Sandbox bcce04

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Imaginary Protein

spinqualitylabelsall models PDB ID 1iat Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Imaginaryase (alternatively known as imaginary isomerase or imaginary-8-phosphate isomerase) are a group of enzymes of the isomerase family (EC 5.3.a.b), so named for their main function in metabolism. In this pathway imaginary isomerase (IGI) is used to inter-convert imaginary-8-phosphate and reality-6-phosphate. This reaction is driven by the relative concentrations of these molecules in the imaginary/reality matrix of the cell [1]. Imaginaryase is also known for a list of activities: Something cool [2]. Something cooler[3]. Something my prof thinks is cool [4]. Something really boring [5]. IGI is important for metabolism in many different living organisms. [6]. Structure Figure 1. Multiple alignment PGI - Geobacillus stearothermophilus (white), Homo sapiens (pink), Oryctolagus cuniculus (blue)[7] Phosphoglucose isomerase exists in the cell usually as a , nevertheless outside of the cell, it has been isolated as a structure. PGI has essentially an identical fold in all of the characterized species (see Figure 1). The of phosphoglucose isomerase is charaterized by an αβα conformation, on each of its two domains. The smaller domain is characterized by 5 parallel β-sheets, while the larger domain if formed out of 6 parallel/antiparallel β-sheets. Furthermore, another characteristic trait is a residue extension at the C-terminus, which wraps around the other monomer in the dimeric conformation. A "hook" that can potentially be involved in the previously mentioned extracellular activities. Phosphoglucose isomerase has a monomer molecular mass of proximately 55 kDa. Active Site - Mammalian PGI shows a degree of ( dark red for highly conserved regions - dark blue for variable reigions) of about 90 %. The is the region with highest observed conservation, containing a number of residues that are crucial in the enzyme-substrate interaction mechanism (Lys210, Gln353, Glu357, Gln511, Lys518, His388b). Lys518(His388) and Glu357 are the main components of ring opening, while many of the other residues can be used for stabliziation and orientation. Another characteristic of phosphoglucose isomerase is that binding of substrate at the active site induces a small movement in the conformation of the enzyme. This can be seen in Figure 2 as change in the position of an α helix. Figure 2. Substrate induced movement

Mechanism

The proposed reaction mechanism of PGI for the reversible conversion of glucose-6-phosphate to fructose 6-phosphate involves an acid/base catalysis by the enzyme. The basic mechanism involves the isomerization of an aldose to a ketose. This is performed by a ring opening, followed by an isomeration of the opened ring, then a ring closing. A detailed step by step mechanism of this process can be seen as follows ^[8]:

Step 1. The substrate binds to the enzyme.

Step 2. The residue Lys518 (or His388b) acts as an enzymatic acid catalyzing the opening of the ring.

Step 3. Conserved Glu357 abstracts the acidic proton from C2 forming a cis-enendiol intermediate.

Step 4. Glu357 donates back the proton at the C1 position.

Step 5. Lys518 (or His388b) abstracts back the proton from the sugar ring oxygen, resulting in a ring closure, to give the product.

Regulation and Inhibition

Regulation of phosphoglucoisomerase is only done by the relative concentrations of glucose-6-phosphate and fructose 6-phosphate, towards equilibrium. Nevertheless, it was found that the kinetic parameters of PGI does depend on the pH and temperature of the environment. The following kinetic parameters are proposed for rabbit PGI at pH 8.5 and 30°C ^[9]

It is interesting to point the regulation of PGI in other aspects that are not involved in metabolism. For example, PGI acts as a "cytokine" outside the cell in that it can be used as a cell signalling protein. PGI has been found to to be associated with AMF cells, which is found to regulate tumor cell motility. Regulation of these extracellular "cytokine" PGI/AMF can be seen. The amount of PGI/AMF that is secreted inside and outside the cell based on infection ^[10].

Inhibition of the phosphoglucoisomerase regulated reaction of glucose-6-phosphate to fructose-6-phosphate can also occur. Competitive competition can take place from inhibitors such as 5PAH. 5PAH resembles PGI, differing only in a nitrogen atom at the first carbon position. 5PAH is reported to have a Ki of .0000002 M ^[11].

Links

• Crystal Structure of human phosphoglucose isomerase (PDB=1iat)

• Crystal Structure of rabbit phosphoglucose isomerase complexed fructose 6-phosphate (PDB=1hox^[12])

• Other available structures 1dqr, 1g98, 1gzd, 1gzv, 1hm5, 1iri, 1jiq, 1jlh, 1koj, 1n8t, 1nuh, 1xtb.

3D structures of phosphoglucose isomerase

PGI

2pgi, 1b0z – GsPGI – Geobacillus stearothermophilus
1dqr, 1hm5, 1n8t – rPGI – rabbit
1iat, 1jlh – hPGI – human
1qxj, 1x8e, 3sxw – PfPGI – Pyrococcus furiosus
1j3p, 1j3q – TlPGI – Thermococcus litoralis
1q50 – LmPGI – Leishmania Mexicana
1u0e, 2cvp – mPGI – mouse
2q8n – PGI – Thermotoga maritima
3hjb – PGI – Vibrio cholera
3ifs – PGI – Bacillus anthracis
2wu8 – PGI – Mycobacterium tuberculosis
3ljk – FtPGI (mutant) – Francisella tularensis
3nbu – PGI – Escherichia coli

PGI complex with fructose-6-phosphate

1hox – rPGI + fructose-6-phosphate
1t10 - LmPGI + fructose-6-phosphate
2gc2 - PfPGI + fructose-6-phosphate
2cxs, 2cxt - mPGI + fructose-6-phosphate
3m5p - FtPGI (mutant) + fructose-6-phosphate

PGI complex with sorbitol-6-phosphate

1xtb - rPGI + sorbitol-6-phosphate
2gc1 - PfPGI + sorbitol-6-phosphate
2cxq - mPGI + sorbitol-6-phosphate

PGI complex with phosphoarabinose

1gzd, 1gzv – PGI + phosphoarabinose – pig
1c7r - GsPGI + phosphoarabinose
2cxp – mPGI + phosphoarabinose
1nuh - hPGI + phosphoarabinose
1qsr, 1x7n, 1x82 - PfPGI + phosphoarabinose
2gc0 - PfPGI + phosphoarabinose derivative
1koj – rPGI + phosphoarabinose derivative

PGI complex with gluconate-6-phosphate

1qy4 - PfPGI + gluconate-6-phosphate
1j3r - TlPGI + gluconate-6-phosphate
2cxr - mPGI + gluconate-6-phosphate
3q7i - FtPGI (mutant) + gluconate-6-phosphate

PGI complex with glucose-6-phosphate

1u0f - mPGI + glucose-6-phosphate
3ff1 - PGI + glucose-6-phosphate – Staphylococcus aureus
2o2c - TbPGI + glucose-6-phosphate – Trypanosoma brucei

Other PGI binary complexes

2o2d – TbPGI + citrate
1u0g, 2cxo - mPGI + erythrose-4-phosphate
3q88 – FtPGI (mutant) + ribose bisphosphate
1c7q – GsPGI + phosphate inhibitor
2cxn, 2cxu – mPGI + phosphate
1g98 – rPGI + transition state analog
2gc3 - PfPGI + mannose-6-phosphate

Additional Resources

For additional information, see: Carbohydrate Metabolism

References

1. ↑ 1
2. ↑ 2
3. ↑ 3
4. ↑ 4
5. ↑ 5
6. ↑ 5
7. ↑ Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 Oct;25(13):1605-12.
8. ↑ Voet D, Voet J, and Pratt C. Fundamentals of Biochemistry Life at the Molecular Level. New York: John Wiley & Sons, 2008. Print.
9. ↑ Dyson JE, Noltmann EA. The effect of pH and temperature on the kinetic parameters of phosphoglucose isomerase. Participation of histidine and lysine in a proposed dual function mechanism. J Biol Chem. 1968 Apr 10;243(7):1401-14. PMID:5647261
10. ↑ Funasaka T, Hu H, Yanagawa T, Hogan V, Raz A. Down-Regulation of Phosphoglucose Isomerase/Autocrine Motility Factors Results in Mesenchymal-to-Epithelial Transition of Human Lung Fibrosarcoma Cells. (2007) Cancer Res, 76(9)
11. ↑ Arsenieva D, Hardre R, Salmon L, Jeffery CJ. The crystal structure of rabbit phosphoglucose isomerase complex with 5-phospho-D-arabinonohydroxamic acid. (2002),PNAS, 99(9)
12. ↑ Lee JH, Chang KZ, Patel V, Jeffery CJ. Crystal structure of rabbit phosphoglucose isomerase complexed with its substrate D-fructose 6-phosphate. Biochemistry. 2001 Jul 3;40(26):7799-805. PMID:11425306