The atlas of contacts

1.Introduction

This page shows the information about protein complex between human phosphopantenil transferase and acyl-carrier protein (ACP) [1]. Experimental data has gotten using X-Ray difraction. Acyl-carrier protein forms a part of fatty acid synthetase. It is a multi-domeins proteins consisted of 6 subunits (ACP is not counted). Reactions of fatty acids' synthesis are shown on picture 1.

Picture 1. Reactions of fatty acids' synthesis [2]

2. Description of proteins included in complex 2CG5

*Таблица 1. General сharacteristics of proteins, included in 2CG5 complex*
	L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	Acyl-carrier protein (as a part of fatty acid synthetase )
Short name	AASD-PPT	ACP
Gene name	AASDHPPT	Fasn
PDB ID	2BYD	2PNG
UniProtKB AC	Q9NRN7	P12785
Molecular function	Transferase	Transferase
Catalytic activity	CoA-[4'-phosphopantetheine] + apo-[acyl-carrier-protein] = adenosine 3',5'-bisphosphate + holo-[acyl-carrier-protein].	Fatty acids synthesis (pic.1)
Ligands	Magnesium, CoA, Br	B5
Cellular localisation	Cytosol	Cytosol

Phosphopantetheinyl transferase - it is an enzyme, capable to transfer 4'-phosphopantetheine residue of CoA to conserved serine-2156 residue of APB. It is also able to phosphopantetheinylate peptid- and acyl-carrier procariotic proteins. Moreover, this enzyme takes part in lysine catabolism.[3].

Рicture 2.Reaction Catalyzed by Human PPT [4]

Acyl-carrier protein is a important component in fatty-acids and polycetide (secondary metabolite [5]) biosynthesis. It is synthesized in inactive form and activated throw joining 4'-phosphopantetheine. Phosphopantetheine have two vital functions: joininf of synthesing intermediate to fatty-acid synthase throw energy-rich link and because of flexibility of its chain allows to bring together intermediates and enzyme active center [6].

3. Protein-protein contcts


Generalconfiguration	Script
Cores	Script
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Aromatic	Script
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If you pull 'General configuration' -button, you will see cartoon-structure of this complex (grey-ACP, yellow and pink-transferase). Conserved serine-2156 residue displayed in green. It is changed to ALA (to facilitate crystallization of a stable ternary complex). As we can see, serine residue points directly toward the CoA. transferase forms a clift, in which one ACP can be placed. Also we can see that there are no covalent bonds between two proteins.
Hydrophobic interactions . There are lots of alpha-helixes in either proteins so we can suppose that there are lots of hydrophobic interactions between them.
Using server [7] we identified hydrophobic cores of proteins. Using within-command (average distance between two covalent not-binded atoms we know from the previous task-4 angstrems [8]) we studied that only 4 from overall 10 cores takes part in protein-protein contacts. If you pull 'Cores'-buttom, you will see a general view of these cores (red-transferase, black-ACP, another colors-different cores). If you pull 'Resume'-button, you will se a general scheme of hydrophobic interactions (List of aminoacids, takes part in it ACP:[ALA]2130 [ILE]2134 [ILE]2137 [LEU]2152 [ALA]2156 [LEU]2157 [VAL]2160 [GLU]2161 [THR]2165 [VAL]2176 Transferase: [PHE]61 [VAL]62 [PHE]63 [GLN]122 [PHE]154 [ILE]157 [TYR]184 [TRP]187 [LEU]201). Transferase displayed in grey, ACP in green, aminoacids from transferase, taking part in hydrophobic interactions, in pink, from ACP in blue. It is clearly seen that hydrophobic contacts are aggregated in two regions, keeping ACP from two sides. One of them is situated between 'twist-region' of secondary structure (pull 'Resume'-button) and one of them between alpha-helixes (pull 'Resume'-button). We suppose that hydrophobic interactions help to orientate correct the movements of two proteins relative to one another and keeping the right position for some time, necessary for reaction.
Polar interactions. As a rule, it is different to draw a line between polar interactions and hydrogen bonds, so we mean that there are bonds between positive and negative charged residues not lonfer than 5 angstrom.
We have found only three polar bonds ([GLU]2161:B -[Arg]148:A, [Thr]2165:B -[Arg]148:A и [Asp]2151:B-[Gln]60:A). Pull 'Polar interactions'-button to see a genera view, where ACP is diplayed in green, transferase in grey, negative charged residues in blue, positive charged in pink. Press 'Resume'-button to see them closer. On picture 4 you can see a snapshot of ASP2151-GLN60 where high atoms of aminoacids are marked.

Picture 4. Polar interactions between GLN60 and ASP2151

In the case of small amount of detected polar bonds we suppose that they play minor role in protein-protein interactions.
Hydrogen bonds.There is only one hydrogen bond between oxygen of ASP2151 and nitrogen of VAL62. For visualisation press 'Hydrogen bond'-buttom. This link is unusual because of the fact, that it is not between lateral-lateral residues but between lateral residue and backbone.

Picture 5. The variety of stacking-interactions[9]

Stacking-interactions. Stacking-interaction - it is attractive, noncovalent interaction between aromatic rings, containing pi bonds [9]. Using within command we found aromatic (phe, trp, tyr, his) aminoacids, siteated on the contacts' broad between transferase and ACP (trp187, phe154, phe63, phe 61, his2133, tyr184). For visualisation press 'Aromatic'-buttom. As it seen, all of them are situated too far from each other to form a stacking-bond (1,26 nm and 1,09 nm).
However we found information about stacking berween aromatic aminoacids and nitrogen atoms of glu, arg and asp [10]. Authors of that article said that there are stacking-interactions no longer than 5 angstrom. Press 'Resume'-button to see PHE63-ARG65 and ARG2138-HIS2133. We assume that these interactions help to stabilize 'twist-structure' of alpha-helix. It can play role in pritein positioning (press 'Resume'-button to see general view).

4.Ligands in complex 2CG5, 2BYD, 2JBZ.

In this chapter we review protein-ligand contacts in 2CG5 complex, and, separately, in 2BYD and 2JBZ. There are 6 different ligands in total, their features are presented in Table 2.


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*Table 2. General information about the ligands*
Ligand	CoA	Br^-	Ni²⁺	K¹⁺	Mg²⁺	PO₄^3-
PDBID	2CG5 and 2JBZ	2BYD	2CG5	2JBZ	2CG5 and 2JBZ	2CG5
IUPAC	S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-2-hydroxy-3,3-dimethylbutanoyl]amino]propanoylamino]ethyl] ethanethioate	Bromide	Nickel(2+)	Potassium(1+)	Magnesium(2+)	Phosphate
Chemical formula
Gross formula	C₂₃H₃₈N₇O₁₇P₃S	Br	Ni	K	Mg	PO₄
Molar mass	809,57	79.90	58.69	39.10	24.30	94,97
PubChem	444493	259	934	813	888	1061

5.Conclusions

Taking everything into account we can say that our proteins connected to each other with hydrophobic interactions and polar interactions do not play a main role in this process. Opposite, polar small ligands positioned in proteins by binding with polar residues of aminoacids.

6.References

[1] http://www.rcsb.org/pdb/explore/explore.do?structureId=2CG5
[2] Наглядная биохимия. Кольман Я., Рём К.-Г. М.: 2000. - 469 с
[3] Joshi A.K. et al. Cloning, Expression, and Characterization of a Human 4’-Phosphopantetheinyl Transferase with Broad Substrate Specificity // J. Biol. Chem. 2003. Vol. 278, № 35. P. 33142–33149.
[4] Bunkoczi G. et al. Mechanism and Substrate Recognition of Human Holo ACP Synthase // Chem. Biol. 2007. Vol. 14, № 11. P. 1243–1253.
[5] https://ru.wikipedia.org/wiki/Поликетиды
[6] https://meshb.nlm.nih.gov/#/record/ui?name=Acyl%20Carrier%20Protein
[7] http://mouse.belozersky.msu.ru/npidb/cgi-bin/hftri.pl
[8] http://kodomo.fbb.msu.ru/~azbukinanadezda/term2/pr2/pr2.html
[9] https://en.wikipedia.org/wiki/Stacking_(chemistry)
[10] Flocco M.M., Mowbray S.L. Planar stacking interactions of arginine and aromatic side-chains in proteins. // Journal of molecular biology. 1994. Vol. 235. P. 709–717.