Pyruvate dehydrogenase

From Wikipedia, the free encyclopedia
Jump to: navigation, search
This article is about the enzyme that precedes the citric acid cycle. For the enzyme that forms acetaldehyde, see pyruvate decarboxylase.
pyruvate dehydrogenase (acetyl-transferring)
PDwhole1.jpg
Crystallographic structure of pyruvate dehydrogenase (PDH). PH is a six domain dimer with α (blue), α’ (yellow), β (red), and β’ (teal) regions denoted by the different colors. Thiamine pyrophosphate (TPP) is shown in grey ball and stick form, two magnesium ions in purple undergoing metal ligation with the TPP, and two potassium ions in orange.[1][2]
Identifiers
EC number 1.2.4.1
CAS number 9014-20-4
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

Pyruvate dehydrogenase (E1) is the first component enzyme of pyruvate dehydrogenase complex (PDC). The pyruvate dehydrogenase complex contributes to transforming pyruvate into acetyl-CoA by a process called pyruvate decarboxylation. Acetyl-CoA may then be used in the citric acid cycle to carry out cellular respiration, so pyruvate dehydrogenase contributes to linking the glycolysis metabolic pathway to the citric acid cycle and releasing energy via NADH.

Function[edit]

Pyruvate dehydrogenase (E1) performs the first two reactions within the pyruvate dehydrogenase complex (PDC): a decarboxylation of substrate 1 (pyruvate) and a reductive acetylation of substrate 2 (lipoic acid). Lipoic acid is covalently bound to dihydrolipoamide acetyltransferase (E2), which is the second catalytic component enzyme of PDC. The reaction catalyzed by pyruvate dehydrogenase (E1) is considered to be the rate-limiting step for the pyruvate dehydrogenase complex (PDHc).

Regulation[edit]

Phosphorylation of E1 by pyruvate dehydrogenase kinase (PDK) inactivates E1 and subsequently the entire complex. This is reversed by pyruvate dehydrogenase phosphatase. Pyruvate dehydrogenase phosphatase is stimulated by insulin, PEP, and AMP, but competitively inhibited by ATP, NADH, and Acetyl-CoA.

Regulation of Pyruvate Dehydrogenase

Mechanism[edit]

Pyruvate Dehydrogenase Mechanism

The ylide resonance form of thiamine pyrophosphate (TPP) begins by attacking the electrophilic ketone of pyruvate. The intermediate β-alkoxide then decarboxylates and the resulting enol is deprotonated on the carbon atom to form a stabilized 1,3-dipole involving a positively charged nitrogen atom of the thiamine heterocycle. This 1,3-dipole undergoes a reductive acetylation with lipoamide-E2.

Biochemical and structural data for E1 revealed a mechanism of activation of TPP cofactor by forming the conserved hydrogen bond with glutamate residue (Glu59 in human E1) and by imposing a V-conformation that brings the N4’ atom of the aminopyrimidine to intramolecular hydrogen bonding with the thiazolium C2 atom. This unique combination of contacts and conformations of TPP leads to formation of the reactive C2-carbanion, eventually. After the cofactor TPP decarboxylates pyruvate, the acetyl portion becomes a hydroxyethyl derivative covalently attached to TPP.[1]

Structure[edit]

E1 is a multimeric protein. Mammalian E1s, including human E1, are tetrameric, composed of two α- and two β- subunits.[1] Some bacterial E1s, including E1 from Escherichia coli, are composed of two similar subunits, each being as large as the sum of molecular masses of α- and β- subunits.[3]

Pyruvate dehydrogenase E1 subunit of E. coli. Colors represent different chains. Structure determined by Arjunan et al. Biochemistry 2002. Created with PyMol.

Active site[edit]

PDActiveSite2.jpg

E1 has two catalytic sites, each providing thiamine pyrophosphate (TPP) and magnesium ion as cofactors. The α- subunit binds magnesium ion and pyrophosphate fragment while the β-subunit binds pyrimidine fragment of TPP, forming together a catalytic site at the interface of subunits. [1]

The active site for pyruvate dehydrogenase (image created from PDB 1NI4) holds TPP through metal ligation to a magnesium ion (purple sphere) and through hydrogen bonding to amino acids. While over 20 amino acids can be found in the active site, amino acids Tyr 89, Arg 90, Gly 136, Val 138, Asp 167, Gly 168, Ala 169, Asn, 196, and His 263 actually participate in hydrogen bonding to hold TPP and pyruvate (not shown here) in the active site. The amino acids are shown as wires, and the TPP is in ball and stick form. The active site also aids in the transfer of the acyl on the TPP to a lipoamide waiting on E2.[1][2]

Pathology[edit]

Pyruvate dehydrogenase is an autoantigen recognized in primary biliary cirrhosis. These antibodies appear to recognize oxidized protein that has resulted from inflammatory immune responses. Some of these inflammatory responses could be related to gluten sensitivity as over 50% of the acute liver failure patients in one study exhibited a nonmitochondrial autoantibody against tissue transglutaminase.[4] Other mitochondrial autoantigens include oxoglutarate dehydrogenase and branched-chain alpha-keto acid dehydrogenase complex, which are antigens recognized by anti-mitochondrial antibodies.

Pyruvate dehydrogenase (PDH) deficiency is a congenital degenerative metabolic disease resulting from a mutation of the pyruvate dehydrogenase complex (PDC) located on the X chromosome. While defects have been identified in all 3 enzymes of the complex, the E1-α subunit is predominantly the culprit. Malfunction of the citric acid cycle due to PDH deficiency deprives the body of energy and leads to an abnormal buildup of lactate. PDH deficiency is a common cause of lactic acidosis in newborns and often presents with severe lethargy, poor feeding, tachypnea, and cases of death have occurred.[5]

Examples[edit]

Human proteins that possess pyruvate dehydrogenase activity include:

Pyruvate dehydrogenase (lipoamide) alpha 1
Identifiers
Symbol PDHA1
Alt. symbols PDHA
Entrez 5160
HUGO 8806
OMIM 300502
RefSeq NM_000284
UniProt P08559
Other data
EC number 1.2.4.1
Locus Chr. X p22.1
pyruvate dehydrogenase (lipoamide) alpha 2
Identifiers
Symbol PDHA2
Alt. symbols PDHAL
Entrez 5161
HUGO 8807
OMIM 179061
RefSeq NM_005390
UniProt P29803
Other data
EC number 1.2.4.1
Locus Chr. 4 q22-q23
pyruvate dehydrogenase (lipoamide) beta
Identifiers
Symbol PDHB
Alt. symbols PHE1B
Entrez 5162
HUGO 8808
OMIM 179060
RefSeq NM_000925
UniProt P11177
Other data
EC number 1.2.4.1
Locus Chr. 3 p21.1-14.2

Related enzymes[edit]

In bacteria, a form of pyruvate dehydrogenase (also called pyruvate oxidase, EC 1.2.2.2) exists that links the oxidation of pyruvate into acetate and carbon dioxide to the reduction of ferrocytochrome. In E. coli this enzyme is encoded by the pox B gene and the protein has a flavin cofactor.[6] This enzyme increases the efficiency of growth of E. coli under aerobic conditions.[7]

See also[edit]

References[edit]

  1. ^ a b c d e PDB 1ni4; Ciszak EM, Korotchkina LG, Dominiak PM, Sidhu S, Patel MS (June 2003). "Structural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase". J. Biol. Chem. 278 (23): 21240–6. doi:10.1074/jbc.M300339200. PMID 12651851. 
  2. ^ a b Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco; Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (October 2004). "UCSF Chimera—a visualization system for exploratory research and analysis". J Comput Chem 25 (13): 1605–12. doi:10.1002/jcc.20084. PMID 15264254. 
  3. ^ Arjunan P, Nemeria N, Brunskill A, Chandrasekhar K, Sax M, Yan Y, Jordan F, Guest JR, Furey W. (2002). "Structure of the pyruvate dehydrogenase multienzyme complex E1 component from Escherichia coli at 1.85 A resolution". Biochemistry 41 (16): 5213–21. doi:10.1021/bi0118557. PMID 11955070. 
  4. ^ Leung PS, Rossaro L, Davis PA, et al. (2007). "Antimitochondrial antibodies in acute liver failure: Implications for primary biliary cirrhosis". Hepatology 46 (5): 1436–42. doi:10.1002/hep.21828. PMC 3731127. PMID 17657817. 
  5. ^ Frye, Richard E., and Paul J. Benke. "Pyruvate Dehydrogenase Complex Deficiency." EMedicine. 11 Dec. 2007. WebMD. 14 Dec. 2008 <http://emedicine.medscape.com/article/948360-overview>.
  6. ^ Recny MA, Hager LP (1982). "Reconstitution of native Escherichia coli pyruvate oxidase from apoenzyme monomers and FAD". J. Biol. Chem. 257 (21): 12878–86. PMID 6752142. 
  7. ^ Abdel-Hamid AM, Attwood MM, Guest JR (2001). "Pyruvate oxidase contributes to the aerobic growth efficiency of Escherichia coli". Microbiology (Reading, Engl.) 147 (Pt 6): 1483–98. PMID 11390679. 

External links[edit]