superpathway of microbial D-galacturonate and D-glucuronate degradation

Andberg M, Maaheimo H, Boer H, Penttilä M, Koivula A, Richard P. Characterization of a novel Agrobacterium tumefaciens Galactarolactone Cycloisomerase Enzyme for Direct Conversion of d-Galactarolactone to 3-Deoxy-2-keto-l-threo-hexarate. Journal of Biological Chemistry. 2012 May;287(21):17662–71. doi: 10.1074/jbc.m111.335240.; Martens-Uzunova ES, Schaap PJ. An evolutionary conserved d-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet Biol. 2008 Nov;45(11):1449–57. doi: 10.1016/j.fgb.2008.08.002. PMID: 18768163.; ISHIKAWA T, MASUMOTO I, IWASA N, NISHIKAWA H, SAWA Y, SHIBATA H, NAKAMURA A, YABUTA Y, SHIGEOKA S. Functional Characterization ofD-Galacturonic Acid Reductase, a Key Enzyme of the Ascorbate Biosynthesis Pathway, fromEuglena gracilis. Bioscience, Biotechnology, and Biochemistry. 2006 Nov 23;70(11):2720–6. doi: 10.1271/bbb.60327.; Agius F, González-Lamothe R, Caballero JL, Muñoz-Blanco J, Botella MA, Valpuesta V. Engineering increased vitamin C levels in plants by overexpression of a D-galacturonic acid reductase. Nat Biotechnol. 2003 Feb;21(2):177–81. doi: 10.1038/nbt777. PMID: 12524550.

Metabolites

1,10-Phenanthroline

Formula: C12H8N2 (180.0687448)

CAS ID: 66-71-7

Adenine

Formula: C5H5N5 (135.054493)

CAS ID: 73-24-5

Adenosine

Formula: C10H13N5O4 (267.09674980000005)

CAS ID: 58-61-7

Bromide

Formula: Br (78.918336)

CAS ID: 24959-67-9

Calcium cation

Formula: Ca (39.962591)

CAS ID: 14127-61-8

Cl-

Formula: Cl (34.968853)

CAS ID: 16887-00-6

CO2

Formula: CO2 (43.98983)

CAS ID: 124-38-9

Cobalt ion

Formula: Co (58.933198)

CAS ID: 22541-53-3

Copper

Formula: Cu (62.929599)

CAS ID: 7440-50-8

D-Galacturonate

Formula: C6H10O7 (194.042651)

CAS ID: 685-73-4

D-Sorbitol

Formula: C6H14O6 (182.0790344)

CAS ID: 50-70-4

Diphosphate

Formula: H4P2O7 (177.9432294)

CAS ID: 2466-09-3

Fe2+

Formula: Fe (55.934939)

CAS ID: 15438-31-0

Fluoride

Formula: F (18.9984032)

CAS ID: 7782-41-4

Glycerol

Formula: C3H8O3 (92.0473418)

CAS ID: 56-81-5

H+

Formula: H (1.0078246)

CAS ID: 12408-02-5

H2O

Formula: H2O (18.0105642)

CAS ID: 7732-18-5

Hydrogen cyanide

Formula: CHN (27.010898599999997)

CAS ID: 74-90-8

Magnesium cation

Formula: Mg (23.98505)

CAS ID: 22537-22-0

Manganese(2+)

Formula: Mn (54.938046)

CAS ID: 7439-96-5

Mannitol

Formula: C6H14O6 (182.0790344)

CAS ID: 69-65-8

Mercaptoethanol

Formula: C2H6OS (78.0139346)

CAS ID: 60-24-2

Mercury(2+)

Formula: Hg (201.970632)

CAS ID: 14302-87-5

N-Ethylmaleimide

Formula: C6H7NO2 (125.0476762)

CAS ID: 128-53-0

Silver

Formula: Ag (106.905095)

CAS ID: 7440-22-4

Sodium cyanide

Formula: NaCN (48.992844)

CAS ID: 143-33-9

Zinc cation

Formula: Zn (63.929145)

CAS ID: 23713-49-7

Nitrate

Formula: NO3 (61.987819)

CAS ID: 14797-55-8

iodoacetamide

Formula: C2H4INO (184.9337644)

CAS ID: 144-48-9

potassium cyanide

Formula: CKN (64.966782)

CAS ID: 151-50-8

L-tartrate(2-)

Formula: C4H4O6 (148.0007884)

CAS ID: 87-69-4

gluconate

Formula: C6H11O7 (195.0504756)

CAS ID: 608-59-3

D-mannonate

Formula: C6H11O7 (195.0504756)

CAS ID:

D-glucopyranuronate

Formula: C6H9O7 (193.0348264)

CAS ID: 148-00-5

2-dehydro-3-deoxy-D-gluconate

Formula: C6H9O6 (177.0399114)

CAS ID: 19992-86-0

2-oxoglutarate(2-)

Formula: C5H4O5 (144.00587339999998)

CAS ID: 64-15-3

acetate

Formula: C2H3O2 (59.0133038)

CAS ID: 71-50-1

pyruvate

Formula: C3H3O3 (87.00821880000001)

CAS ID: 57-60-3

citrate(3-)

Formula: C6H5O7 (189.00352800000002)

CAS ID: 126-44-3

dimethylarsinate

Formula: C2H6AsO2 (136.9583736)

CAS ID: 15132-04-4

NADPH(4-)

Formula: C21H26N7O17P3 (741.0598016)

CAS ID: 53-57-6

ATP(4-)

Formula: C10H12N5O13P3 (502.9644492)

CAS ID:

NAD(1-)

Formula: C21H26N7O14P2 (662.1012936000001)

CAS ID: 53-84-9

ADP(3-)

Formula: C10H12N5O10P2 (424.0059412)

CAS ID:

3',5'-cyclic AMP(1-)

Formula: C10H11N5O6P (328.0446936)

CAS ID: 62906-31-4

NADP(3-)

Formula: C21H25N7O17P3 (740.051977)

CAS ID: 53-59-8

beta-D-glucuronamide

Formula: C6H11NO6 (193.0586346)

CAS ID: 61914-43-0



Enzyme

EC Number name full name note
1.1.1.-
1.1.1.127 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase 2-dehydro-3-deoxy-D-gluconate:NAD+ 5-oxidoreductase
1.1.1.203 uronate dehydrogenase uronate:NAD+ 1-oxidoreductase
1.1.1.365 D-galacturonate reductase L-galactonate:NADP+ oxidoreductase
1.1.1.372 D/L-glyceraldehyde reductase glycerol:NADP+ oxidoreductase (D/L-glyceraldehyde-forming)
1.1.1.57 fructuronate reductase D-mannonate:NAD+ 5-oxidoreductase
1.1.1.58 tagaturonate reductase D-altronate:NAD+ 3-oxidoreductase
1.1.1.60 2-hydroxy-3-oxopropionate reductase D-glycerate:NAD(P)+ oxidoreductase
1.2.1.26 2,5-dioxovalerate dehydrogenase 2,5-dioxopentanoate:NADP+ 5-oxidoreductase
2.7.1.165 glycerate 2-kinase ATP:(R)-glycerate 2-phosphotransferase
2.7.1.31 glycerate 3-kinase ATP:D-glycerate 3-phosphotransferase
2.7.1.45 2-dehydro-3-deoxygluconokinase ATP:2-dehydro-3-deoxy-D-gluconate 6-phosphotransferase
3.2.1.31 beta-glucuronidase beta-D-glucuronoside glucuronosohydrolase
4.1.1.112 oxaloacetate decarboxylase oxaloacetate carboxy-lyase (pyruvate-forming)
4.1.2.14 2-dehydro-3-deoxy-phosphogluconate aldolase 2-dehydro-3-deoxy-6-phosphate-D-gluconate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
4.1.2.20 2-dehydro-3-deoxyglucarate aldolase 2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase (pyruvate-forming)
4.1.2.54 L-threo-3-deoxy-hexylosonate aldolase 2-dehydro-3-deoxy-L-galactonate L-glyceraldehyde-lyase (pyruvate-forming)
4.1.3.42 (4S)-4-hydroxy-2-oxoglutarate aldolase (4S)-4-hydroxy-2-oxoglutarate glyoxylate-lyase (pyruvate-forming)
4.2.1.146 L-galactonate dehydratase L-galactonate hydro-lyase (2-dehydro-3-deoxy-L-galactonate-forming)
4.2.1.40 glucarate dehydratase D-glucarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)
4.2.1.41 5-dehydro-4-deoxyglucarate dehydratase 5-dehydro-4-deoxy-D-glucarate hydro-lyase (decarboxylating; 2,5-dioxopentanoate-forming)
4.2.1.42 galactarate dehydratase galactarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)
4.2.1.7 altronate dehydratase D-altronate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)
4.2.1.8 mannonate dehydratase D-mannonate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)
5.3.1.12 glucuronate isomerase D-glucuronate aldose-ketose-isomerase
5.3.1.17 5-dehydro-4-deoxy-D-glucuronate isomerase 5-dehydro-4-deoxy-D-glucuronate aldose-ketose-isomerase
5.4.1.4 D-galactarolactone isomerase D-galactaro-1,5-lactone isomerase (D-galactaro-1,4-lactone-forming)
5.5.1.27 D-galactarolactone cycloisomerase D-galactaro-1,4-lactone lyase (ring-opening)


Proteins

Protein ID name full name
A2QEQ6 GUS79_ASPNC Beta-glucuronidase
A6Y9S5 lga1 L-threo-3-deoxy-hexylosonate aldolase
A9CEQ7 GLI_AGRFC D-galactarolactone isomerase
A9CEQ8 gci D-galactarolactone cycloisomerase
P05804 uidA Beta-glucuronidase
P0A6L7 uxaB Altronate oxidoreductase
P0A8G3 uxaC Uronate isomerase
P0A955 eda KHG/KDPG aldolase
P0ABQ2 garR 2-hydroxy-3-oxopropionate reductase
P0AES2 gudD Glucarate dehydratase
P23522 garL 5-keto-4-deoxy-D-glucarate aldolase
P23524 garK Glycerate 2-kinase
P24215 uxuA Mannonate dehydratase
P37647 kdgK 2-dehydro-3-deoxygluconokinase
P37769 kduD 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase
P38448 eda 2-dehydro-3-deoxy-phosphogluconate aldolase
P39160 uxuB D-mannonate oxidoreductase
P39829 garD Galactarate dehydratase (L-threo-forming)
P42206 gudD Glucarate dehydratase
P42604 uxaA Altronate dehydratase
P45416 kdgK 2-dehydro-3-deoxygluconokinase
P77364 glxK Glycerate 3-kinase
Q05528 kduD 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase
Q05529 kduI 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
Q0GYU5 gld1 D/L-glyceraldehyde reductase
Q0QWS4 lgd1 L-galactonate dehydratase
Q3ZFI7 gar1 D-galacturonate reductase
Q46938 kduI 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
Q6FFQ0 KGSDH_ACIAD Alpha-ketoglutaric semialdehyde dehydrogenase
Q6FFQ1 KDGD_ACIAD Probable 5-dehydro-4-deoxyglucarate dehydratase
Q6FFQ2 gudD Glucarate dehydratase
Q7CRQ0 udh Uronate dehydrogenase
Q888H1 PSPTO_1053 conserved hypothetical protein