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Literature summary extracted from

  • Carter, M.; Zhang, X.; Huang, H.; Bouvier, J.; Francisco, B.; Vetting, M.; Al-Obaidi, N.; Bonanno, J.; Ghosh, A.; Zallot, R.; Andersen, H.; Almo, S.; Gerlt, J.
    Functional assignment of multiple catabolic pathways for D-apiose article (2018), Nat. Chem. Biol., 14, 696-705 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.420 expressed in Escherichia coli BL21(DE3) cells Agrobacterium tumefaciens
1.1.1.421 expressed in Escherichia coli BL21(DE3) cells Agrobacterium tumefaciens
1.1.1.421 expressed in Escherichia coli BL21(DE3) cells Blautia hydrogenotrophica
1.1.1.421 expressed in Escherichia coli BL21(DE3) cells Cupriavidus necator
1.1.1.421 expressed in Escherichia coli BL21(DE3) cells Pectobacterium atrosepticum

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.7.1.231 Mg2+ 2 mM used in assay conditions Paraburkholderia graminis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.420 D-apiofuranose + NAD+ Agrobacterium tumefaciens
-
 D-apionolactone + NADH + H+
-
 r
1.1.1.420 D-apiofuranose + NAD+ Agrobacterium tumefaciens K84
-
 D-apionolactone + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+ Agrobacterium tumefaciens
-
 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+ Blautia hydrogenotrophica
-
 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+ Cupriavidus necator
-
 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+ Pectobacterium atrosepticum
-
 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+ Agrobacterium tumefaciens K84
-
 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+ Cupriavidus necator ATCC 43291
-
 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+ Blautia hydrogenotrophica DSM 10507
-
 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+ Pectobacterium atrosepticum SCRI 1043
-
 3-oxo-D-isoapionate + NADH + H+
-
 r
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate Actinobacillus succinogenes the enzyme is involved in a catabolic pathway for D-apiose D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate Phocaeicola vulgatus the enzyme is involved in a catabolic pathway for D-apiose D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate Phocaeicola vulgatus ATCC 8482 the enzyme is involved in a catabolic pathway for D-apiose D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate Actinobacillus succinogenes ATCC 55618 the enzyme is involved in a catabolic pathway for D-apiose D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.7.1.231 ATP + 3-oxoisoapionate Paraburkholderia graminis
-
 ADP + 3-oxoisoapionate 4-phosphate
-
 ?
2.7.1.231 ATP + 3-oxoisoapionate Paraburkholderia graminis C4D1M
-
 ADP + 3-oxoisoapionate 4-phosphate
-
 ?
2.7.1.233 ATP + D-apulose Pectobacterium atrosepticum
-
 ADP + apulose 4-phosphate
-
 ?
2.7.1.233 ATP + D-apulose Pectobacterium atrosepticum SCRI 1043
-
 ADP + apulose 4-phosphate
-
 ?
3.1.1.115 D-apionolactone + H2O Brucella anthropi the enzyme is involved in a catabolic pathway for D-apiose D-apionate
-
 ?
3.1.1.115 D-apionolactone + H2O Brucella anthropi ATCC 49188 the enzyme is involved in a catabolic pathway for D-apiose D-apionate
-
 ?
3.7.1.28 3-oxoisoapionate 4-phosphate + H2O Xanthobacter autotrophicus
-
 glycolate + 3-phospho-D-glycerate
-
 ?
3.7.1.28 3-oxoisoapionate 4-phosphate + H2O Xanthobacter autotrophicus ATCC BAA-1158
-
 glycolate + 3-phospho-D-glycerate
-
 ?
4.1.1.120 3-oxoisoapionate Pectobacterium atrosepticum
-
 L-erythrulose + CO2
-
 ?
4.1.1.120 3-oxoisoapionate Pectobacterium atrosepticum SCRI 1043
-
 L-erythrulose + CO2
-
 ?
4.1.1.121 3-oxoisoapionate 4-phosphate Agrobacterium tumefaciens
-
 L-erythrulose 1-phosphate + CO2
-
 ?
4.1.1.121 3-oxoisoapionate 4-phosphate Agrobacterium tumefaciens K84
-
 L-erythrulose 1-phosphate + CO2
-
 ?
5.3.1.36 D-apiose Pectobacterium atrosepticum the enzyme is involved in the catabolic pathways for D-apiose apulose
-
 r
5.3.1.36 D-apiose Pectobacterium atrosepticum SCRI 1043 the enzyme is involved in the catabolic pathways for D-apiose apulose
-
 r

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.420 Agrobacterium tumefaciens B9JK80
-
-
1.1.1.420 Agrobacterium tumefaciens K84 B9JK80
-
-
1.1.1.421 Agrobacterium tumefaciens B9JK75
-
-
1.1.1.421 Agrobacterium tumefaciens K84 B9JK75
-
-
1.1.1.421 Blautia hydrogenotrophica C0CMQ7
-
-
1.1.1.421 Blautia hydrogenotrophica DSM 10507 C0CMQ7
-
-
1.1.1.421 Cupriavidus necator F8GV06
-
-
1.1.1.421 Cupriavidus necator ATCC 43291 F8GV06
-
-
1.1.1.421 Pectobacterium atrosepticum Q6D8V3
-
-
1.1.1.421 Pectobacterium atrosepticum SCRI 1043 Q6D8V3
-
-
2.2.1.13 Actinobacillus succinogenes A6VKQ3 AND A6VKQ4 A6VKQ3: subunit B, A6VKQ4: subunit A
-
2.2.1.13 Actinobacillus succinogenes ATCC 55618 A6VKQ3 AND A6VKQ4 A6VKQ3: subunit B, A6VKQ4: subunit A
-
2.2.1.13 Phocaeicola vulgatus A6KXB3 AND A6KXB4 A6KXB3: subunit B, A6KXB4: subunit A
-
2.2.1.13 Phocaeicola vulgatus ATCC 8482 A6KXB3 AND A6KXB4 A6KXB3: subunit B, A6KXB4: subunit A
-
2.7.1.231 Paraburkholderia graminis B1G889
-
-
2.7.1.231 Paraburkholderia graminis C4D1M B1G889
-
-
2.7.1.233 Pectobacterium atrosepticum Q6D5T8
-
-
2.7.1.233 Pectobacterium atrosepticum SCRI 1043 Q6D5T8
-
-
3.1.1.115 Brucella anthropi A6X3G3
-
-
3.1.1.115 Brucella anthropi ATCC 49188 A6X3G3
-
-
3.7.1.28 Xanthobacter autotrophicus A7IJG7
-
-
3.7.1.28 Xanthobacter autotrophicus ATCC BAA-1158 A7IJG7
-
-
4.1.1.120 Pectobacterium atrosepticum Q6D8V4
-
-
4.1.1.120 Pectobacterium atrosepticum SCRI 1043 Q6D8V4
-
-
4.1.1.121 Agrobacterium tumefaciens B9JK73
-
-
4.1.1.121 Agrobacterium tumefaciens K84 B9JK73
-
-
5.3.1.36 Pectobacterium atrosepticum Q6D5T7
-
-
5.3.1.36 Pectobacterium atrosepticum SCRI 1043 Q6D5T7
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.420 Ni-NTA resin column chromatography Agrobacterium tumefaciens
1.1.1.421 Ni-NTA resin column chromatography Agrobacterium tumefaciens
1.1.1.421 Ni-NTA resin column chromatography Blautia hydrogenotrophica
1.1.1.421 Ni-NTA resin column chromatography Cupriavidus necator
1.1.1.421 Ni-NTA resin column chromatography Pectobacterium atrosepticum

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.420 D-apiofuranose + NAD+
-
 Agrobacterium tumefaciens D-apionolactone + NADH + H+
-
 r
1.1.1.420 D-apiofuranose + NAD+
-
 Agrobacterium tumefaciens K84 D-apionolactone + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+
-
 Agrobacterium tumefaciens 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+
-
 Blautia hydrogenotrophica 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+
-
 Cupriavidus necator 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+
-
 Pectobacterium atrosepticum 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+
-
 Agrobacterium tumefaciens K84 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+
-
 Cupriavidus necator ATCC 43291 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+
-
 Blautia hydrogenotrophica DSM 10507 3-oxo-D-isoapionate + NADH + H+
-
 r
1.1.1.421 D-apionate + NAD+
-
 Pectobacterium atrosepticum SCRI 1043 3-oxo-D-isoapionate + NADH + H+
-
 r
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate the enzyme is involved in a catabolic pathway for D-apiose Actinobacillus succinogenes D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate the enzyme is involved in a catabolic pathway for D-apiose Phocaeicola vulgatus D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate apulose i..e. 1,3,4-trihydroxy-3-(hydroxymethyl)butan-2-one Actinobacillus succinogenes D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate apulose i..e. 1,3,4-trihydroxy-3-(hydroxymethyl)butan-2-one Phocaeicola vulgatus D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate the enzyme is involved in a catabolic pathway for D-apiose Phocaeicola vulgatus ATCC 8482 D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate apulose i..e. 1,3,4-trihydroxy-3-(hydroxymethyl)butan-2-one Phocaeicola vulgatus ATCC 8482 D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate the enzyme is involved in a catabolic pathway for D-apiose Actinobacillus succinogenes ATCC 55618 D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.2.1.13 apulose 4-phosphate + D-glyceraldehyde 3-phosphate apulose i..e. 1,3,4-trihydroxy-3-(hydroxymethyl)butan-2-one Actinobacillus succinogenes ATCC 55618 D-xylulose 5-phosphate + glycerone phosphate
-
 ?
2.7.1.231 ATP + 3-oxoisoapionate
-
 Paraburkholderia graminis ADP + 3-oxoisoapionate 4-phosphate
-
 ?
2.7.1.231 ATP + 3-oxoisoapionate
-
 Paraburkholderia graminis C4D1M ADP + 3-oxoisoapionate 4-phosphate
-
 ?
2.7.1.233 ATP + D-apulose
-
 Pectobacterium atrosepticum ADP + apulose 4-phosphate
-
 ?
2.7.1.233 ATP + D-apulose
-
 Pectobacterium atrosepticum SCRI 1043 ADP + apulose 4-phosphate
-
 ?
3.1.1.115 D-apionolactone + H2O the enzyme is involved in a catabolic pathway for D-apiose Brucella anthropi D-apionate
-
 ?
3.1.1.115 D-apionolactone + H2O D-apionolactone i.e. (3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-one Brucella anthropi D-apionate
-
 ?
3.1.1.115 D-apionolactone + H2O the enzyme is involved in a catabolic pathway for D-apiose Brucella anthropi ATCC 49188 D-apionate
-
 ?
3.1.1.115 D-apionolactone + H2O D-apionolactone i.e. (3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-one Brucella anthropi ATCC 49188 D-apionate
-
 ?
3.7.1.28 3-oxoisoapionate 4-phosphate + H2O
-
 Xanthobacter autotrophicus glycolate + 3-phospho-D-glycerate
-
 ?
3.7.1.28 3-oxoisoapionate 4-phosphate + H2O
-
 Xanthobacter autotrophicus ATCC BAA-1158 glycolate + 3-phospho-D-glycerate
-
 ?
4.1.1.120 3-oxoisoapionate
-
 Pectobacterium atrosepticum L-erythrulose + CO2
-
 ?
4.1.1.120 3-oxoisoapionate
-
 Pectobacterium atrosepticum SCRI 1043 L-erythrulose + CO2
-
 ?
4.1.1.121 3-oxoisoapionate 4-phosphate
-
 Agrobacterium tumefaciens L-erythrulose 1-phosphate + CO2
-
 ?
4.1.1.121 3-oxoisoapionate 4-phosphate
-
 Agrobacterium tumefaciens K84 L-erythrulose 1-phosphate + CO2
-
 ?
5.3.1.36 D-apiose the enzyme is involved in the catabolic pathways for D-apiose Pectobacterium atrosepticum apulose
-
 r
5.3.1.36 D-apiose apulose i.e. 1,3,4-trihydroxy-3-(hydroxymethyl)butan-2-one Pectobacterium atrosepticum apulose
-
 r
5.3.1.36 D-apiose the enzyme is involved in the catabolic pathways for D-apiose Pectobacterium atrosepticum SCRI 1043 apulose
-
 r
5.3.1.36 D-apiose apulose i.e. 1,3,4-trihydroxy-3-(hydroxymethyl)butan-2-one Pectobacterium atrosepticum SCRI 1043 apulose
-
 r

Subunits

EC Number Subunits Comment Organism
2.2.1.13 heterodimer
-
 Actinobacillus succinogenes
2.2.1.13 heterodimer
-
 Phocaeicola vulgatus

Synonyms

EC Number Synonyms Comment Organism
2.2.1.13 aptAB
-
 Actinobacillus succinogenes
2.2.1.13 aptAB
-
 Phocaeicola vulgatus
2.7.1.231 3-oxo-isoapionate kinase
-
 Paraburkholderia graminis
2.7.1.233 D-apulose kinase
-
 Pectobacterium atrosepticum
3.1.1.115 apnL
-
 Brucella anthropi
3.1.1.115 D-apionate lactonase
-
 Brucella anthropi
3.7.1.28 oiaT
-
 Xanthobacter autotrophicus
3.7.1.28 RLP transcarboxylase/hydrolase
-
 Xanthobacter autotrophicus
4.1.1.120 3-oxo-isoapionate decarboxylase
-
 Pectobacterium atrosepticum
4.1.1.121 3-oxo-isoapionate 4-phosphate decarboxylase
-
 Agrobacterium tumefaciens

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.420 NAD+
-
 Agrobacterium tumefaciens
1.1.1.420 NADH
-
 Agrobacterium tumefaciens
1.1.1.421 NAD+
-
 Agrobacterium tumefaciens
1.1.1.421 NAD+
-
 Blautia hydrogenotrophica
1.1.1.421 NAD+
-
 Cupriavidus necator
1.1.1.421 NAD+
-
 Pectobacterium atrosepticum
1.1.1.421 NADH
-
 Agrobacterium tumefaciens
1.1.1.421 NADH
-
 Blautia hydrogenotrophica
1.1.1.421 NADH
-
 Cupriavidus necator
1.1.1.421 NADH
-
 Pectobacterium atrosepticum

General Information

EC Number General Information Comment Organism
2.2.1.13 metabolism the enzyme is involved in a catabolic pathway for D-apiose Actinobacillus succinogenes
2.2.1.13 metabolism the enzyme is involved in a catabolic pathway for D-apiose Phocaeicola vulgatus
3.1.1.115 physiological function the enzyme is involved in a catabolic pathway for D-apiose Brucella anthropi