View source for Malate dehydrogenase

{{Short description|Class of enzymes}}
{{other uses}}

{{infobox enzyme
| Name       = Malate dehydrogenase
| EC_number  = 1.1.1.37
| CAS_number = 9001-64-3
| GO_code    =
| image      = Malate_dehydrogenase_structure.png
| width      = 
| caption    = Structure of the protein with attached cofactors 
}}

'''Malate dehydrogenase''' ({{EC number|1.1.1.37}}) ('''MDH''') is an [[enzyme]] that [[reversible reaction|reversibly catalyzes]] the [[redox|oxidation]] of [[malic acid|malate]] to [[oxaloacetic acid|oxaloacetate]] using the reduction of [[Nicotinamide adenine dinucleotide|NAD<sup>+</sup>]] to NADH. This reaction is part of many [[metabolic pathway]]s, including the [[citric acid cycle]]. Other malate [[dehydrogenase]]s, which have other EC numbers and catalyze other reactions oxidizing malate, have qualified names like [[malate dehydrogenase (NADP+)|malate dehydrogenase (NADP<sup>+</sup>)]].

== Isozymes ==

Several [[isozymes]] of malate dehydrogenase exist. There are two main [[isoforms]] in eukaryotic cells.<ref name="Minárik_2002">{{cite journal | vauthors = Minárik P, Tomásková N, Kollárová M, Antalík M | title = Malate dehydrogenases--structure and function | journal = General Physiology and Biophysics | volume = 21 | issue = 3 | pages = 257–65 | date = September 2002 | pmid = 12537350 }}</ref> One is found in the mitochondrial matrix, participating as a key enzyme in the citric acid cycle that catalyzes the oxidation of malate. The other is found in the [[cytoplasm]], assisting the [[malate-aspartate shuttle]] with exchanging reducing equivalents so that malate can pass through the mitochondrial membrane to be transformed into oxaloacetate for further cellular processes.<ref>{{cite journal | vauthors = Musrati RA, Kollárová M, Mernik N, Mikulásová D | title = Malate dehydrogenase: distribution, function and properties | journal = General Physiology and Biophysics | volume = 17 | issue = 3 | pages = 193–210 | date = September 1998 | pmid = 9834842 }}</ref>

Humans and most other mammals express the following two malate dehydrogenases:
{{col-begin|width=auto}}
{{col-break}}
{{infobox protein|align=left
| Name = [[MDH1|malate dehydrogenase 1]], NAD (cytoplasmic)
| caption = 
| image = 
| width = 
| HGNCid = 6970
| Symbol = [[MDH1]]
| AltSymbols = 
| EntrezGene = 4190
| OMIM = 154200
| RefSeq = NM_005917
| UniProt = P40925
| PDB = 
| ECnumber = 1.1.1.37
| Chromosome = 2
| Arm = p
| Band = 23
| LocusSupplementaryData = 
}}
{{col-break}}
{{infobox protein|align=left
| Name = [[malate dehydrogenase 2]], NAD (mitochondrial)
| caption = Malate dehydrogenase 2, homotetramer, Human
| image = 2dfd.jpg
| width = 
| HGNCid = 6971
| Symbol = [[Malate dehydrogenase 2|MDH2]]
| AltSymbols = 
| EntrezGene = 4191
| OMIM = 154100
| RefSeq = NM_005918
| UniProt = P40926
| PDB = 
| ECnumber = 1.1.1.37
| Chromosome = 7
| Arm = 
| Band = 
| LocusSupplementaryData = cen-q22
}}
{{col-end}}

==Protein families==
{{col-begin|width=auto}}
{{col-break}}
{{Infobox protein family
| Symbol = Ldh_1_N
| Name =  lactate/malate dehydrogenase, NAD binding domain
| image = 
| width = 
| caption = 
| Pfam = PF00056
| Pfam_clan = CL0063
| InterPro = IPR001236
| SMART = 
| PROSITE = 
| MEROPS =
| SCOP = 6ldh
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD =
}}
{{col-break}}
{{Infobox protein family
| Symbol = Ldh_1_C
| Name = lactate/malate dehydrogenase, alpha/beta C-terminal domain
| image = 
| width = 
| caption = 
| Pfam = PF02866
| Pfam_clan = CL0341
| InterPro = IPR022383
| SMART = 
| PROSITE = PDOC00066
| MEROPS =
| SCOP = 6ldh
| TCDB = 
| OPM family = 
| OPM protein = 
| CAZy = 
| CDD =
}}
{{col-end}}[[File:Malate dehydrogenase Mobile Loop Region.png|thumb|3-D crystal structure of the mobile loop region in malate dehydrogenase in the closed and open conformation. The MDH closed conformation is shown in pink (indicated by the pink arrow) while the open conformation is shown in cyan (indicated by the cyan arrow).]]The malate dehydrogenase family contains L-lactate dehydrogenase and [[L-2-hydroxyisocaproate dehydrogenases]]. L-lactate dehydrogenases catalyzes the conversion of [[L-lactate]] to [[pyruvate]], the last step in anaerobic glycolysis. The [[N-terminus]] is a Rossmann NAD-binding fold and the [[C-terminus]] is an unusual alpha+beta fold.<ref name="pmid10075524">{{cite journal | vauthors = Chapman AD, Cortés A, Dafforn TR, Clarke AR, Brady RL | title = Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD | journal = Journal of Molecular Biology | volume = 285 | issue = 2 | pages = 703–12 | date = January 1999 | pmid = 10075524 | doi = 10.1006/jmbi.1998.2357 | doi-access = free }}</ref><ref name="pmid12029364">{{cite journal | vauthors = Madern D | title = Molecular evolution within the L-malate and L-lactate dehydrogenase super-family | journal = Journal of Molecular Evolution | volume = 54 | issue = 6 | pages = 825–40 | date = June 2002 | pmid = 12029364 | doi = 10.1007/s00239-001-0088-8 | bibcode = 2002JMolE..54..825M | s2cid = 469660 }}</ref>

== Evolution and structure ==
In most organisms, malate dehydrogenase (MDH) exists as a [[homodimeric]] molecule and is closely related to [[lactate dehydrogenase]] (LDH) in structure. It is a large protein molecule with subunits weighing between 30 and 35 kDa.<ref>{{cite book | vauthors = Banaszak LJ, Bradshaw RA | editor = Boyer PD | title = The Enzymes | edition = 3rd | volume = 11 | year = 1975 | publisher = Academic Press | location = New York | pages = 369–396 | chapter = Malate dehydrogenase }}</ref> Based on the amino acid sequences, it seems that MDH has diverged into two main phylogenetic groups that closely resemble either mitochondrial isozymes or cytoplasmic/chloroplast isozymes.<ref name="Goward1994">{{cite journal | vauthors = Goward CR, Nicholls DJ | title = Malate dehydrogenase: a model for structure, evolution, and catalysis | journal = Protein Science | volume = 3 | issue = 10 | pages = 1883–8 | date = October 1994 | pmid = 7849603 | pmc = 2142602 | doi = 10.1002/pro.5560031027 }}</ref> Because the sequence identity of malate dehydrogenase in the mitochondria is more closely related to its prokaryotic ancestors in comparison to the cytoplasmic isozyme, the theory that mitochondria and chloroplasts were developed through [[endosymbiosis]] is plausible.<ref>{{cite journal | vauthors = McAlister-Henn L | title = Evolutionary relationships among the malate dehydrogenases | journal = Trends in Biochemical Sciences | volume = 13 | issue = 5 | pages = 178–81 | date = May 1988 | pmid = 3076279 | doi = 10.1016/0968-0004(88)90146-6 }}</ref> The amino acid sequences of [[archaeal]] MDH are more similar to that of LDH than that of MDH of other organisms. This indicates that there is a possible evolutionary linkage between lactate dehydrogenase and malate dehydrogenase.<ref>{{cite journal | vauthors = Cendrin F, Chroboczek J, Zaccai G, Eisenberg H, Mevarech M | title = Cloning, sequencing, and expression in Escherichia coli of the gene coding for malate dehydrogenase of the extremely halophilic archaebacterium Haloarcula marismortui | journal = Biochemistry | volume = 32 | issue = 16 | pages = 4308–13 | date = April 1993 | pmid = 8476859 | doi = 10.1021/bi00067a020 }}</ref>

Each subunit of the malate dehydrogenase dimer has two distinct domains that vary in structure and functionality. A parallel [[β-sheet]] structure makes up the NAD+ binding domain, while four β-sheets and one [[α-helix]] comprise the central NAD<sup>+</sup> binding site. The subunits are held together through extensive [[hydrogen-bonding]] and hydrophobic interactions.<ref>{{cite journal | vauthors = Hall MD, Levitt DG, Banaszak LJ | title = Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87 A resolution | journal = Journal of Molecular Biology | volume = 226 | issue = 3 | pages = 867–82 | date = August 1992 | pmid = 1507230 | doi = 10.1016/0022-2836(92)90637-Y }}</ref>

Malate dehydrogenase has also been shown to have a mobile loop region that plays a crucial role in the enzyme's catalytic activity. Studies have shown that conformational change of this loop region from the open conformation to the closed conformation after binding of substrate enhances MDH catalysis through shielding of substrate and catalytic amino acids from solvent. Studies have also indicated that this loop region is highly conserved in malate dehydrogenase.<ref name="Goward1994" />

== Mechanism ==

[[Image:Malate dehydrogenase active site.svg|thumb|300px|Active site of malate dehydrogenase]]

The active site of malate dehydrogenase is a hydrophobic cavity within the protein complex that has specific binding sites for the substrate and its [[coenzyme]], NAD<sup>+</sup>. In its active state, MDH undergoes a conformational change that encloses the substrate to minimize solvent exposure and to position key residues in closer proximity to the substrate.<ref name="Goward1994" /> The three residues in particular that comprise a catalytic triad are [[histidine]] (His-195), [[aspartate]] (Asp-168), both of which work together as a proton transfer system, and [[arginine]]s (Arg-102, Arg-109, Arg-171), which secure the substrate.<ref>{{cite journal | vauthors = Lamzin VS, Dauter Z, Wilson KS | title = Dehydrogenation through the looking-glass | journal = Nature Structural Biology | volume = 1 | issue = 5 | pages = 281–2 | date = May 1994 | pmid = 7664032 | doi = 10.1038/nsb0594-281 | s2cid = 26167967 }}</ref>

Mechanistically, malate dehydrogenase catalyzes the oxidation of the hydroxyl group of malate by utilizing NAD<sup>+</sup> as an electron acceptor. This oxidation step results in the elimination of a proton and a hydride ion from the substrate. NAD<sup>+</sup> receives the hydride ion (specifically, the hydride ion is transferred to the nicotinamide ring of the NAD<sup>+</sup>) and becomes reduced to NADH while concomitantly, the His-195 residue on the enzyme accepts the proton.<ref name=":0">{{cite book | title = Fundamentals of Biochemistry: Life at the Molecular Level | edition = 4th | last1 = Voet | first1 = Donald | last2 = Voet | first2 = Judith G. | last3 = Pratt | first3 = Charlotte W. | name-list-style = vanc | publisher = Wiley | year = 2015 | isbn = 978-0-470-54784-7 | location = Hoboken, NJ | pages = 574–5 }}</ref> The positively charged His-195 residue, which is involved in [[base catalysis]] of the substrate, is stabilized by the adjacent, negatively charged Asp-168 residue. This electrostatic stabilization helps facilitate the transfer of the proton.<ref name="Minárik_2002" /> Arg-102, Arg-109, and Arg-171 (which are protonated, and thus positively charged) participate in [[Enzyme catalysis|electrostatic catalysis]] and help to bind the negatively charged carboxylates on the substrate. Additionally, the Arginine residues on the enzyme provide additional substrate specificity and binding through hydrogen bonding between the guanidinium side chain of the Arginine amino acid residues and the carboxylates of the substrate.<ref name="Bernstein_1978">{{cite journal | vauthors = Bernstein LH, Everse J | title = Studies on the mechanism of the malate dehydrogenase reaction | journal = The Journal of Biological Chemistry | volume = 253 | issue = 24 | pages = 8702–7 | date = December 1978 | doi = 10.1016/S0021-9258(17)34234-5 | pmid = 31361 | url = http://www.jbc.org/content/253/24/8702.full.pdf | doi-access = free }}</ref>

Studies have also identified a mobile loop in malate dehydrogenase that participates in the catalytic activity of the enzyme. The loop undergoes a conformational change to shield the substrate and catalytic amino acids from the solvent in response to the binding of the malate dehydrogenase:coenzyme complex to substrate. This flipping of the loop to the up position to cover the active site also promotes enhanced interaction of the catalytically important amino residues on the enzyme with the substrate. Additionally, the movement of the loop has been shown to correlate with the rate determining step of the enzyme.<ref>{{cite journal | vauthors = Waldman AD, Hart KW, Clarke AR, Wigley DB, Barstow DA, Atkinson T, Chia WN, Holbrook JJ | title = The use of genetically engineered tryptophan to identify the movement of a domain of B. stearothermophilus lactate dehydrogenase with the process which limits the steady-state turnover of the enzyme | journal = Biochemical and Biophysical Research Communications | volume = 150 | issue = 2 | pages = 752–9 | date = January 1988 | pmid = 3422557 | doi = 10.1016/0006-291X(88)90455-X | bibcode = 1988BBRC..150..752W }}</ref>

== Function ==
=== Reaction ===
[[File:General Malate Dehydrogenase Catalyzed Reaction.jpg|thumb|400px|General reaction showing malate dehydrogenase catalyzed oxidation of malate through reduction of NAD<sup>+</sup>.]]Malate dehydrogenases catalyzes the interconversion of malate to oxaloacetate. In the citric acid cycle, malate dehydrogenase is responsible for catalyzing the regeneration of oxaloacetate This reaction occurs through the oxidation of hydroxyl group on malate and reduction of NAD<sup>+</sup>. The mechanism of the transfer of the hydride ion to NAD<sup>+</sup> is carried out in a similar mechanism seen in lactate dehydrogenase and alcohol dehydrogenase. The ΔG'° of malate dehydrogenase is +29.7 kJ/mol and the ΔG (in the cell) is 0 kJ/mol.<ref name=":0" />

=== Other pathways ===
Malate dehydrogenase is also involved in [[gluconeogenesis]], the synthesis of glucose from smaller molecules. Pyruvate in the mitochondria is acted upon by pyruvate carboxylase to form oxaloacetate, a [[citric acid cycle]] intermediate. In order to get the oxaloacetate out of the mitochondria, malate dehydrogenase reduces it to malate, and it then traverses the inner mitochondrial membrane. Once in the cytosol, the malate is oxidized back to oxaloacetate by cytosolic malate dehydrogenase. Finally, [[phosphoenolpyruvate carboxykinase]] (PEPCK) converts oxaloacetate to [[phosphoenolpyruvate]] (PEP).<ref>{{cite journal | vauthors = Hung GC, Brown CR, Wolfe AB, Liu J, Chiang HL | title = Degradation of the gluconeogenic enzymes fructose-1,6-bisphosphatase and malate dehydrogenase is mediated by distinct proteolytic pathways and signaling events | journal = The Journal of Biological Chemistry | volume = 279 | issue = 47 | pages = 49138–50 | date = November 2004 | pmid = 15358789 | doi = 10.1074/jbc.M404544200 | doi-access = free }}</ref>

=== Kinetics ===
Kinetic studies show that malate dehydrogenase enzymatic activity is ordered. The cofactor NAD<sup>+</sup>/NADH is bound to the enzyme before the substrate.<ref>{{cite journal | vauthors = Shows TB, Chapman VM, Ruddle FH | title = Mitochondrial malate dehydrogenase and malic enzyme: Mendelian inherited electrophoretic variants in the mouse | journal = Biochemical Genetics | volume = 4 | issue = 6 | pages = 707–18 | date = December 1970 | pmid = 5496232 | doi = 10.1007/BF00486384 | s2cid = 35435579 }}</ref> The Km value for malate, i.e., the concentration at which the enzyme activity is half-maximal, is 2 mM. The Kcat value is 259.2 s<sup>−1</sup>.<ref>{{cite journal | vauthors = Wood DC, Jurgensen SR, Geesin JC, Harrison JH | title = Subunit interactions in mitochondrial malate dehydrogenase. Kinetics and mechanism of reassociation | journal = The Journal of Biological Chemistry | volume = 256 | issue = 5 | pages = 2377–82 | date = March 1981 | doi = 10.1016/S0021-9258(19)69790-5 | pmid = 7462244 | doi-access = free }}</ref>

== Effect of pH on catalytic activity ==
Additionally, pH levels control specificity of substrate binding by malate dehydrogenase due to proton transfer in the catalytic mechanism.<ref>{{cite journal | vauthors = Dasika SK, Vinnakota KC, Beard DA | title = Determination of the catalytic mechanism for mitochondrial malate dehydrogenase | journal = Biophysical Journal | volume = 108 | issue = 2 | pages = 408–19 | date = January 2015 | pmid = 25606688 | pmc = 4302198 | doi = 10.1016/j.bpj.2014.11.3467 }}</ref> A histidine moiety with a pK value of 7.5 has been suggested to play a role in the pH-dependency of the enzyme. Studies have indicated that the binding of the enol form oxaloacetate with the malate dehydrogenase:NADH complex forms much more rapidly at higher pH values.<ref name="Bernstein_1978" /> Additionally, L-malate binding to malate dehydrogenase is promoted at alkaline conditions. Consequently, the non-protonated form malate dehydrogenase binds preferentially to L-malate and the enol form of oxaloacetate. In contrast, D-malate, hydroxymalonate, and the keto form of oxaloacetate have been found to bind exclusively to the protonated form of the enzyme. Specifically, when the histidine is protonated, the His residue can form a hydrogen bond with the substrate's carbonyl oxygen, which shifts electron density away from the oxygen and makes it more susceptible to nucleophilic attack by hydride. This promotes the binding of malate dehydrogenase to these substrates. As a result, at lower pH values malate dehydrogenase binds preferentially to D-malate, hydroxymalonate, and keto-oxaloacetate.<ref>{{cite journal | vauthors = Lodola A, Shore JD, Parker DM, Holbrook J | title = Malate dehydrogenase of the cytosol. A kinetic investigation of the reaction mechanism and a comparison with lactate dehydrogenase | journal = The Biochemical Journal | volume = 175 | issue = 3 | pages = 987–98 | date = December 1978 | pmid = 217361 | pmc = 1186162 | doi = 10.1042/bj1750987 }}</ref>

== Allosteric regulation ==

Because malate dehydrogenase is closely tied to the citric acid cycle, studies have proposed and experimentally demonstrated that citrate is an allosteric regulator of malate dehydrogenase depending on the concentrations of L-malate and NAD<sup>+</sup>. This may be due to deviations observed in the kinetic behavior of malate dehydrogenase at high oxaloacetate and L-malate concentrations. Experiments have shown that [[Citrate]] can both allosterically activate and inhibit the enzymatic activity of malate dehydrogenase. Citrate has been shown to inhibit the oxidation of L-malate when there are low levels of L-malate and NAD<sup>+</sup>. However, in the presence of high levels of malate and NAD<sup>+</sup>, citrate can stimulate the production of oxaloacetate. Although malate dehydrogenase is typically considered a reversible enzyme, it is believed that there is an allosteric regulatory site on the enzyme where citrate can bind to and drive the reaction equilibrium in either direction.<ref>{{cite journal | vauthors = Gelpí JL, Dordal A, Montserrat J, Mazo A, Cortés A | title = Kinetic studies of the regulation of mitochondrial malate dehydrogenase by citrate | journal = The Biochemical Journal | volume = 283 ( Pt 1) | issue = Pt 1 | pages = 289–97 | date = April 1992 | pmid = 1567375 | pmc = 1131027 | doi = 10.1042/bj2830289 }}</ref>

Glutamate has also been shown to inhibit malate dehydrogenase activity. Furthermore, it has been shown that alpha ketoglutarate dehydrogenase can interact with mitochondrial aspartate aminotransferase to form a complex, which can then bind to malate dehydrogenase, forming a ternary complex that reverses inhibitory action on malate dehydrogenase enzymatic activity by glutamate. Additionally, the formation of this complex enables glutamate to react with aminotransferase without interfering activity of malate dehydrogenase. The formation of this ternary complex also facilitates the release of oxaloacetate from malate dehydrogenase to aminotransferase. Kinetically, the binding of malate dehydrogenase to the binary complex of alpha ketoglutarate dehydrogenase and aminotrannferase has been shown to increase reaction rate of malate dehydrogenase because the Km of malate dehydrogenase is decreased when it is bound as part of this complex.<ref>{{cite journal | vauthors = Fahien LA, Kmiotek EH, MacDonald MJ, Fibich B, Mandic M | title = Regulation of malate dehydrogenase activity by glutamate, citrate, alpha-ketoglutarate, and multienzyme interaction | journal = The Journal of Biological Chemistry | volume = 263 | issue = 22 | pages = 10687–97 | date = August 1988 | doi = 10.1016/S0021-9258(18)38026-8 | pmid = 2899080 | url = http://www.jbc.org/content/263/22/10687.full.pdf | doi-access = free }}</ref>

== Interactive pathway map ==
{{GlycolysisGluconeogenesis_WP534|highlight=Malate_dehydrogenase}}

== References ==
{{reflist|33em}}

== Further reading ==
{{refbegin|33em}}
* {{cite journal | vauthors = Guha A, Englard S, Listowsky I | title = Beef heart malic dehydrogenases. VII. Reactivity of sulfhydryl groups and conformation of the supernatant enzyme | journal = The Journal of Biological Chemistry | volume = 243 | issue = 3 | pages = 609–15 | date = February 1968 | doi = 10.1016/S0021-9258(18)93648-3 | pmid = 5637713 | doi-access = free }}
* {{cite journal | vauthors = McReynolds MS, Kitto GB | title = Purification and properties of Drosophila malate dehydrogenases | journal = Biochimica et Biophysica Acta (BBA) - Enzymology | volume = 198 | issue = 2 | pages = 165–75 | date = February 1970 | pmid = 4313528 | doi = 10.1016/0005-2744(70)90048-3 }}
* {{cite journal | vauthors = Wolfe RG, Neilands JB | title = Some molecular and kinetic properties of heart malic dehydrogenase | journal = The Journal of Biological Chemistry | volume = 221 | issue = 1 | pages = 61–9 | date = July 1956 | doi = 10.1016/S0021-9258(18)65228-7 | pmid = 13345798 | doi-access = free }}

{{refend}}

== External links ==

* {{MeSH name|Malate+dehydrogenase}}

{{Alcohol oxidoreductases}}
{{Citric acid cycle enzymes}}
{{Mitochondrial enzymes}}
{{Enzymes}}
{{Portal bar|Biology|border=no}}

{{DEFAULTSORT:Malate Dehydrogenase}}
[[Category:EC 1.1.1]]
[[Category:Enzymes of known structure]]
[[Category:Cellular respiration]]