Pyruvate, phosphate dikinase

The systematic name of this enzyme class is ATP:pyruvate, phosphate phosphotransferase. Other names in common use include pyruvate, orthophosphate dikinase, pyruvate-phosphate dikinase (phosphorylating), pyruvate phosphate dikinase, pyruvate-inorganic phosphate dikinase, pyruvate-phosphate dikinase, pyruvate-phosphate ligase, pyruvic-phosphate dikinase, pyruvic-phosphate ligase, pyruvate, Pi dikinase, and PPDK.

PPDK catalyses the conversion of pyruvate to phosphoenolpyruvate (PEP), consuming 1 molecule of ATP, and producing one molecule of AMP in the process. The mechanism consists of 3 reversible reactions:{{cite journal | vauthors = Evans HJ, Wood HG | title = The mechanism of the pyruvate, phosphate dikinase reaction | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 61 | issue = 4 | pages = 1448–53 | date = December 1968 | pmid = 4303480 | pmc = 225276 | doi = 10.1073/pnas.61.4.1448 | bibcode = 1968PNAS...61.1448E | doi-access = free }}

1. The enzyme PPDK binds to ATP, to produce AMP and a diphosphorylated PPDK.
2. The diphosphorylated PPDK binds to inorganic phosphate, producing diphosphate and (mono)phosphorylated PPDK.
3. Phosphorylated PPDK binds to pyruvate, producing phosphoenolpyruvate, and regenerating PPDK.

The reaction is similar to the reaction catalysed by pyruvate kinase, which also converts pyruvate to PEP.{{cite journal | vauthors = Herzberg O, Chen CC, Liu S, Tempczyk A, Howard A, Wei M, Ye D, Dunaway-Mariano D | display-authors = 6 | title = Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis | journal = Biochemistry | volume = 41 | issue = 3 | pages = 780–7 | date = January 2002 | pmid = 11790099 | doi = 10.1021/bi011799+ }} However, pyruvate kinase catalyses an irreversible reaction, and does not consume ATP. By contrast, PPDK catalyses a reversible reaction, and consumes 1 molecule of ATP for each molecule of pyruvate converted.

Currently, the details of each mechanistic step is unknown

In its active form, PPDK is a homotetramer with subunits about 95 kDa{{cite journal | vauthors = Chastain CJ, Failing CJ, Manandhar L, Zimmerman MA, Lakner MM, Nguyen TH | title = Functional evolution of C(4) pyruvate, orthophosphate dikinase | journal = Journal of Experimental Botany | volume = 62 | issue = 9 | pages = 3083–91 | date = May 2011 | pmid = 21414960 | doi = 10.1093/jxb/err058 | doi-access = free }}

There are two different reaction centres about 45 Angstroms apart, in which different substrates bind.{{cite journal | vauthors = Herzberg O, Chen CC, Kapadia G, McGuire M, Carroll LJ, Noh SJ, Dunaway-Mariano D | title = Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 93 | issue = 7 | pages = 2652–7 | date = April 1996 | pmid = 8610096 | pmc = 39685 | doi = 10.1073/pnas.93.7.2652 | bibcode = 1996PNAS...93.2652H | doi-access = free }} The nucleotide (ATP) binding site is on the N-terminus, has 240 amino acids, and a characteristic ATP-grasp. The pyruvate/PEP binding site is on the C-terminus, has 340 amino acids, and an α/β-barrel fold. There is also a central domain, which contains His455, the primary residue responsible for catalysis. His455 is the phosphoryl acceptor or donor residue. The structure of the enzyme suggests that the His455 arm undergoes a swivelling motion to shuttle a phosphoryl group between the two reaction centres.{{cite journal | vauthors = Lim K, Read RJ, Chen CC, Tempczyk A, Wei M, Ye D, Wu C, Dunaway-Mariano D, Herzberg O | display-authors = 6 | title = Swiveling domain mechanism in pyruvate phosphate dikinase | journal = Biochemistry | volume = 46 | issue = 51 | pages = 14845–53 | date = December 2007 | pmid = 18052212 | doi = 10.1021/bi701848w | citeseerx = 10.1.1.421.2653 }} During this swivelling, the central domain rotates at least 92 degrees, and translates 0.5 Angstroms.{{cite journal | vauthors = Nakanishi T, Nakatsu T, Matsuoka M, Sakata K, Kato H | title = Crystal structures of pyruvate phosphate dikinase from maize revealed an alternative conformation in the swiveling-domain motion | journal = Biochemistry | volume = 44 | issue = 4 | pages = 1136–44 | date = February 2005 | pmid = 15667207 | doi = 10.1021/bi0484522 }}

Studies of crystal structures of PPDK show that the central domain is located in different proximity to the two other domains depending on the source of the enzyme. In maize, it is closer to the C-terminal, while in Clostridium symbiosum, it is closer to the N-terminal.

Research has shown that the PPDK binding mechanisms are similar to that of D-Ala-D-Ala ligase and pyruvate kinase. In particular, PPDK is very similar to pyruvate kinase, which also catalyses the conversion of pyruvate to phosphoenolpyruvate; however, it does so without a phosphorylated-enzyme intermediate. Though their amino acid sequences are different, residues key to catalysis are preserved in both enzymes. Point-mutagenesis experiments have shown that catalytic residues include Arg561, Arg617, Glu745, Asn768, and Cys831 (numbering relative to the C, symbiosum protein, {{PDB|1KBL|1KC7}}).

PPDK is used in the C4 pathway, to improve the efficiency of carbon dioxide fixation.{{cite book |last1= Berg|first1= Jeremy|last2 = Tymoczko | first2 = John | last3 = Stryer | first3 = Lubert | name-list-style = vanc | year= 2012 |chapter = The Calvin Cycle and the Pentose Phosphate Pathway |title= Biochemistry | edition = 7th | location= New York |publisher= W.H Freeman | pages = 599–600 |isbn= 9780716787242 }} In environments where there is a lot of light, the rate of photosynthesis in plants is limited by the rate of carbon dioxide (CO₂) uptake. This can be improved by using a series of chemical reactions to transport CO₂ from mesophyll cells (which are located on the outside of a leaf) to bundle sheath cells (which are located inside the cells). PPDK converts pyruvate to PEP, which reacts with CO₂ to produce oxaloacetate. When CO₂ is released in the bundle sheath cells, pyruvate is regenerated, and the cycle continues.

Though the reaction catalysed by PPDK is reversible, PEP is favoured as the product in biological conditions. This is due to the basic pH in the stroma, where the reaction occurs, as well as high concentrations of adenylate kinase and pyrophosphatase. Because these two enzymes catalyse exergonic reactions involving AMP, and disphosphate, respectively, they drive the PPDK-catalysed reaction forward.{{cite book | last = Chastain | first = Chris | editor-first = Agepati | editor-last = Raghavendra | name-list-style = vanc | year = 2010 | chapter = Structure, Function, and Post-Translational Regulation of C4 Pyruvate Orthophosphate Dikinase | title = C4 Photosynthesis and Related CO2 Concentrating Mechanisms. | pages = 301–305 | publisher = Springer | isbn = 9789048194063 }} Because PPDK consumes ATP, the C4 pathway is unfavourable for plants in environments with little access to light, as they are unable to produce large quantities of ATP.

PPDK is highly abundant in C4 leaves, comprising up to 10% of total protein.{{cite journal | vauthors = Chastain CJ, Fries JP, Vogel JA, Randklev CL, Vossen AP, Dittmer SK, Watkins EE, Fiedler LJ, Wacker SA, Meinhover KC, Sarath G, Chollet R | display-authors = 6 | title = Pyruvate,orthophosphate dikinase in leaves and chloroplasts of C(3) plants undergoes light-/dark-induced reversible phosphorylation | journal = Plant Physiology | volume = 128 | issue = 4 | pages = 1368–78 | date = April 2002 | pmid = 11950985 | pmc = 154264 | doi = 10.1104/pp.010806 }} Research has shown that the enzyme is about 96% identical in different species of plants. Hybridization experiments revealed that the genetic differences correlate with the extent to which the plants perform the C4 pathway – the uncommon sequences exist in plants which also display C3 characteristics.{{cite journal | vauthors = Rosche E, Streubel M, Westhoff P | title = Primary structure of the photosynthetic pyruvate orthophosphate dikinase of the C3 plant Flaveria pringlei and expression analysis of pyruvate orthophosphate dikinase sequences in C3, C3-C4 and C4 Flaveria species | journal = Plant Molecular Biology | volume = 26 | issue = 2 | pages = 763–9 | date = October 1994 | pmid = 7948930 | doi = 10.1007/bf00013761 | s2cid = 23276817 }} PPDK is also found in small quantities in C3 plants. Evolutionary history suggests that it once had a role in glycolysis like the similar pyruvate kinase, and eventually evolved into the C4 pathway.

Besides plants, PPDK is also found in the parasitic ameoba Entamoeba histolytica ({{UniProt|P37213}}) and the bacteria Clostridium symbiosum ({{UniProt|P22983}}; as well as other bacteria).UniProt 50%-90% clusters: [https://www.uniprot.org/uniref/?query=cluster:UniRef50_P22983+identity:0.9 From Clostridium PPDK] In those two organisms PPDK functions similarly to (and sometimes in place of) pyruvate kinase, catalyzing the reaction in the ATP-producing direction as a part of glycolysis. Inhibitors for the Entamoeba PPDK have been proposed as amebicides against this organism.{{cite journal | vauthors = Stephen P, Vijayan R, Bhat A, Subbarao N, Bamezai RN | title = Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors | journal = Journal of Computer-Aided Molecular Design | volume = 22 | issue = 9 | pages = 647–60 | date = September 2008 | pmid = 17710553 | doi = 10.1007/s10822-007-9130-2 | bibcode = 2008JCAMD..22..647S | s2cid = 25026913 }}

File:PPDK Regulatory Protein.jpg

Plant PPDK is regulated by the pyruvate, phosphate dikinase regulatory protein (PDRP). When levels of light are high, PDRP dephosphorylates Thr456 on PPDK using AMP, thus activating the enzyme. PDRP deactivates PPDK by phosphorylating the same threonine residue, using diphosphate. PDRP is a unique regulator because it catalyses both activation and deactivation of PPDK, through two different mechanisms.

Research on maize PPDK suggests that introns, terminator sequences, and perhaps other enhancer sequences, act cooperatively to increase the level of functional and stable mRNA. PPDK cDNA was expressed only slightly in transgenic rice, compared to intact DNA which saw significant expression.{{cite journal | vauthors = Fukayama H, Tsuchida H, Agarie S, Nomura M, Onodera H, Ono K, Lee BH, Hirose S, Toki S, Ku MS, Makino A, Matsuoka M, Miyao M | display-authors = 6 | title = Significant accumulation of C(4)-specific pyruvate, orthophosphate dikinase in a C(3) plant, rice | journal = Plant Physiology | volume = 127 | issue = 3 | pages = 1136–46 | date = November 2001 | pmid = 11706193 | pmc = 129282 | doi = 10.1104/pp.010641 }}

As of early 2018, 14 structures have been solved for this class of enzymes, with PDB accession codes {{PDB link|1DIK}}, {{PDB link|1GGO}}, {{PDB link|1H6Z}}, {{PDB link|1JDE}}, {{PDB link|1KBL}}, {{PDB link|1KC7}}, {{PDB link|1VBG}}, {{PDB link|1VBH}}, {{PDB link|2DIK}}, {{PDB link|2FM4}}, {{PDB link|5JVJ}}, {{PDB link|5JVL}}, {{PDB link|5JVN}}, {{PDB link|5LU4}}.

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• {{cite journal | vauthors = Hatch MD, Slack CR | title = A new enzyme for the interconversion of pyruvate and phosphopyruvate and its role in the C4 dicarboxylic acid pathway of photosynthesis | journal = The Biochemical Journal | volume = 106 | issue = 1 | pages = 141–6 | date = January 1968 | pmid = 4305612 | pmc = 1198479 | doi = 10.1042/bj1060141 }}
• {{cite journal | vauthors = Reeves RE | title = A new enzyme with the glycolytic function of pyruvate kinase | journal = The Journal of Biological Chemistry | volume = 243 | issue = 11 | pages = 3202–4 | date = June 1968 | doi = 10.1016/S0021-9258(18)93395-8 | pmid = 4297474 | doi-access = free }}
• {{cite journal | vauthors = Reeves RE | title = Pyruvate,phosphate dikinase from Bacteroides symbiosus | journal = The Biochemical Journal | volume = 125 | issue = 2 | pages = 531–9 | date = November 1971 | pmid = 5144757 | pmc = 1178089 | doi = 10.1042/bj1250531 }}
• {{cite journal | vauthors = Reeves RE, Menzies RA, Hsu DS | title = The pyruvate-phosphate dikinase reaction. The fate of phosphate and the equilibrium | journal = The Journal of Biological Chemistry | volume = 243 | issue = 20 | pages = 5486–91 | date = October 1968 | doi = 10.1016/S0021-9258(18)91972-1 | pmid = 4302788 | doi-access = free }}

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{{Kinases}}

{{Enzymes}}

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Category:EC 2.7.9

Category:Enzymes of known structure