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2  structures 200  species 1  interaction 212  sequences 2  architectures

Family: Lact-deh-memb (PF09330)

Summary: D-lactate dehydrogenase, membrane binding

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This is the Wikipedia entry entitled "Lactate dehydrogenase". More...

Lactate dehydrogenase Edit Wikipedia article

Lactate dehydrogenase
1i10.jpg
Lactate dehydrogenase M tetramer (LDH5), Human
Identifiers
EC number 1.1.1.27
CAS number 9001-60-9
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO

Lactate dehydrogenase (LDH or LD) is an enzyme found in nearly all living cells (animals, plants, and prokaryotes). LDH catalyzes the conversion of lactate to pyruvic acid and back, as it converts NAD+ to NADH and back. A dehydrogenase is an enzyme that transfers a hydride from one molecule to another.

LDH exist in four distinct enzyme classes. This article is specifically about the NAD(P)-dependent L-lactate dehydrogenase. Other LDHs act on D-lactate and/or are dependent on cytochrome c: D-lactate dehydrogenase (cytochrome)) and L-lactate (L-lactate dehydrogenase (cytochrome)).

LDH is expressed extensively in body tissues, such as blood cells and heart muscle. Because it is released during tissue damage, it is a marker of common injuries and disease such as heart failure.

Reaction

Lactate dehydrogenase catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of NADH and NAD+. It converts pyruvate, the final product of glycolysis, to lactate when oxygen is absent or in short supply, and it performs the reverse reaction during the Cori cycle in the liver. At high concentrations of lactate, the enzyme exhibits feedback inhibition, and the rate of conversion of pyruvate to lactate is decreased. It also catalyzes the dehydrogenation of 2-Hydroxybutyrate, but it is a much poorer substrate than lactate.

Reaction catalyzed by lactate dehydrogenase
Arrow pushing mechanism for the reaction catalyzed by lactate dehydrogenase

Active site

LDH in humans uses His(193) as the proton acceptor, and works in unison with the coenzyme (Arg99 and Asn138), and substrate (Arg106; Arg169; Thr248) binding residues.[1] The His(193) active site, is not only found in the human form of LDH, but is found in many different animals, showing the convergent evolution of LDH. The two different subunits of LDH: LDHA also known as the M subunit of LDH, and LDHB also known as the H subunit of LDH both retain the same active site, and the same amino acids participating in the reaction. The noticeable difference between the two subunits that make up LDH's tertiary structure is the replacement of alanine (in the M chain) with a glutamine (in the H chain). This tiny but notable change is believed to be the reason the H subunit can bind faster, and the M subunit's catalytic activity isn't reduced when subjected to the same conditions as the H subunit; while the H subunits activity is reduced fivefold.[2]

Isozymes

Lactate dehydrogenase is composed of four subunits (tetramer). The two most common subunits are the LDH-M and LDH-H protein, encoded by the LDHA and LDHB genes, respectively. These two subunits can form five possible tetramers (isoenzymes): 4H, 4M, and the three mixed tetramers (3H1M, 2H2M, 1H3M). These five isoforms are enzymatically similar but show different tissue distribution: The major isoenzymes of skeletal muscle and liver, M4, has four muscle (M) subunits, while H4 is the main isoenzymes for heart muscle in most species, containing four heart (H) subunits.

Usually LDH-2 is the predominant form in the serum. A LDH-1 level higher than the LDH-2 level (a "flipped pattern") suggests myocardial infarction (damage to heart tissues releases heart LDH, which is rich in LDH-1, into the bloodstream). The use of this phenomenon to diagnose infarction has been largely superseded by the use of Troponin I or T measurement.[citation needed]

There are two more mammalian LDH subunits that can be included in LDH tetramers: LDHC and LDHBx. LDHC is a testes-specific LDH protein, that is encoded by the LDHC gene. LDHBx is a peroxisome-specific LDH protein. LDHBx is the readthrough-form of LDHB. LDHBx is generated by translation of the LDHB mRNA, but the stop codon is interpreted as an amino acid-encoding codon. In consequence, translation continues to the next stop codon. This leads to the addition of seven amino acid acids to the normal LDH-H protein. The extension contains a peroxisomal targeting signal, so that LDHBx is imported into the peroxisome.[4]

Protein families

The family also contains L-lactate dehydrogenases that catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. Malate dehydrogenases that catalyse the interconversion of malate to oxaloacetate and participate in the citric acid cycle, and L-2-hydroxyisocaproate dehydrogenases are also members of the family. The N-terminus is a Rossmann NAD-binding fold and the C-terminus is an unusual alpha+beta fold.[5][6]

Interactive pathway map

Click on genes, proteins and metabolites below to link to respective articles. [§ 1]

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GlycolysisGluconeogenesis_WP534 go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to article go to Entrez go to article go to article go to article go to article go to article go to WikiPathways go to article go to Entrez go to article
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Glycolysis and Gluconeogenesis edit
  1. ^ The interactive pathway map can be edited at WikiPathways: "GlycolysisGluconeogenesis_WP534". 

Enzyme regulation

This protein may use the morpheein model of allosteric regulation.[7]

Ethanol-induced hypoglycemia

Ethanol is dehydrogenated to acetaldehyde by alcohol dehydrogenase, and further into acetic acid by acetaldehyde dehydrogenase. During this reaction 2 NADH are produced. If large amounts of ethanol are present, then large amounts of NADH are produced, leading to a depletion of NAD+. Thus, the conversion of pyruvate to lactate is increased due to the associated regeneration of NAD+. Therefore, anion-gap metabolic acidosis (lactic acidosis) may ensue in ethanol poisoning.

The increased NADH/NAD+ ratio also can cause hypoglycemia in an (otherwise) fasting individual who has been drinking and is dependent on gluconeogenesis to maintain blood glucose levels. Alanine and lactate are major gluconeogenic precursors that enter gluconeogenesis as pyruvate. The high NADH/NAD+ ratio shifts the lactate dehydrogenase equilibrium to lactate, so that less pyruvate can be formed and, therefore, gluconeogenesis is impaired.

Substrate regulation

LDH is also regulated by the relative concentrations of its substrates. LDH becomes more active under periods of extreme muscular output due to an increase in substrates for the LDH reaction. When skeletal muscles are pushed to produce high levels of power, the demand for ATP in regards to aerobic ATP supply leads to an accumulation of free ADP, AMP, and Pi. The subsequent glycolytic flux, specifically production of NADH and pyruvate, exceeds the capacity for pyruvate dehydrogenase and other shuttle enzymes to metabolize pyruvate. The flux through LDH increases in response to increased levels of pyruvate and NADH to metabolize pyruvate into lactate.[8]

Transcriptional regulation

LDH undergoes transcriptional regulation by PGC-1α. PGC-1α regulates LDH by decreasing LDH A mRNA transcription and the enzymatic activity of pyruvate to lactate conversion.[9]

Genetics

The M and H subunits are encoded by two different genes:

Mutations of the M subunit have been linked to the rare disease exertional myoglobinuria (see OMIM article), and mutations of the H subunit have been described but do not appear to lead to disease.

Mutations

This is a mutant version of the LDH-5 enzyme, which is usually found in skeletal muscle

In rare cases, a mutation in the genes controlling the production of lactate dehydrogenase will lead to a medical condition known as lactate dehydrogenase deficiency. Depending on which gene carries the mutation, one of two types will occur: either lactate dehydrogenase-A deficiency (also known as glycogen storage disease XI) or lactate dehydrogenase-B deficiency. Both of these conditions affect how the body breaks down sugars, primarily in certain muscle cells. Lactate dehydrogenase-A deficiency is caused by a mutation to the LDHA gene, while lactate dehydrogenase-B deficiency is caused by a mutation to the LDHB gene.[10]

This condition is inherited in an autosomal recessive pattern, meaning that both parents must contribute a mutated gene in order for this condition to be expressed.[11]

A complete lactate dehydrogenase enzyme consists of four protein subunits.[12] Since the two most common subunits found in lactate dehydrogenase are encoded by the LDHA and LDHB genes, either variation of this disease causes abnormalities in many of the lactate dehydrogenase enzymes found in the body. In the case of lactate dehydrogenase-A deficiency, mutations to the LDHA gene results in the production of an abnormal lactate dehydrogenase-A subunit that cannot bind to the other subunits to form the complete enzyme. This lack of a functional subunit reduces the amount of enzyme formed, leading to an overall decrease in activity. During the anaerobic phase of glycolysis (the Cori Cycle), the mutated enzyme is unable to convert pyruvate into lactate to produce the extra energy the cells need. Since this subunit has the highest concentration in the LDH enzymes found in the skeletal muscles (which are the primary muscles responsible for movement), high-intensity physical activity will lead to an insufficient amount of energy being produced during this anaerobic phase.[13] This in turn will cause the muscle tissue to weaken and eventually break down, a condition known as rhabdomyolysis. The process of rhabdomyolysis also releases myoglobin into the blood, which will eventually end up in the urine and cause it to become red or brown: another condition known as myoglobinuria.[14] Some other common symptoms are exercise intolerance, which consists of fatigue, muscle pain, and cramps during exercise, and skin rashes.[15][16] In severe cases, myoglobinuria can damage the kidneys and lead to life-threatening kidney failure.[17] In order to obtain a definitive diagnosis, a muscle biopsy may be performed to confirm low or absent LDH activity. There is currently no specific treatment for this condition.

In the case of lactate dehydrogenase-B deficiency, mutations to the LDHB gene results in the production of an abnormal lactate dehydrogenase-B subunit that cannot bind to the other subunits to form the complete enzyme. As with lactate dehydrogenase-A deficiency, this mutation reduces the overall effectiveness in the enzyme.[18] However, there are some major differences between these two cases. The first is the location where the condition manifests itself. With lactate dehydrogenase-B deficiency, the highest concentration of B subunits can be found within cardiac muscle, or the heart. Within the heart, lactate dehydrogenase plays the role of converting lactate back into pyruvate so that the pyruvate can be used again to create more energy.[19] With the mutated enzyme, the overall rate of this conversion is decreased. However, unlike lactate dehydrogenase-A deficiency, this mutation does not appear to cause any symptoms or health problems linked to this condition.[16][20] At the present moment, it is unclear why this is the case. Affected individuals are usually discovered only when routine blood tests indicate low LDH levels present within the blood.

Role in muscular fatigue

The onset of acidosis during periods of intense exercise is commonly been attributed to accumulation of lactic acid. From this reasoning, the idea of lactate production being a primary cause of muscle fatigue during exercise has been widely adopted. A closer, mechanistic analysis of lactate production under anaerobic conditions shows that there is no biochemical evidence for the production of lactate through LDH contributing to acidosis. While LDH activity is correlated to muscle fatigue,[21] the production of lactate by means of the LDH complex works as a system to delay the onset of muscle fatigue.

LDH works to prevent muscular failure and fatigue in multiple ways. The lactate-forming reaction generates cytosolic NAD+, which feeds into the glyceraldehyde 3-phosphate dehydrogenase reaction to help maintain cytosolic redox potential and promote substrate flux through the second phase of glycolysis to promote ATP generation. This, in effect, provides more energy to contracting muscles under heavy workloads. The production and removal of lactate from the cell also ejects a proton consumed in the LDH reaction- the removal of excess protons produced in the wake of this fermentation reaction serves to act as a buffer system for muscle acidosis. Once proton accumulation exceeds the rate of uptake in lactate production and removal through the LDH symport,[22] muscular acidosis occurs.

Medical relevance

LDH is a protein that normally appears throughout the body in small amounts. Many cancers can raise LDH levels, so LDH may be used as a tumor marker, but at the same time, it is not useful in identifying a specific kind of cancer. Measuring LDH levels can be helpful in monitoring treatment for cancer. Noncancerous conditions that can raise LDH levels include heart failure, hypothyroidism, anemia, pre-eclampsia, meningitis, encephalitis, acute pancreatitis, HIV and lung or liver disease.[23]

Tissue breakdown releases LDH, and therefore LDH can be measured as a surrogate for tissue breakdown, e.g. hemolysis. LDH is measured by the lactate dehydrogenase (LDH) test (also known as the LDH test or lactic acid dehydrogenase test). Comparison of the measured LDH values with the normal range help guide diagnosis.[24]

Cancer cells

Comparison of LDH activity in normal and cancerous cells

LDH is involved in tumor initiation and metabolism. Cancer cells rely on increased glycolysis resulting in increased lactate production in addition to aerobic respiration in the mitochondria, even under oxygen-sufficient conditions (a process known as the Warburg effect[25]). This state of fermentative glycolysis is catalyzed by the A form of LDH. This mechanism allows tumorous cells to convert the majority of their glucose stores into lactate regardless of oxygen availability, shifting use of glucose metabolites from simple energy production to the promotion of accelerated cell growth and replication. For this reason, LDH A and the possibility of inhibiting its activity has been identified as a promising target in cancer treatments focused on preventing carcinogenic cells from proliferating.

Chemical inhibition of LDH A has demonstrated marked changes in metabolic processes and overall survival carcinoma cells. Oxamate is a cytosolic inhibitor of LDH A that significantly decreases ATP production in tumorous cells as well as increasing production of reactive oxygen species (ROS). These ROS drive cancer cell proliferation by activating kinases that drive cell cycle progression growth factors at low concentrations,[26] but can damage DNA through oxidative stress at higher concentrations. Secondary lipid oxidation products can also inactivate LDH and impact its ability to regenerate NADH,[27] directly disrupting the enzymes ability to convert lactate to pyruvate.

While recent studies have shown that LDH activity is not necessarily an indicator of metastatic risk,[28] LDH expression can act as a general marker in the prognosis of cancers. Expression of LDH5 and VEGF in tumors and the stroma has been found to be a strong prognostic factor for diffuse or mixed-type gastric cancers.[29]

Hemolysis

In medicine, LDH is often used as a marker of tissue breakdown as LDH is abundant in red blood cells and can function as a marker for hemolysis. A blood sample that has been handled incorrectly can show false-positively high levels of LDH due to erythrocyte damage.

It can also be used as a marker of myocardial infarction. Following a myocardial infarction, levels of LDH peak at 3–4 days and remain elevated for up to 10 days. In this way, elevated levels of LDH (where the level of LDH1 is higher than that of LDH2, i.e. the LDH Flip, as normally, in serum, LDH2 is higher than LDH1) can be useful for determining whether a patient has had a myocardial infarction if they come to doctors several days after an episode of chest pain.

Tissue turnover

Other uses are assessment of tissue breakdown in general; this is possible when there are no other indicators of hemolysis. It is used to follow up cancer (especially lymphoma) patients, as cancer cells have a high rate of turnover, with destroyed cells leading to an elevated LDH activity.

Exudates and transudates

Measuring LDH in fluid aspirated from a pleural effusion (or pericardial effusion) can help in the distinction between exudates (actively secreted fluid, e.g. due to inflammation) or transudates (passively secreted fluid, due to a high hydrostatic pressure or a low oncotic pressure). The usual criterion (included in Light's criteria) is that a ratio of fluid LDH versus upper limit of normal serum LDH of more than 0.6[30] or 23[31] indicates an exudate, while a ratio of less indicates a transudate. Different laboratories have different values for the upper limit of serum LDH, but examples include 200[32] and 300[32] IU/L.[33] In empyema, the LDH levels, in general, will exceed 1000 IU/L.

Meningitis and encephalitis

High levels of lactate dehydrogenase in cerebrospinal fluid are often associated with bacterial meningitis.[34] In the case of viral meningitis, high LDH, in general, indicates the presence of encephalitis and poor prognosis.

HIV

LDH is often measured in HIV patients as a non-specific marker for pneumonia due to Pneumocystis jirovecii (PCP). Elevated LDH in the setting of upper respiratory symptoms in an HIV patient suggests, but is not diagnostic for, PCP. However, in HIV-positive patients with respiratory symptoms, a very high LDH level (>600 IU/L) indicated histoplasmosis (9.33 more likely) in a study of 120 PCP and 30 histoplasmosis patients.[35]

Dysgerminoma

Elevated LDH can be an early clinical sign of a rare malignant cell tumor called a dysgerminoma. Not all dysgerminomas produce LDH, and this is often a non-specific finding.

Prokaryotes

A cap-membrane-binding domain is found in prokaryotic lactate dehydrogenase. This consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. It allows for membrane association.[36]

See also

References

This article incorporates text from the public domain Pfam and InterPro IPR015409

  1. ^ Holmes RS, Goldberg E (Oct 2009). "Computational analyses of mammalian lactate dehydrogenases: human, mouse, opossum and platypus LDHs". Computational Biology and Chemistry. 33 (5): 379–85. doi:10.1016/j.compbiolchem.2009.07.006. PMC 2777655Freely accessible. PMID 19679512. 
  2. ^ Eventoff W, Rossmann MG, Taylor SS, Torff HJ, Meyer H, Keil W, Kiltz HH (Jul 1977). "Structural adaptations of lactate dehydrogenase isozymes" (PDF). Proceedings of the National Academy of Sciences of the United States of America. 74 (7): 2677–81. doi:10.1073/pnas.74.7.2677. PMC 431242Freely accessible. PMID 197516. 
  3. ^ Van Eerd JP, Kreutzer EK (1996). Klinische Chemie voor Analisten deel 2. pp. 138–139. ISBN 978-90-313-2003-5. 
  4. ^ a b Schueren F, Lingner T, George R, Hofhuis J, Gartner J, Thoms S (2014). "Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals". eLife. 3: e03640. doi:10.7554/eLife.03640. PMID 25247702. 
  5. ^ Chapman AD, Cortés A, Dafforn TR, Clarke AR, Brady RL (1999). "Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD.". J Mol Biol. 285 (2): 703–12. doi:10.1006/jmbi.1998.2357. PMID 10075524. 
  6. ^ Madern D (2002). "Molecular evolution within the L-malate and L-lactate dehydrogenase super-family.". J Mol Evol. 54 (6): 825–40. doi:10.1007/s00239-001-0088-8. PMID 12029364. 
  7. ^ Selwood T, Jaffe EK (March 2012). "Dynamic dissociating homo-oligomers and the control of protein function". Arch. Biochem. Biophys. 519 (2): 131–43. doi:10.1016/j.abb.2011.11.020. PMC 3298769Freely accessible. PMID 22182754. 
  8. ^ Spriet LL, Howlett RA, Heigenhauser GJ (2000). "An enzymatic approach to lactate production in human skeletal muscle during exercise.". Med Sci Sports Exerc. 32 (4): 756–63. doi:10.1097/00005768-200004000-00007. PMID 10776894. 
  9. ^ Summermatter S, Santos G, Pérez-Schindler J, Handschin C (2013). "Skeletal muscle PGC-1α controls whole-body lactate homeostasis through estrogen-related receptor α-dependent activation of LDH B and repression of LDH A.". Proc Natl Acad Sci U S A. 110 (21): 8738–43. doi:10.1073/pnas.1212976110. PMC 3666691Freely accessible. PMID 23650363. 
  10. ^ "Lactate dehydrogenase deficiency". Genetics Home Reference. 2016-02-29. Retrieved 2016-03-02. 
  11. ^ "Diseases - Metabolic Diseases - Causes/Inheritance". Muscular Dystrophy Association. Retrieved 2016-03-02. 
  12. ^ Millar DB, Frattali V, Willick GE (Jun 1969). "The quaternary structure of lactate dehydrogenase. I. The subunit molecular weight and the reversible association at acid pH". Biochemistry. 8 (6): 2416–21. doi:10.1021/bi00834a025. PMID 5816379. 
  13. ^ Kanno T, Sudo K, Maekawa M, Nishimura Y, Ukita M, Fukutake K (Mar 1988). "Lactate dehydrogenase M-subunit deficiency: a new type of hereditary exertional myopathy". Clinica Chimica Acta; International Journal of Clinical Chemistry. 173 (1): 89–98. doi:10.1016/0009-8981(88)90359-2. PMID 3383424. 
  14. ^ "Myoglobinuria; Rhabdomyolysis". neuromuscular.wustl.edu. Retrieved 2016-03-02. 
  15. ^ Hoffmann GF (2002-01-01). Inherited Metabolic Diseases. Lippincott Williams & Wilkins. ISBN 9780781729000. 
  16. ^ a b "Glycogenoses". neuromuscular.wustl.edu. Retrieved 2016-03-02. 
  17. ^ "Glycogen storage disease XI - Conditions - GTR - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2016-03-02. 
  18. ^ "LDHB gene". Genetics Home Reference. 2016-02-29. Retrieved 2016-03-02. 
  19. ^ "Lactate Dehydrogenase - Worthington Enzyme Manual". www.worthington-biochem.com. Retrieved 2016-03-02. 
  20. ^ "OMIM Entry # 614128 - LACTATE DEHYDROGENASE B DEFICIENCY; LDHBD". www.omim.org. Retrieved 2016-03-02. 
  21. ^ Tesch P, Sjödin B, Thorstensson A, Karlsson J (1978). "Muscle fatigue and its relation to lactate accumulation and LDH activity in man.". Acta Physiol Scand. 103 (4): 413–20. doi:10.1111/j.1748-1716.1978.tb06235.x. PMID 716962. 
  22. ^ Juel C, Klarskov C, Nielsen JJ, Krustrup P, Mohr M, Bangsbo J (2004). "Effect of high-intensity intermittent training on lactate and H+ release from human skeletal muscle.". Am J Physiol Endocrinol Metab. 286 (2): E245–51. doi:10.1152/ajpendo.00303.2003. PMID 14559724. 
  23. ^ Stanford Cancer Center. "Cancer Diagnosis - Understanding Cancer". Understanding Cancer. Stanford Medicine. 
  24. ^ "Lactate dehydrogenase test: MedlinePlus Medical Encyclopedia". MedlinePlus. U.S. National Library of Medicine. 
  25. ^ Warburg O (1956). "On the origin of cancer cells.". Science. 123 (3191): 309–14. doi:10.1126/science.123.3191.309. PMID 13298683. 
  26. ^ Irani K, Xia Y, Zweier JL, Sollott SJ, Der CJ, Fearon ER, Sundaresan M, Finkel T, Goldschmidt-Clermont PJ (1997). "Mitogenic signaling mediated by oxidants in Ras-transformed fibroblasts.". Science. 275 (5306): 1649–52. doi:10.1126/science.275.5306.1649. PMID 9054359. 
  27. ^ Ramanathan R, Mancini RA, Suman SP, Beach CM (2014). "Covalent Binding of 4-Hydroxy-2-nonenal to Lactate Dehydrogenase Decreases NADH Formation and Metmyoglobin Reducing Activity.". J Agric Food Chem. 62 (9): 2112–7. doi:10.1021/jf404900y. PMID 24552270. 
  28. ^ Xu HN, Kadlececk S, Profka H, Glickson JD, Rizi R, Li LZ (2014). "Is Higher Lactate an Indicator of Tumor Metastatic Risk? A Pilot MRS Study Using Hyperpolarized (13)C-Pyruvate.". Acad Radiol. 21 (2): 223–31. doi:10.1016/j.acra.2013.11.014. PMID 24439336. 
  29. ^ Kim HS, Lee HE, Yang HK, Kim WH (2014). "High lactate dehydrogenase 5 expression correlates with high tumoral and stromal vascular endothelial growth factor expression in gastric cancer.". Pathobiology. 81 (2): 78–85. doi:10.1159/000357017. PMID 24401755. 
  30. ^ Heffner JE, Brown LK, Barbieri CA (April 1997). "Diagnostic value of tests that discriminate between exudative and transudative pleural effusions. Primary Study Investigators". Chest. 111 (4): 970–80. doi:10.1378/chest.111.4.970. PMID 9106577. 
  31. ^ Light RW, Macgregor MI, Luchsinger PC, Ball WC (October 1972). "Pleural effusions: the diagnostic separation of transudates and exudates". Ann. Intern. Med. 77 (4): 507–13. doi:10.7326/0003-4819-77-4-507. PMID 4642731. 
  32. ^ a b Joseph J, Badrinath P, Basran GS, Sahn SA (November 2001). "Is the pleural fluid transudate or exudate? A revisit of the diagnostic criteria". Thorax. 56 (11): 867–70. doi:10.1136/thorax.56.11.867. PMC 1745948Freely accessible. PMID 11641512. 
  33. ^ Joseph J, Badrinath P, Basran GS, Sahn SA (March 2002). "Is albumin gradient or fluid to serum albumin ratio better than the pleural fluid lactate dehydroginase in the diagnostic of separation of pleural effusion?". BMC Pulm Med. 2: 1. doi:10.1186/1471-2466-2-1. PMC 101409Freely accessible. PMID 11914151. 
  34. ^ Stein JH (1998). Internal Medicine. Elsevier Health Sciences. pp. 1408–. ISBN 978-0-8151-8698-4. Retrieved 12 August 2013. 
  35. ^ Butt AA, Michaels S, Greer D, Clark R, Kissinger P, Martin DH (July 2002). "Serum LDH level as a clue to the diagnosis of histoplasmosis". AIDS Read. 12 (7): 317–21. PMID 12161854. 
  36. ^ Dym O, Pratt EA, Ho C, Eisenberg D (August 2000). "The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme". Proc. Natl. Acad. Sci. U.S.A. 97 (17): 9413–8. doi:10.1073/pnas.97.17.9413. PMC 16878Freely accessible. PMID 10944213. 

Further reading

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

D-lactate dehydrogenase, membrane binding Provide feedback

Members of this family are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for membrane association [1].

Literature references

  1. Dym O, Pratt EA, Ho C, Eisenberg D; , Proc Natl Acad Sci U S A. 2000;97:9413-9418.: The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme. PUBMED:10944213 EPMC:10944213


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015409

Members of this entry are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for membrane association [PUBMED:10944213].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan FAD-oxidase_C (CL0277), which has the following description:

This clan consists of a duplicated subdomain in a variety of FAD-liked oxidase/dehydrogenase enzymes.

The clan contains the following 6 members:

ALO BBE Chol_subst-bind Cytokin-bind FAD-oxidase_C Lact-deh-memb

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(73)
Full
(212)
Representative proteomes UniProt
(1933)
NCBI
(3087)
Meta
(215)
RP15
(23)
RP35
(102)
RP55
(277)
RP75
(638)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(73)
Full
(212)
Representative proteomes UniProt
(1933)
NCBI
(3087)
Meta
(215)
RP15
(23)
RP35
(102)
RP55
(277)
RP75
(638)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(73)
Full
(212)
Representative proteomes UniProt
(1933)
NCBI
(3087)
Meta
(215)
RP15
(23)
RP35
(102)
RP55
(277)
RP75
(638)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: pdb_1f0x
Previous IDs: none
Type: Domain
Author: Sammut SJ
Number in seed: 73
Number in full: 212
Average length of the domain: 283.40 aa
Average identity of full alignment: 55 %
Average coverage of the sequence by the domain: 50.94 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 27.2 25.7
Noise cut-off 24.5 23.9
Model length: 290
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There is 1 interaction for this family. More...

FAD_binding_4

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Lact-deh-memb domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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