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MetaCyc Enzyme: L-1,2-propanediol dehydrogenase / glycerol dehydrogenase

Gene: gldA Accession Numbers: EG11904 (MetaCyc), b3945, ECK3937

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of L-1,2-propanediol dehydrogenase / glycerol dehydrogenase = [GldA]8

Summary:
The physiological function of the GldA enzyme has long been unclear. The enzyme was independently isolated as a glycerol dehydrogenase and a D-1-amino-2-propanol:NAD+ oxidoreductase. At that time, D-1-amino-2-propanol was thought to be an intermediate for the biosynthesis of vitamin B12, and although E. coli is unable to synthesize vitamin B12 de novo, enzymes catalyzing the synthesis of this compound were sought [Campbell73]. It was later found that GldA was responsible for both activities [Kelley85].

The primary in vivo role of GldA was recently proposed to be the removal of dihydroxyacetone by converting it to glycerol [Subedi08]. However, a dual role in the fermentation of glycerol has also recently been established [Gonzalez08]. Glycerol dissimilation in E. coli can be accomplished by two different pathways in E. coli. The glycerol and glycerophosphodiester degradation pathway requires the presence of a terminal electron acceptor and utilizes an ATP-dependent kinase of the Glp system, which phosphorylates glycerol to glycerol-3-phosphate. However, upon inactivation of the kinase and selection for growth on glycerol [St77, Jin83], it was found that an NAD+-linked dehydrogenase, GldA, was able to support glycerol fermentation [Tang82] (see glycerol degradation V). Recently, [Gonzalez08] showed that GldA was involved in glycerol fermentation both as a glycerol dehydrogenase, producing dihydroxyacetone, and as a 1,2-propanediol dehydrogenase, regenerating NAD+ by producing 1,2-propanediol from acetol.

The enzyme is found in two catalytically active forms, a large form of eight subunits and a small form of two subunits. The large form appears to be the major species [Campbell78, Tang79, Jin83, Kelley84].

Kinetic modeling and metabolic control analysis showed that during glycerol fermentation in E. coli, calculated flux control coefficients indicated that the glycolytic flux is almost exclusively controlled by glycerol dehydrogenase (GldA) and dihydroxyacetone kinase (DhaKLM). Overexpression of GldA and DhaKLM led to significant increase in glycerol utilization and ethanol synthesis, suggesting a potential industrial scale production of ethanol from crude glycerol under anaerobic conditions [Cintolesi12, Wong14].

Conversely, a broad survey of aldehyde reductases showed that YahK was one of several endogenous aldehyde reductases that contribute to the degradation of desired aldehyde end products of metabolic engineering [Rodriguez14].

Expression of gldA is induced by hydroxyacetone in stationary phase [Truniger94].

Citations: [Tang82a, Dharmadi06, Murarka08, Durnin09, Zhou13]

Locations: cytosol

Map Position: [4,135,955 <- 4,137,058]

Molecular Weight of Polypeptide: 38.712 kD (from nucleotide sequence), 39 kD (experimental) [Tang79 ]

Molecular Weight of Multimer: 310.0 kD (experimental) [Tang79]

pI: 5.08

Unification Links: ASAP:ABE-0012912 , CGSC:34147 , DIP:DIP-47916N , EchoBASE:EB1849 , EcoGene:EG11904 , EcoliWiki:b3945 , Entrez-Nucleotide:U00006 , ModBase:P0A9S5 , OU-Microarray:b3945 , PortEco:gldA , PR:PRO_000022774 , Pride:P0A9S5 , Protein Model Portal:P0A9S5 , RefSeq:NP_418380 , RegulonDB:EG11904 , SMR:P0A9S5 , String:511145.b3945 , Swiss-Model:P0A9S5 , UniProt:P0A9S5

Relationship Links: InterPro:IN-FAMILY:IPR001670 , InterPro:IN-FAMILY:IPR016205 , InterPro:IN-FAMILY:IPR018211 , Pfam:IN-FAMILY:PF00465 , Prosite:IN-FAMILY:PS00060 , Prosite:IN-FAMILY:PS00913

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0019588 - anaerobic glycerol catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Gonzalez08]
GO:0051596 - methylglyoxal catabolic process Inferred from experiment [Gonzalez08]
GO:0006071 - glycerol metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0008888 - glycerol dehydrogenase [NAD+] activity Inferred from experiment Inferred by computational analysis [GOA01a, Truniger94, Tang79]
GO:0019147 - (R)-aminopropanol dehydrogenase activity Inferred from experiment [Campbell78]
GO:0042802 - identical protein binding Inferred from experiment [Kelley84]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]

MultiFun Terms: metabolism central intermediary metabolism misc. glycerol metabolism

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: L-1,2-propanediol dehydrogenase

(S)-propane-1,2-diol + NAD+ <=> acetol + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Tang79]

In Pathways: superpathway of methylglyoxal degradation , methylglyoxal degradation III

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
The enzyme accepts 1,2-propanediol as a substrate with the same [Tang82] or even higher [Tang79] activity as with glycerol or D-1-amino-2-propanol [Kelley84]. However, the Km for 1,2-propanediol (1.1 mM) is much lower than that for glycerol (140 mM) [Kelley85].

Kinetic Parameters:

Substrate
Km (μM)
Citations
NAD+
150.0
[Kelley84]


Enzymatic reaction of: D-aminopropanol dehydrogenase (L-1,2-propanediol dehydrogenase / glycerol dehydrogenase)

Synonyms: D-1-amino-2-propanol oxidoreductase, D-1-aminopropan-2-ol:NAD+ oxidoreductase

EC Number: 1.1.1.75

aminoacetone + NADH + H+ <=> (R)-1-aminopropan-2-ol + NAD+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown. [Dekker68]

Alternative Products for (R)-1-aminopropan-2-ol [Comment 1 ]: glycerol [Campbell78 , Kelley84 ] , 3-amino-1,2-propanediol [Kelley84 ] , 3-chloro-1,2-propanediol [Kelley84 ] , 3-mercapto-1,2-propanediol [Kelley84 ] , a propane-1,2-diol [Kelley84 ] , 1,2-butanediol [Kelley84 ] , a 2,3-butanediol [Kelley84 , Campbell78 ]

In Pathways: aminopropanol phosphate biosynthesis II

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
The reaction equilibrium heavily favors reduction of the aminoketone [Dekker68].

Inhibitors (Unknown Mechanism): Zn2+ [Kelley84, Campbell78] , Ni2+ [Kelley84, Campbell78] , Fe2+ [Kelley84] , Mn2+ [Kelley84, Campbell78] , Cu2+ [Kelley84, Campbell78] , Co2+ [Kelley84, Campbell78] , Hg2+ [Kelley84, Comment 2]

Kinetic Parameters:

Substrate
Km (μM)
Citations
(R)-1-aminopropan-2-ol
14500.0
[Kelley84]
NAD+
1230.0
[Kelley84]

pH(opt): 8.4-8.8 [Campbell78]


Enzymatic reaction of: glycerol dehydrogenase

Synonyms: glycerol:NAD+ 2-oxidoreductase, GLDH

EC Number: 1.1.1.6

glycerol + NAD+ <=> dihydroxyacetone + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [St77]

Alternative Substrates for dihydroxyacetone [Tang79 ]: isobutanal [Rodriguez14 ] , acetol [Tang79 , St77 ]

Alternative Substrates for glycerol [Tang79 ]: (S)-propane-1,2-diol [Tang82 , St77 , Tang79 ]

In Pathways: glycerol degradation V

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
The optimal pH for the oxidation of glycerol is 9.5-10, while the optimum pH of the reverse reaction, reduction of dihydroxyacetone, is 5.5-6 [Tang79].

Enzyme activity with isobutanal as the substrate is NADPH-dependent [Rodriguez14].

The enzyme was first partially purified from E. coli strain ECFS [ASNIS53].

Alternative Cofactors for NADH [Tang79 ]: NADPH [Comment 3 ]

Activators (Unknown Mechanism): ammonium [Tang79, Comment 4] , K+ [Tang79, Comment 4] , Rb+ [Tang79, Comment 5]

Inhibitors (Unknown Mechanism): N-ethylmaleimide [Tang79] , 8-hydroxyquinoline [Tang79] , o-phenanthroline [Tang79] , Cu2+ [Tang79] , Ca2+ [Tang79]

Kinetic Parameters:

Substrate
Km (μM)
Citations
dihydroxyacetone
1000.0
[Tang79]
glycerol
1400.0
[Tang79]

pH(opt) (forward direction): 10 [Tang79]

pH(opt) (reverse direction): 5.5-6 [Tang79]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 37
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 94 -> 98
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 116 -> 119
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 121
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 125
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 127
[UniProt10]
UniProt: NAD; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 131
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 171
[UniProt10]
UniProt: Zinc; catalytic; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 254
[UniProt10]
UniProt: Zinc; catalytic; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 271
[UniProt10]
UniProt: Zinc; catalytic; Non-Experimental Qualifier: by similarity;

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b3945 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11904; confirmed by SwissProt match.


References

ASNIS53: ASNIS RE, BRODIE AF (1953). "A glycerol dehydrogenase from Escherichia coli." J Biol Chem 203(1);153-9. PMID: 13069498

Campbell73: Campbell RL, Dekker EE (1973). "Formation of D-1-amino-2-propanol from L-threonine by enzymes from Escherichia coli K-12." Biochem Biophys Res Commun 53(2);432-8. PMID: 4577583

Campbell78: Campbell RL, Swain RR, Dekker EE (1978). "Purification, separation, and characterization of two molecular forms of D-1-amino-2-propanol:NAD+ oxidoreductase activity from extracts of Escherichia coli K-12." J Biol Chem 253(20);7282-8. PMID: 359547

Cintolesi12: Cintolesi A, Clomburg JM, Rigou V, Zygourakis K, Gonzalez R (2012). "Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli." Biotechnol Bioeng 109(1);187-98. PMID: 21858785

Dekker68: Dekker EE, Swain RR (1968). "Formation of Dg-1-amino-2-propanol by a highly purified enzyme from Escherichia coli." Biochim Biophys Acta 158(2);306-7. PMID: 4385233

Dharmadi06: Dharmadi Y, Murarka A, Gonzalez R (2006). "Anaerobic fermentation of glycerol by Escherichia coli: a new platform for metabolic engineering." Biotechnol Bioeng 94(5);821-9. PMID: 16715533

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Durnin09: Durnin G, Clomburg J, Yeates Z, Alvarez PJ, Zygourakis K, Campbell P, Gonzalez R (2009). "Understanding and harnessing the microaerobic metabolism of glycerol in Escherichia coli." Biotechnol Bioeng 103(1);148-61. PMID: 19189409

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Gonzalez08: Gonzalez R, Murarka A, Dharmadi Y, Yazdani SS (2008). "A new model for the anaerobic fermentation of glycerol in enteric bacteria: trunk and auxiliary pathways in Escherichia coli." Metab Eng 10(5);234-45. PMID: 18632294

Jin83: Jin RZ, Tang JC, Lin EC (1983). "Experimental evolution of a novel pathway for glycerol dissimilation in Escherichia coli." J Mol Evol 1983;19(6);429-36. PMID: 6361270

Kelley84: Kelley JJ, Dekker EE (1984). "D-1-amino-2-propanol:NAD+ oxidoreductase. Purification and general properties of the large molecular form of the enzyme from Escherichia coli K12." J Biol Chem 1984;259(4);2124-9. PMID: 6365902

Kelley85: Kelley JJ, Dekker EE (1985). "Identity of Escherichia coli D-1-amino-2-propanol:NAD+ oxidoreductase with E. coli glycerol dehydrogenase but not with Neisseria gonorrhoeae 1,2-propanediol:NAD+ oxidoreductase." J Bacteriol 1985;162(1);170-5. PMID: 3920199

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Murarka08: Murarka A, Dharmadi Y, Yazdani SS, Gonzalez R (2008). "Fermentative utilization of glycerol by Escherichia coli and its implications for the production of fuels and chemicals." Appl Environ Microbiol 74(4);1124-35. PMID: 18156341

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Rodriguez14: Rodriguez GM, Atsumi S (2014). "Toward aldehyde and alkane production by removing aldehyde reductase activity in Escherichia coli." Metab Eng 25;227-37. PMID: 25108218

St77: St Martin EJ, Freedberg WB, Lin EC (1977). "Kinase replacement by a dehydrogenase for Escherichia coli glycerol utilization." J Bacteriol 131(3);1026-8. PMID: 197059

Subedi08: Subedi KP, Kim I, Kim J, Min B, Park C (2008). "Role of GldA in dihydroxyacetone and methylglyoxal metabolism of Escherichia coli K12." FEMS Microbiol Lett 279(2);180-7. PMID: 18179582

Tang79: Tang CT, Ruch FE, Lin CC (1979). "Purification and properties of a nicotinamide adenine dinucleotide-linked dehydrogenase that serves an Escherichia coli mutant for glycerol catabolism." J Bacteriol 1979;140(1);182-7. PMID: 40950

Tang82: Tang JC, Forage RG, Lin EC (1982). "Immunochemical properties of NAD+-linked glycerol dehydrogenases from Escherichia coli and Klebsiella pneumoniae." J Bacteriol 1982;152(3);1169-74. PMID: 6183251

Tang82a: Tang JC, St Martin EJ, Lin EC (1982). "Derepression of an NAD-linked dehydrogenase that serves an Escherichia coli mutant for growth on glycerol." J Bacteriol 152(3);1001-7. PMID: 6754692

Truniger94: Truniger V, Boos W (1994). "Mapping and cloning of gldA, the structural gene of the Escherichia coli glycerol dehydrogenase." J Bacteriol 1994;176(6);1796-800. PMID: 8132480

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Wong14: Wong MS, Li M, Black RW, Le TQ, Puthli S, Campbell P, Monticello DJ (2014). "Microaerobic conversion of glycerol to ethanol in Escherichia coli." Appl Environ Microbiol 80(10);3276-82. PMID: 24584248

Zhou13: Zhou YJ, Yang W, Wang L, Zhu Z, Zhang S, Zhao ZK (2013). "Engineering NAD+ availability for Escherichia coli whole-cell biocatalysis: a case study for dihydroxyacetone production." Microb Cell Fact 12;103. PMID: 24209782


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sun Dec 21, 2014, biocyc13.