Pyruvate Phosphate Dikinase

Pyruvate Phosphate Dikinase
Structure of the PPDK from Zea mays ( PDB  1VBH ). The nucleotide binding domain (green), PEP / pyruvate binding domain (blue) with the substrate PEP and an Mg2 + ion, the phosphohistidine domain (yellow) and the linker peptides (red) are highlighted in color. The catalytic histidine residue is highlighted by an arrow. The overlay (gray) shows the PPDK from Clostridium symbiosum ( PDB  1KBL ).
Existing structural data : 1VBG , 1VBH , 1KBL , 1DIK , 2X0S
Mass / length primary structure	947 amino acids ( Zea mays )
Secondary to quaternary structure	Homotetramer
Cofactor	Mg 2+ , NH 4 +
Identifier
Gene name (s)	pdk (MaizeGDB)
External IDs	UniProt :  P11155 CAS number : 9027-40-1
Enzyme classification
EC, category	2.7.9.1 ,  phosphotransferase
Substrate	ATP + pyruvate + phosphate
Products	AMP + phosphoenolpyruvate + diphosphate
Occurrence
Parent taxon	Plants , various bacteria and protozoa

The pyruvate phosphate dikinase (PPDK) ( EC 2.7.9.1) belongs to the class of enzymes Phoshphotransferasen and catalyzes the ATP -dependent phosphorylation of pyruvate to phosphoenolpyruvate .

PPDK was first described in grasses and the parasitic amoeba Entamoeba histolytica . Some mainly anaerobically living bacteria and protozoa use this reaction in the opposite direction, which forms pyruvate to produce ATP.

Catalyzed reaction

${\displaystyle \mathrm {ATP\ +} }$ ${\displaystyle \mathrm {\ +\ P_{i}\ \rightleftharpoons \ AMP\ +\ } }$ ${\displaystyle \mathrm {\ +\ PP_{i}} }$

ATP , pyruvate and phosphate are converted to AMP , phosphoenolpyruvate (PEP) and diphosphate .

Structural functionality

Taking into account sequence homologies and structural data, the PPDK can be divided into three domains :

1. Nucleotide binding domain
2. Central phosphohistidine domain
3. PEP / pyruvate binding domain

Within the nucleotide binding domain, 240 amino acid residues form an ATP-grasp , 340 residues of the C-terminal PEP / pyruvate binding domain form a so-called TIM barrel . The three domains are connected to one another via flexible linker peptides.

Schematic representation of the swiveling domain mechanism for transferring the phosphate group between the nucleotide and the PEP / pyruvate binding domain. The catalytic histidine residue is shown as a blue circle.

The distance between the nucleotide and the PEP / pyruvate binding domain is about 45 Å. A direct interaction of the two substrate binding domains is not possible over this distance. Instead, the phosphate transfer is made possible by a torsional movement of the phosphohistidine domain.

Function in C ₄ plants

In C ₄ plants , the PPDK is located in the chloroplasts of the mesophyll cells and there catalyzes the regeneration of the primary CO ₂ acceptor phosphoenolpyruvate.

literature

• CJ Chastain, CJ Failing, L. Manandhar, M. Zimmerman, MM Lakner, THT Nguyen: Functional evolution of C ₄ pyruvate, orthophosphate dikinase . In: Journal of Experimental Botany . tape 62 , no. 9 , May 17, 2011, p. 3083-3091 , doi : 10.1093 / jxb / err058 , PMID 21414960 .
• AS Raghavendra, RF Sage (Ed.): C ₄ Photosynthesis and Related CO ₂ Concentrating Mechanisms (=  Advances in Photosynthesis and Respiration . Volume 32 ). Springer Netherlands, Dordrecht 2011, ISBN 978-90-481-9406-3 , doi : 10.1007 / 978-90-481-9407-0 .

Individual evidence

1. ↑ MD Hatch, CR Slack: A new enzyme for the interconversion of pyruvate and phosphopyruvate and its role in the C ₄ dicarboxylic acid pathway of photosynthesis . In: The Biochemical Journal . tape 106 , no. 1 , January 1968, p. 141–146 , doi : 10.1042 / bj1060141 , PMID 4305612 , PMC 1198479 (free full text).
2. ^ RE Reeves: A new enzyme with the glycolytic function of pyruvate kinase . In: The Journal of Biological Chemistry . tape 243 , no. 11 , June 10, 1968, pp. 3202-3204 , PMID 4297474 .
3. ↑ DJ Pocalyko, LJ Carroll, BM Martin, PC Babbitt, D. Dunaway-Mariano: Analysis of sequence homologies in plant and bacterial pyruvate phosphate dikinase, enzyme I of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and other PEP-utilizing enzymes. Identification of potential catalytic and regulatory motifs . In: Biochemistry . tape 29 , no. 48 , December 4, 1990, pp. 10757-10765 , doi : 10.1021 / bi00500a006 , PMID 2176881 (English).
4. ↑ O. Herzberg, CC Chen, S. Liu, A. Tempczyk, A. Howard, M. Wei, D. Ye, D. Dunaway-Mariano: Pyruvate Site of Pyruvate Phosphate Dikinase: Crystal Structure of the Enzyme - Phosphonopyruvate Complex, and Mutant Analysis . In: Biochemistry . tape 41 , no. 3 , January 22, 2002, p. 780-787 , doi : 10.1021 / bi011799 + , PMID 11790099 .
5. ↑ O. Herzberg, CC Chen, G. Kapadia, M. McGuire, LJ Carroll, SJ Noh, D. Dunaway-Mariano: Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites . In: Proceedings of the National Academy of Sciences of the United States of America . tape 93 , no. 7 , April 2, 1996, pp. 2652-2657 , doi : 10.1073 / pnas.93.7.2652 , PMID 8610096 , PMC 39685 (free full text).