Phosphoglycerate kinase, domains

Fig. 71. Examples of protein domains with different numbers of layers of backbone structure (a) two-layer cytochrome c (b) three-layer phosphoglycerate kinase domain 2 (c) four-layer triosephosphate isomerase. The arrows above each drawing point to the backbone layers.

Classic doubly wound /3 sheets Lactate dehydrogenase domain 1 Alcohol dehydrogenase domain 2 Aspartate transcarbamylase catalytic domain 2 Phosphoglycerate kinase domain 1 Tyrosyl-tRNA synthetase domain 1( )... 

Arabinose-binding protein domains 1 and 2 Dihydrofolate reductase Adenylate kinase Rhodanese domains 1 and 2 Glutathione reductase domains 1 and 2 Phosphoglycerate mutase Phosphoglycerate kinase domain 2 Pyruvate kinase domain 3 Hexokinase domains 1 and 2 Catalase domain 3 Aspartate aminotransferase... 

FIGURE 6.28 Examples of protein domains with different numbers of layers of backbone strnctnre. (a) Cytochrome c with two layers of a-helix. (b) Domain 2 of phosphoglycerate kinase, composed of a /3-sheet layer between two layers of helix, three layers overall, (c) An nnnsnal five-layer strnctnre, domain 2 of glycogen phosphorylase, a /S-sheet layer sandwiched between four layers of a-helix. (d) The concentric layers of /S-sheet (inside) and a-helix (outside) in triose phosphate isomerase. Hydrophobic residnes are bnried between these concentric layers in the same manner as in the planar layers of the other proteins. The hydrophobic layers are shaded yellow. (Jane Richarelson)... 

M20. Michelson, A. M Blake, C. C., Evans, S. T and Orkin, S. H., Structure of the human phosphoglycerate kinase gene and the intron-mediated evolution and dispersal of the nucleotidebinding domain. Proc. Natl. Acad. Sci. U.S.A. 82,6965-6969 (1985). 

Fig. 65. The dumbbell domain organization of phosphoglycerate kinase, with a relatively narrow neck between two well-separated domains.

Zaiss, K. and R. Jaenicke. 1999. Thermodynamic study of phosphoglycerate kinase from Thermotoga maritima and its isolated domains reversible thermal unfolding monitored by differential scanning calorimetry and circular dichroism spectroscopy. Biochemistry 38 4633 -639. 

Sherman, M.A. Chen, Y. Mas, M.T. An engineered amino-terminal domain of yeast phosphoglycerate kinase with native-like structure. Protein Sci., 6, 882-891 (1997)... 

Szilagyi, A.N. Vas, M. Anion activation of 3-phosphoglycerate kinase requires domain closure. Biochemistry, 37, 8551-8563 (1998)... 

RNS, ribonuclease LZM, lysozyme SNS, staphylococcal nuclease LZ4, T4 lysozyme PAP, papain TLS, thermolysin, TRX, thioiedoxin FLN, flavodoxin ADH, alcohol dehydrogenase coenzyme domain AKN, adenyl kinase MDG, malate dehydrogenase TIM, triosephosphate isomerase SUB, subtilisin CPA, carboxypeptidase LDH, lactate dehydrogenase PGK, phosphoglycerate kinase GPD, glyceraldehyde 3-phosphate dehydrogenase, HKN, hexokinase. 

The separateness of two domains within a subunit varies all the way from independent globular domains joined only by a flexible length of polypeptide chain, to domains with tight and extensive contact and a smooth globular surface for the outside of the entire subunit, as in the proteolytic enzyme elastase (fig. 4.20). An intermediate level of domain separateness, characterized by a definite neck or cleft between the domains, is found in phosphoglycerate kinase (fig. 4.21). 

The dumbbell domain organization of phosphoglycerate kinase, with a relatively narrow neck between two well-separated domains. (Copyright 1994 by the Scripps Research Institute/Molecular Graphics Images by Michael Pique using software by Yng Chen, Michael Connolly, Michael Carson, Alex Shah, and AVS, Inc. Visualization advice by Holly Miller, Wake Forest University Medical Center.)... 

Phosphoglycerate kinase is a protein composed of two structural domains of approximately equal molecular weight (N-terminal do-mainMr 20,814 C-terminal domain Afr 23,735). The crystallographic structure has been determined (Watson et al., 1982) and can be used to calculate the hydrophobic surface exposed to water on total or partial unfolding as well as the number of hydrogen bonds and other bonds involved in the stabilization of the folded conformation. 

Analysis of the crystallographic structure indicates that on complete unfolding of the phosphoglycerate kinase (PGK) molecule a total of 1828 apolar hydrogens (814 from the N domain and 1014 from the C domain) become exposed to the solvent. Also, an average of 73% of the amino acid residues are hydrogen bonded (Chothia, 1976) and... 

Fig. 8. Experimental ( — ) and theoretical heat capacity functions for the thermal folding/unfolding transition of phosphoglycerate kinase at pH 6.5 in the presence of 0.7 M GuHCl. The heat denaturation transition is characterized by a single peak, whereas the cold denaturation displays two peaks corresponding to the independent unfolding of the N and C domains. The experimental curve has been published before (Griko et al., 1989). As discussed in the text, the theoretical curve does not represent the best fit to the experimental data, but rather the calculated curve using structural information in conjunction with thermodynamic information for elementary interactions. [Reprinted from Freire et al. (1991).]...

A physical technique for the study of conformation based on measuring changes in heat capacity of a molecule under various conditions. See Zecchinon, L., Oriol, A., Netzel, U. et al.. Stability domains, substrate-induced conformational changes, and hinge-bending motions in a psychro-philic phosphoglycerate kinase. A microcalorimetric study, J. Biol. Chem. 280, 41307-41314, 2005. 

Some proteins can show either two-state or multistate behavior depending on the conditions of denaturation. For example, heat dena-turation of phosphoglycerate kinase complies with the two-state approximation, but not its cold denaturation [58] this has been quantitatively analyzed as resulting from the existence of two domains, interacting mainly through hydrophobic contacts, that unfold almost independently at low temperature but behave as a single cooperative unit at high temperature, as a consequence of the temperature dependence of hydrophobic interactions [59,63]. 

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