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Escherichia coli K-12 substr. MG1655 Enzyme: malate dehydrogenase



Gene: mdh Accession Numbers: EG10576 (EcoCyc), b3236, ECK3225

Regulation Summary Diagram: ?

Subunit composition of malate dehydrogenase = [Mdh]2
         malate dehydrogenase = Mdh

Summary:
Malate dehydrogenase (Mdh) catalyzes the reversible oxidation of malate to generate oxaloacetate, using NAD+ as an electron acceptor [Sutherland85, Fernley81]. Mdh carries out the oxidation reaction as part of the TCA cycle, the glyoxylate cycle, and gluconeogenesis. It reduces oxaloacetate to generate malate as part of anaerobic respiration and mixed-acid fermentation.

Malate dehydrogenase comprises a dimer of Mdh monomers [Fernley81]. A crystal structure of this dimer shows that Arg-81, Arg-153 and His-177 may all be involved in substrate interaction [Hall92]. Although Mdh does not interact directly with the oxaloacetate-utilizing enzyme aspartate aminotransferase, PLP-dependent, it does appear to directly transfer NADH to NADH:ubiquinone oxidoreductase I [Geck99, Amarneh05].

Mdh activity is depressed during anaerobic conditions [Sutherland85]. There is a 2-fold difference between expression of Mdh under aerobic versus anaerobic conditions. In addition, Mdh expression increases during growth on pyruvate, is low during growth on glucose, and is increased 5-fold by heme limitation during anaerobic growth [Park95a].

mdh is one of a network of genes believed to play a role in promoting the stress-induced mutagenesis (SIM) response of E. coli K-12 [Al12].

Citations: [vanderRest00]

Gene Citations: [Yamamoto08, Iuchi90]

Locations: cytosol, membrane

Map Position: [3,381,352 <- 3,382,290] (72.88 centisomes)
Length: 939 bp / 312 aa

Molecular Weight of Polypeptide: 32.337 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010613 , CGSC:523 , DIP:DIP-35924N , EchoBASE:EB0571 , EcoGene:EG10576 , EcoliWiki:b3236 , ModBase:P61889 , OU-Microarray:b3236 , PortEco:mdh , PR:PRO_000023174 , Pride:P61889 , Protein Model Portal:P61889 , RefSeq:NP_417703 , RegulonDB:EG10576 , SMR:P61889 , UniProt:P61889

Relationship Links: InterPro:IN-FAMILY:IPR001236 , InterPro:IN-FAMILY:IPR001252 , InterPro:IN-FAMILY:IPR001557 , InterPro:IN-FAMILY:IPR010097 , InterPro:IN-FAMILY:IPR015955 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR022383 , InterPro:IN-FAMILY:IPR023958 , Panther:IN-FAMILY:PTHR11540 , PDB:Structure:1CME , PDB:Structure:1EMD , PDB:Structure:1IB6 , PDB:Structure:1IE3 , PDB:Structure:2CMD , PDB:Structure:2PWZ , PDB:Structure:3HHP , Pfam:IN-FAMILY:PF00056 , Pfam:IN-FAMILY:PF02866 , Prosite:IN-FAMILY:PS00068

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006096 - glycolytic process Inferred from experiment [Sutherland85]
GO:0006099 - tricarboxylic acid cycle Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Sutherland85]
GO:0006108 - malate metabolic process Inferred from experiment Inferred by computational analysis [GOA01a, Murphey67]
GO:0006113 - fermentation Inferred from experiment [Sutherland85]
GO:0009061 - anaerobic respiration Inferred from experiment [Sutherland85]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01a]
GO:0044262 - cellular carbohydrate metabolic process Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0016491 - oxidoreductase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Murphey67]
GO:0016615 - malate dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA01a, Murphey67, Sutherland85, Courtright70]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01a]
GO:0030060 - L-malate dehydrogenase activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Courtright70]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0019898 - extrinsic component of membrane Inferred from experiment [Amarneh05]

MultiFun Terms: metabolism carbon utilization carbon compounds
metabolism central intermediary metabolism glyoxylate degradation
metabolism central intermediary metabolism
metabolism energy metabolism, carbon fermentation
metabolism energy metabolism, carbon TCA cycle

Essentiality data for mdh knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 11-Sep-2006 by Shearer A , SRI International


Enzymatic reaction of: malate dehydrogenase

Synonyms: malate oxidoreductase, L-malate oxidoreductase, L-malate:NAD(+) oxidoreductase

EC Number: 1.1.1.37

(S)-malate + NAD+ <=> oxaloacetate + 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.

In Pathways: superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass , superpathway of glyoxylate bypass and TCA , glyoxylate cycle , TCA cycle I (prokaryotic) , mixed acid fermentation , gluconeogenesis I

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
oxaloacetate
49.0
[Muslin95, BRENDA14]
oxaloacetate
23.0, 26.0, 56.0
[Kim99, BRENDA14]
oxaloacetate
40.0
931.0
[Yin07, BRENDA14]
(S)-malate
2600.0
[Muslin95, BRENDA14]
NADH
61.0
[Muslin95, BRENDA14]
NAD+
260.0
[Muslin95, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 7 -> 13
[UniProt10]
UniProt: NAD;
Amino-Acid-Sites-That-Bind 34
[UniProt10]
UniProt: NAD;
Sequence-Conflict 37
[Sutherland85, UniProt10]
Alternate sequence: P → S; UniProt: (in Ref. 5);
Sequence-Conflict 70
[Vogel87a, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 2);
Extrinsic-Sequence-Variant 71
[UniProt10]
Alternate sequence: D → N; UniProt: (in strain: EC47, EC49, EC50 and RT272);
Sequence-Conflict 80
[Vogel87a, McAlisterHenn87, UniProt10]
Alternate sequence: A → R; UniProt: (in Ref. 1 and 2);
Amino-Acid-Sites-That-Bind 81
[UniProt10]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 87
[UniProt10]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 94
[UniProt10]
UniProt: NAD;
Acetylation-Modification 99
[Yu08]
 
Extrinsic-Sequence-Variant 106
[UniProt10]
Alternate sequence: A → S; UniProt: (in strain: ECOR 27 and RT082);
Sequence-Conflict 116
[Vogel87a, UniProt10]
Alternate sequence: I → N; UniProt: (in Ref. 2);
Nucleotide-Phosphate-Binding-Region 117 -> 119
[UniProt10]
UniProt: NAD;
Amino-Acid-Sites-That-Bind 119
[UniProt10]
UniProt: Substrate;
Acetylation-Modification 140
[Yu08]
 
Sequence-Conflict 144
[McAlisterHenn87, UniProt10]
Alternate sequence: F → L; UniProt: (in Ref. 1);
Mutagenesis-Variant 153
[Bell01, UniProt11]
Alternate sequence: R → C; UniProt: Loss of interaction with substrate.
Amino-Acid-Sites-That-Bind 153
[UniProt10]
UniProt: Substrate;
Active-Site 177
[UniProt10]
UniProt: Proton acceptor;
Extrinsic-Sequence-Variant 209
[UniProt10]
Alternate sequence: A → P; UniProt: (in strain: MB001D);
Extrinsic-Sequence-Variant 218
[UniProt10]
Alternate sequence: A → R; UniProt: (in strain: A8190, E2666-74, E830587, E851819, E3406, EC10, EC14, EC32, EC35, EC38, EC40, EC44, EC46, EC47, EC49, EC50, EC52, EC58, E64 and EC70);
Amino-Acid-Sites-That-Bind 227
[UniProt10]
UniProt: NAD;
Extrinsic-Sequence-Variant 232
[UniProt10]
Alternate sequence: A → T; UniProt: (in strain: ECO R37);
Extrinsic-Sequence-Variant 249
[UniProt10]
Alternate sequence: V → I; UniProt: (in strain: RT083);
Extrinsic-Sequence-Variant 289
[UniProt10]
Alternate sequence: Q → K; UniProt: (in strain: EC35, EC38, EC40, EC44, EC46, EC47 and RT272);
Extrinsic-Sequence-Variant 290
[UniProt10]
Alternate sequence: N → S; UniProt: (in strain: E2666-74, ECOR 27, ECOR 45, RL012A, RT104 and RT174);
Extrinsic-Sequence-Variant 291
[UniProt10]
Alternate sequence: A → S; UniProt: (in strain: EC35);
Extrinsic-Sequence-Variant 294
[UniProt10]
Alternate sequence: G → A; UniProt: (in strain: ECOR 45);
Extrinsic-Sequence-Variant 297
[UniProt10]
Alternate sequence: D → N; UniProt: (in strain: E830587);
Sequence-Conflict 305 -> 312
[Vogel87a, UniProt10]
Alternate sequence: LGEEFVNK → WAKSSLISN; UniProt: (in Ref. 2);
Sequence-Conflict 307
[McAlisterHenn87, UniProt10]
Alternate sequence: E → Q; UniProt: (in Ref. 1);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3236 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10576; confirmed by SwissProt match.


References

Al12: Al Mamun AA, Lombardo MJ, Shee C, Lisewski AM, Gonzalez C, Lin D, Nehring RB, Saint-Ruf C, Gibson JL, Frisch RL, Lichtarge O, Hastings PJ, Rosenberg SM (2012). "Identity and function of a large gene network underlying mutagenic repair of DNA breaks." Science 338(6112);1344-8. PMID: 23224554

Amarneh05: Amarneh B, Vik SB (2005). "Direct transfer of NADH from malate dehydrogenase to complex I in Escherichia coli." Cell Biochem Biophys 42(3);251-61. PMID: 15976458

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bell01: Bell JK, Yennawar HP, Wright SK, Thompson JR, Viola RE, Banaszak LJ (2001). "Structural analyses of a malate dehydrogenase with a variable active site." J Biol Chem 276(33);31156-62. PMID: 11389141

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Courtright70: Courtright JB, Henning U (1970). "Malate dehydrogenase mutants in Escherichia coli K-12." J Bacteriol 102(3);722-8. PMID: 4914076

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Fernley81: Fernley RT, Lentz SR, Bradshaw RA (1981). "Malate dehydrogenase: isolation from E. coli and comparison with the eukaryotic mitochondrial and cytoplasmic forms." Biosci Rep 1(6);497-507. PMID: 7028159

Geck99: Geck MK, Kirsch JF (1999). "A novel, definitive test for substrate channeling illustrated with the aspartate aminotransferase/malate dehydrogenase system." Biochemistry 38(25);8032-7. PMID: 10387047

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hall92: Hall MD, Levitt DG, Banaszak LJ (1992). "Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87 A resolution." J Mol Biol 226(3);867-82. PMID: 1507230

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Iuchi90: Iuchi S, Matsuda Z, Fujiwara T, Lin EC (1990). "The arcB gene of Escherichia coli encodes a sensor-regulator protein for anaerobic repression of the arc modulon." Mol Microbiol 1990;4(5);715-27. PMID: 2201868

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kim99: Kim SY, Hwang KY, Kim SH, Sung HC, Han YS, Cho Y (1999). "Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum." J Biol Chem 274(17);11761-7. PMID: 10206992

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

McAlisterHenn87: McAlister-Henn L, Blaber M, Bradshaw RA, Nisco SJ (1987). "Complete nucleotide sequence of the Escherichia coli gene encoding malate dehydrogenase." Nucleic Acids Res 15(12);4993. PMID: 3299262

Murphey67: Murphey WH, Barnaby C, Lin FJ, Kaplan NO (1967). "Malate dehydrogenases. II. Purification and properties of Bacillus subtilis, Bacillus stearothermophilus, and Escherichia coli malate dehydrogenases." J Biol Chem 242(7);1548-59. PMID: 4960671

Muslin95: Muslin EH, Li D, Stevens FJ, Donnelly M, Schiffer M, Anderson LE (1995). "Engineering a domain-locking disulfide into a bacterial malate dehydrogenase produces a redox-sensitive enzyme." Biophys J 68(6);2218-23. PMID: 7647229

Park95a: Park SJ, Cotter PA, Gunsalus RP (1995). "Regulation of malate dehydrogenase (mdh) gene expression in Escherichia coli in response to oxygen, carbon, and heme availability." J Bacteriol 177(22);6652-6. PMID: 7592446

Sutherland85: Sutherland P, McAlister-Henn L (1985). "Isolation and expression of the Escherichia coli gene encoding malate dehydrogenase." J Bacteriol 163(3);1074-9. PMID: 2993232

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

vanderRest00: van der Rest ME, Frank C, Molenaar D (2000). "Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Escherichia coli." J Bacteriol 2000;182(24);6892-9. PMID: 11092847

Vogel87a: Vogel RF, Entian KD, Mecke D (1987). "Cloning and sequence of the mdh structural gene of Escherichia coli coding for malate dehydrogenase." Arch Microbiol 1987;149(1);36-42. PMID: 3322223

Yamamoto08: Yamamoto K, Matsumoto F, Oshima T, Fujita N, Ogasawara N, Ishihama A (2008). "Anaerobic regulation of citrate fermentation by CitAB in Escherichia coli." Biosci Biotechnol Biochem 72(11);3011-4. PMID: 18997424

Yin07: Yin Y, Kirsch JF (2007). "Identification of functional paralog shift mutations: conversion of Escherichia coli malate dehydrogenase to a lactate dehydrogenase." Proc Natl Acad Sci U S A 104(44);17353-7. PMID: 17947381

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Other References Related to Gene Regulation

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Lynch96: Lynch AS, Lin EC (1996). "Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters." J Bacteriol 1996;178(21);6238-49. PMID: 8892825

Marzan13: Marzan LW, Hasan CM, Shimizu K (2013). "Effect of acidic condition on the metabolic regulation of Escherichia coli and its phoB mutant." Arch Microbiol 195(3);161-71. PMID: 23274360

Pruss01: Pruss BM, Liu X, Hendrickson W, Matsumura P (2001). "FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions." FEMS Microbiol Lett 2001;197(1);91-7. PMID: 11287152

Salmon05: Salmon KA, Hung SP, Steffen NR, Krupp R, Baldi P, Hatfield GW, Gunsalus RP (2005). "Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA." J Biol Chem 280(15);15084-96. PMID: 15699038


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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