in all living species, ranging from bacteria to humans. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Structure |  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Synonyms |
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| CAS number | 58-98-0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Weight | Average: 404.1612 Monoisotopic: 404.002196946 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| InChI Key | XCCTYIAWTASOJW-XVFCMESISA-N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| InChI | InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| IUPAC Name | [({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Traditional IUPAC Name | UDP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Chemical Formula | C9H14N2O12P2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| SMILES | [H]O[C@@]1([H])[C@@]([H])(O[C@]([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])O[H])[C@@]1([H])O[H])N1C([H])=C([H])C(=O)N([H])C1=O | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Chemical Taxonomy | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Description | belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Kingdom | Organic compounds | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Super Class | Nucleosides, nucleotides, and analogues | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Class | Pyrimidine nucleotides | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Sub Class | Pyrimidine ribonucleotides | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Direct Parent | Pyrimidine ribonucleoside diphosphates | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Alternative Parents |
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| Substituents |
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| Molecular Framework | Aromatic heteromonocyclic compounds | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| External Descriptors |
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| Physical Properties | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| State | Solid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Charge | 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Melting point | Not Available | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Experimental Properties |
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| Predicted Properties |
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| Biological Properties | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cellular Locations |
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| Organoleptic Properties | Not Available | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| SMPDB Pathways |
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| KEGG Pathways |
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| SMPDB Reactions |
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| KEGG Reactions |
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| Concentrations | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intracellular Concentrations | Not Available | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Extracellular Concentrations | Not Available | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Spectra | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Spectra |
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| References | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| References: |
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| Synthesis Reference: | Zeng, Bin; Rao, Linfan; Li, Gaowo. Method for manufacturing uridine diphosphate. Faming Zhuanli Shenqing Gongkai Shuomingshu (2007), 14pp. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| External Links: |
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Enzymes
- General function:
- Cell wall/membrane/envelope biogenesis
- Specific function:
- UDP-glucose + dolichyl phosphate = UDP + dolichyl beta-D-glucosyl phosphate
- Gene Name:
- ALG5
- Uniprot ID:
- P40350
- Molecular weight:
- 38346.39844
Reactions
| UDP-glucose + dolichyl phosphate → UDP + dolichyl beta-D-glucosyl phosphate. |
- General function:
- Involved in catalytic activity
- Specific function:
- Phosphatase catalytic subunit of the trehalose synthase complex that catalyzes the production of trehalose from glucose-6- phosphate and UDP-glucose in a two step process
- Gene Name:
- TPS2
- Uniprot ID:
- P31688
- Molecular weight:
- 102976.0
Reactions
| Trehalose 6-phosphate + H(2)O → trehalose + phosphate. |
- General function:
- Involved in hydrolase activity
- Specific function:
- Catalyzes the hydrolysis of phosphoanhydride bonds of nucleoside tri- and di-phosphates. Has equal high activity toward ADP/ATP, GDP/GTP, and UDP/UTP and approximately 50% less toward CDP/CTP and thiamine pyrophosphate. Has no activity toward GMP. Required for Golgi glycosylation and cell wall integrity. Together with CDC55, required for adenovirus E4orf4 (early region 4 open reading frame 4) induced toxicity, the apyrase activity is not required for this function. Plays a role in sphingolipid synthesis
- Gene Name:
- YND1
- Uniprot ID:
- P40009
- Molecular weight:
- 71851.20313
Reactions
| ATP + 2 H(2)O → AMP + 2 phosphate. |
- General function:
- Involved in ATP binding
- Specific function:
- Furnishes the cell with pyrimidines. Accepts UMP, and dUMP as phosphate acceptors with high activity; to a lesser extent, it can also use IMP, GMP, dGMP, 5-iodo-dUMP, XMP, and dTMP as substrates. ATP and dATP are the best phosphate donors; can use GTP, dGTP, dCTP, and dTTP to some degree (30-50%)
- Gene Name:
- URA6
- Uniprot ID:
- P15700
- Molecular weight:
- 22933.0
Reactions
| ATP + UMP → ADP + UDP. |
- General function:
- Involved in transferase activity, transferring hexosyl groups
- Specific function:
- Involved in protein N-glycosylation. Essential for the second step of the dolichol-linked oligosaccharide pathway
- Gene Name:
- ALG13
- Uniprot ID:
- P53178
- Molecular weight:
- 22660.90039
Reactions
| UDP-N-acetyl-D-glucosamine + N-acetyl-D-glucosaminyl-diphosphodolichol → UDP + N,N'-diacetylchitobiosyl-diphosphodolichol. |
- General function:
- Involved in oxidoreductase activity
- Specific function:
- Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR2 provides the diiron-tyrosyl radical center
- Gene Name:
- RNR2
- Uniprot ID:
- P09938
- Molecular weight:
- 46147.0
Reactions
| 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin. |
- General function:
- Involved in nucleoside diphosphate kinase activity
- Specific function:
- Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Required for repair of UV radiation- and etoposide-induced DNA damage
- Gene Name:
- YNK1
- Uniprot ID:
- P36010
- Molecular weight:
- 17166.59961
Reactions
| ATP + nucleoside diphosphate → ADP + nucleoside triphosphate. |
- General function:
- Involved in oxidation-reduction process
- Specific function:
- Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
- Gene Name:
- RNR1
- Uniprot ID:
- P21524
- Molecular weight:
- 99560.20313
Reactions
| 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin. |
- General function:
- Involved in ATP binding
- Specific function:
- RAR (regulation of autonomous replication) is a protein whose activity increases the mitotic stability of plasmids
- Gene Name:
- ERG12
- Uniprot ID:
- P07277
- Molecular weight:
- 48458.89844
Reactions
| ATP + (R)-mevalonate → ADP + (R)-5-phosphomevalonate. |
- General function:
- Involved in transferase activity, transferring glycosyl groups
- Specific function:
- Self-glucosylating initiator of glycogen synthesis. Catalyzes the formation of a short alpha (1,4)-glucosyl chain covalently attached via a glucose 1-O-tyrosyl linkage to internal tyrosine residues. These chains act as primers for the elongation reaction catalyzed by glycogen synthase. Capable of transferring glucosyl residues to unbound acceptors such as free oligoglucans or oligoglucan derivatives
- Gene Name:
- GLG2
- Uniprot ID:
- P47011
- Molecular weight:
- 44545.60156
Reactions
| UDP-alpha-D-glucose + glycogenin → UDP + alpha-D-glucosylglycogenin. |
- General function:
- Involved in 1,3-beta-D-glucan synthase activity
- Specific function:
- Alternate catalytic subunit of the 1,3-beta-glucan synthase (GS). Synthesizes 1,3-beta-glucan, a major structural component of the yeast cell wall. Involved in cell wall synthesis, maintenance and cell wall remodeling
- Gene Name:
- FKS1
- Uniprot ID:
- P38631
- Molecular weight:
- 214849.0
Reactions
| UDP-glucose + ((1->3)-beta-D-glucosyl)(n) → UDP + ((1->3)-beta-D-glucosyl)(n+1). |
- General function:
- Involved in 1,3-beta-D-glucan synthase activity
- Specific function:
- Required for spore wall assembly
- Gene Name:
- FKS3
- Uniprot ID:
- Q04952
- Molecular weight:
- 207481.0
Reactions
| UDP-glucose + ((1->3)-beta-D-glucosyl)(n) → UDP + ((1->3)-beta-D-glucosyl)(n+1). |
- General function:
- Involved in 1,3-beta-D-glucan synthase activity
- Specific function:
- Alternate catalytic subunit of the 1,3-beta-glucan synthase (GS). Synthesizes 1,3-beta-glucan, a major structural component of the yeast cell wall. Required for spore wall assembly. Negative regulation of activity by SMK1 is important for spore wall deposition. Activity is positively regulated by RHO1
- Gene Name:
- GSC2
- Uniprot ID:
- P40989
- Molecular weight:
- 216988.0
Reactions
| UDP-glucose + ((1->3)-beta-D-glucosyl)(n) → UDP + ((1->3)-beta-D-glucosyl)(n+1). |
- General function:
- Involved in nucleotidyltransferase activity
- Specific function:
- Plays a central role as a glucosyl donor in cellular metabolic pathways
- Gene Name:
- UGP1
- Uniprot ID:
- P32861
- Molecular weight:
- 55987.39844
Reactions
| UTP + alpha-D-glucose 1-phosphate → diphosphate + UDP-glucose. |
- General function:
- Involved in catalytic activity
- Specific function:
- Synthase catalytic subunit of the trehalose synthase complex that catalyzes the production of trehalose from glucose-6- phosphate and UDP-glucose in a two step process. Can function independently of the complex
- Gene Name:
- TPS1
- Uniprot ID:
- Q00764
- Molecular weight:
- 56147.5
Reactions
| UDP-glucose + D-glucose 6-phosphate → UDP + alpha,alpha-trehalose 6-phosphate. |
- General function:
- Involved in transferase activity, transferring hexosyl groups
- Specific function:
- May be involved in decane metabolism and autophagy. Involved in the biosynthesis of sterol glucoside
- Gene Name:
- ATG26
- Uniprot ID:
- Q06321
- Molecular weight:
- 136053.0
Reactions
| UDP-glucose + a sterol → UDP + a sterol 3-beta-D-glucoside. |
- General function:
- Involved in transferase activity, transferring glycosyl groups
- Specific function:
- Self-glucosylating initiator of glycogen synthesis. Catalyzes the formation of a short alpha (1,4)-glucosyl chain covalently attached via a glucose 1-O-tyrosyl linkage to internal tyrosine residues. These chains act as primers for the elongation reaction catalyzed by glycogen synthase. Capable of transferring glucosyl residues to unbound acceptors such as free oligoglucans or oligoglucan derivatives
- Gene Name:
- GLG1
- Uniprot ID:
- P36143
- Molecular weight:
- 69723.39844
Reactions
| UDP-alpha-D-glucose + glycogenin → UDP + alpha-D-glucosylglycogenin. |
- General function:
- Involved in phosphatidylinositol N-acetylglucosaminyltr
- Specific function:
- Part of the complex catalyzing the transfer of N- acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis. Involved in cell wall biosynthesis
- Gene Name:
- GPI19
- Uniprot ID:
- Q04082
- Molecular weight:
- 16089.40039
Reactions
| UDP-N-acetyl-D-glucosamine + 1-phosphatidyl-1D-myo-inositol → UDP + 6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol. |
- General function:
- Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
- Specific function:
- Part of the complex catalyzing the transfer of N- acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis
- Gene Name:
- GPI1
- Uniprot ID:
- P53306
- Molecular weight:
- 70353.70313
Reactions
| UDP-N-acetyl-D-glucosamine + 1-phosphatidyl-1D-myo-inositol → UDP + 6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol. |
- General function:
- Involved in biosynthetic process
- Specific function:
- Catalytic subunit in the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis
- Gene Name:
- SPT14
- Uniprot ID:
- P32363
- Molecular weight:
- 51241.80078
Reactions
| UDP-N-acetyl-D-glucosamine + 1-phosphatidyl-1D-myo-inositol → UDP + 6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol. |
- General function:
- Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
- Specific function:
- Part of the complex catalyzing the transfer of N- acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis
- Gene Name:
- GPI2
- Uniprot ID:
- P46961
- Molecular weight:
- 32576.80078
Reactions
| UDP-N-acetyl-D-glucosamine + 1-phosphatidyl-1D-myo-inositol → UDP + 6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol. |
- General function:
- Involved in oxidoreductase activity
- Specific function:
- Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. RNR4 is required for proper folding of RNR2 and assembly with the large subunits
- Gene Name:
- RNR4
- Uniprot ID:
- P49723
- Molecular weight:
- 40054.19922
Reactions
| 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O → ribonucleoside diphosphate + thioredoxin. |
- General function:
- Involved in chitin synthase activity
- Specific function:
- Essential for septum formation and cell division. CHS2 is required for maintaining normal cell morphology
- Gene Name:
- CHS2
- Uniprot ID:
- P14180
- Molecular weight:
- 109881.0
Reactions
| UDP-N-acetyl-D-glucosamine + (1,4-(N-acetyl-beta-D-glucosaminyl))(n) → UDP + (1,4-(N-acetyl-beta-D-glucosaminyl))(n+1). |
- General function:
- Involved in transferase activity, transferring hexosyl groups
- Specific function:
- Appears to be responsible for the synthesis of the majority of the chitin found in the cell wall periphery. It is involved in the synthesis of the chitin ring that forms in the cell wall just before bud emergence. This ring remains at the base of the bud as the bud grows and ultimately forms part of the bud scar marking the division site on the mother cell
- Gene Name:
- CHS3
- Uniprot ID:
- P29465
- Molecular weight:
- 131600.0
Reactions
| UDP-N-acetyl-D-glucosamine + (1,4-(N-acetyl-beta-D-glucosaminyl))(n) → UDP + (1,4-(N-acetyl-beta-D-glucosaminyl))(n+1). |
- General function:
- Involved in chitin synthase activity
- Specific function:
- Septum formation and repair, especially under certain adverse conditions
- Gene Name:
- CHS1
- Uniprot ID:
- P08004
- Molecular weight:
- 129918.0
Reactions
| UDP-N-acetyl-D-glucosamine + (1,4-(N-acetyl-beta-D-glucosaminyl))(n) → UDP + (1,4-(N-acetyl-beta-D-glucosaminyl))(n+1). |
- General function:
- Carbohydrate transport and metabolism
- Specific function:
- Involved in the synthesis of (1->6)- and (1->3)-beta-D- glucan polymers of the yeast cell wall in vivo. It is required for full activity of beta-glucan synthase in vitro. May be involved in the maturation and transport of cell wall proteins (CWP) to the cell wall. May act as a transglucosidase and contribute to the construction of a protein-bound glucan-structure that acts as an acceptor site for the addition of (1->6)-beta-D-glucan at the cell surface
- Gene Name:
- KRE6
- Uniprot ID:
- P32486
- Molecular weight:
- 80122.10156
Reactions
- General function:
- Involved in catalytic activity
- Specific function:
- Regulatory subunit of the trehalose synthase complex that catalyzes the production of trehalose from glucose-6- phosphate and UDP-glucose in a two step process. May stabilize the trehalose synthase complex
- Gene Name:
- TPS3
- Uniprot ID:
- P38426
- Molecular weight:
- 118834.0
Reactions
- General function:
- Involved in glycogen (starch) synthase activity
- Specific function:
- Transfers the glycosyl residue from UDP-Glc to the non- reducing end of alpha-1,4-glucan. Is believed to regulate the synthesis of glycogen
- Gene Name:
- GSY2
- Uniprot ID:
- P27472
- Molecular weight:
- 80078.20313
Reactions
| UDP-glucose ((1->4)-alpha-D-glucosyl)(n) → UDP + ((1->4)-alpha-D-glucosyl)(n+1). |
- General function:
- Involved in glycogen (starch) synthase activity
- Specific function:
- Transfers the glycosyl residue from UDP-Glc to the non- reducing end of alpha-1,4-glucan. Is believed to regulate the synthesis of glycogen
- Gene Name:
- GSY1
- Uniprot ID:
- P23337
- Molecular weight:
- 80509.60156
Reactions
| UDP-glucose ((1->4)-alpha-D-glucosyl)(n) → UDP + ((1->4)-alpha-D-glucosyl)(n+1). |
- General function:
- Carbohydrate transport and metabolism
- Specific function:
- Required for synthesis of the major beta-glucans of the yeast cell wall
- Gene Name:
- SKN1
- Uniprot ID:
- P33336
- Molecular weight:
- 86240.39844
Reactions
- General function:
- Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
- Specific function:
- Part of the complex catalyzing the transfer of N- acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis
- Gene Name:
- GPI15
- Uniprot ID:
- P53961
- Molecular weight:
- 26816.5
Reactions
| UDP-N-acetyl-D-glucosamine + 1-phosphatidyl-1D-myo-inositol → UDP + 6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol. |