Protein disulfide-isomerase

Protein disulfide isomerase, or PDI, is an enzyme in the endoplasmic reticulum (ER) in eukaryotes and the periplasm of bacteria that catalyzes the formation and breakage of disulfide bonds between cysteine residues within proteins as they fold.[1][2][3] This allows proteins to quickly find the correct arrangement of disulfide bonds in their fully folded state, and therefore the enzyme acts to catalyze protein folding.

Protein disulfide-isomerase
Structural picture of human protein disulfide isomerase (PDB 1BJX)
Identifiers
Symbol?
InterProIPR005792
Protein disulfide-isomerase
Identifiers
EC number5.3.4.1
CAS number37318-49-3
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
protein disulfide isomerase family A, member 2
Identifiers
SymbolPDIA2
Alt. symbolsPDIP
NCBI gene64714
HGNC14180
OMIM608012
RefSeqNM_006849
UniProtQ13087
Other data
LocusChr. 16 p13.3
protein disulfide isomerase family A, member 3
Identifiers
SymbolPDIA3
Alt. symbolsGRP58
NCBI gene2923
HGNC4606
OMIM602046
RefSeqNM_005313
UniProtP30101
Other data
LocusChr. 15 q15
protein disulfide isomerase family A, member 4
Identifiers
SymbolPDIA4
NCBI gene9601
HGNC30167
RefSeqNM_004911
UniProtP13667
Other data
LocusChr. 7 q35
protein disulfide isomerase family A, member 5
Identifiers
SymbolPDIA5
NCBI gene10954
HGNC24811
RefSeqNM_006810
UniProtQ14554
Other data
EC number5.3.4.1
LocusChr. 3 q21.1
protein disulfide isomerase family A, member 6
Identifiers
SymbolPDIA6
Alt. symbolsTXNDC7
NCBI gene10130
HGNC30168
RefSeqNM_005742
UniProtQ15084
Other data
LocusChr. 2 p25.1

Structure

Protein disulfide-isomerase has two catalytic thioredoxin-like domains (active sites), each containing the canonical CGHC motif, and two non catalytic domains.[4][5][6] This structure is similar to the structure of enzymes responsible for oxidative folding in the intermembrane space of the mitochondria; an example of this is mitochondrial IMS import and assembly (Mia40), which has 2 catalytic domains that contain a CX9C, which is similar to the CGHC domain of PDI.[7] Bacterial DsbA, responsible for oxidative folding, also has a thioredoxin CXXC domain.[8]

Primary structure of protein disulfide isomerase with sequence of domains

Function

Protein folding

PDI displays oxidoreductase and isomerase properties, both of which depend on the type of substrate that binds to protein disulfide-isomerase and changes in protein disulfide-isomerase's redox state.[4] These types of activities allow for oxidative folding of proteins. Oxidative folding involves the oxidation of reduced cysteine residues of nascent proteins; upon oxidation of these cysteine residues, disulfide bridges are formed, which stabilizes proteins and allows for native structures (namely tertiary and quaternary structures).[4]

Regular oxidative folding mechanism and pathway

PDI is specifically responsible for folding proteins in the ER.[6] In an unfolded protein, a cysteine residue forms a mixed disulfide with a cysteine residue in an active site (CGHC motif) of protein disulfide-isomerase. A second cysteine residue then forms a stable disulfide bridge within the substrate, leaving protein disulfide-isomerase's two active-site cysteine residues in a reduced state.[4]

Afterwards, PDI can be regenerated to its oxidized form in the endoplasmic reticulum by transferring electrons to reoxidizing proteins such ER oxidoreductin 1 (Ero 1), VKOR (vitamin K epoxide reductase), glutathione peroxidase (Gpx7/8), and PrxIV (peroxiredoxin IV).[4][9][10][6] Ero1 is thought to be the main reoxidizing protein of PDI, and the pathway of reoxidation of PDI for Ero1 is more understood than that of other proteins.[10] Ero1 accepts electrons from PDI and donates these electrons to oxygen molecules in the ER, which leads to the formation of hydrogen peroxide.[10]

Misfolded protein mechanism

The reduced (dithiol) form of protein disulfide-isomerase is able to catalyze a reduction of a misformed disulfide bridge of a substrate through either reductase activity or isomerase activity.[11] For the reductase method, a misfolded substrate disulfide bond is converted to a pair of reduced cysteine residues by the transfer of electrons from glutathione and NADPH. Afterwards, normal folding occurs with oxidative disulfide bond formation between the correct pairs of substrate cysteine residues, leading to a properly folded protein. For the isomerase method, intramolecular rearrangement of substrate functional groups is catalyzed near the N terminus of each active site.[4] Therefore, protein disulfide-isomerase is capable of catalyzing the post-translational modification disulfide exchange.

Redox signaling

In the chloroplasts of the unicellular algae Chlamydomonas reinhardtii the protein disulfide-isomerase RB60 serves as a redox sensor component of an mRNA-binding protein complex implicated in the photoregulation of the translation of psbA, the RNA encoding for the photosystem II core protein D1. Protein disulfide-isomerase has also been suggested to play a role in the formation of regulatory disulfide bonds in chloroplasts.[12]

Immune system

Protein disulfide-isomerase helps load antigenic peptides into MHC class I molecules. These molecules (MHC I) are related to the peptide presentation by antigen-presenting cells in the immune response.

Protein disulfide-isomerase has been found to be involved in the breaking of bonds on the HIV gp120 protein during HIV infection of CD4 positive cells, and is required for HIV infection of lymphocytes and monocytes.[13] Some studies have shown it to be available for HIV infection on the surface of the cell clustered around the CD4 protein. Yet conflicting studies have shown that it is not available on the cell surface, but instead is found in significant amounts in the blood plasma.

Chaperone activity

Another major function of protein disulfide-isomerase relates to its activity as a chaperone; its b' domain aids in the binding of misfolded protein for subsequent degradation.[4] This is regulated by three ER membrane proteins, Protein Kinase RNA-like endoplasmic reticulum kinase (PERK), inositol-requiring kinase 1 (IRE1), and activating transcription factor 6 (ATF6).[4][14] They respond to high levels of misfolded proteins in the ER through intracellular signaling cascades that can activate PDI's chaperone activity.[4] These signals can also inactivate translation of these misfolded proteins, because the cascade travels from the ER to the nucleus.[4]

Activity assays

Insulin turbidity assay: protein disulfide-isomerase breaks the two disulfide bonds between two insulin (a and b) chains that results in precipitation of b chain. This precipitation can be monitored at 650 nm, which is indirectly used to monitor protein disulfide-isomerase activity.[15] Sensitivity of this assay is in micromolar range.

ScRNase assay: protein disulfide-isomerase converts scrambled (inactive) RNase into native (active) RNase that further acts on its substrate.[16] The sensitivity is in micromolar range.

Di-E-GSSG assay: This is the fluorometric assay that can detect picomolar quantities of protein disulfide-isomerase and therefore is the most sensitive assay to date for detecting protein disulfide-isomerase activity.[17] Di-E-GSSG has two eosin molecules attached to oxidized glutathione (GSSG). The proximity of eosin molecules leads to the quenching of its fluorescence. However, upon breakage of disulfide bond by protein disulfide-isomerase, fluorescence increases 70-fold.

Stress and inhibition

Effects of nitrosative stress

Redox dysregulation leads to increases in nitrosative stress in the endoplasmic reticulum. Such adverse changes in the normal cellular environment of susceptible cells, such as neurons, leads to nonfunctioning thiol-containing enzymes.[14] More specifically, protein disulfide-isomerase can no longer fix misfolded proteins once its thiol group in its active site has a nitric monoxide group attached to it; as a result, accumulation of misfolded proteins occurs in neurons, which has been associated with the development of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease.[4][14]

Inhibition

Due to the role of protein disulfide-isomerase in a number of disease states, small molecule inhibitors of protein disulfide-isomerase have been developed. These molecules can either target the active site of protein disulfide-isomerase irreversibly[18] or reversibly.[19]

It has been shown that protein disulfide-isomerase activity is inhibited by red wine and grape juice, which could be the explanation for the French paradox.[20]

Members

Human genes encoding protein disulfide isomerases include:[3][21][22]

References
  1. Wilkinson B, Gilbert HF (June 2004). "Protein disulfide isomerase". Biochimica et Biophysica Acta. 1699 (1–2): 35–44. doi:10.1016/j.bbapap.2004.02.017. PMID 15158710.
  2. Gruber CW, Cemazar M, Heras B, Martin JL, Craik DJ (August 2006). "Protein disulfide isomerase: the structure of oxidative folding". Trends in Biochemical Sciences. 31 (8): 455–64. doi:10.1016/j.tibs.2006.06.001. PMID 16815710.
  3. Galligan JJ, Petersen DR (July 2012). "The human protein disulfide isomerase gene family". Human Genomics. 6 (1): 6. doi:10.1186/1479-7364-6-6. PMC 3500226. PMID 23245351.
  4. Perri ER, Thomas CJ, Parakh S, Spencer DM, Atkin JD (2016). "The Unfolded Protein Response and the Role of Protein Disulfide Isomerase in Neurodegeneration". Frontiers in Cell and Developmental Biology. 3: 80. doi:10.3389/fcell.2015.00080. PMC 4705227. PMID 26779479.
  5. Bechtel TJ, Weerapana E (March 2017). "From structure to redox: The diverse functional roles of disulfides and implications in disease". Proteomics. 17 (6): n/a. doi:10.1002/pmic.201600391. PMC 5367942. PMID 28044432.
  6. Soares Moretti AI, Martins Laurindo FR (March 2017). "Protein disulfide isomerases: Redox connections in and out of the endoplasmic reticulum". Archives of Biochemistry and Biophysics. The Chemistry of Redox Signaling. 617: 106–119. doi:10.1016/j.abb.2016.11.007. PMID 27889386.
  7. Erdogan AJ, Riemer J (January 2017). "Mitochondrial disulfide relay and its substrates: mechanisms in health and disease". Cell and Tissue Research. 367 (1): 59–72. doi:10.1007/s00441-016-2481-z. PMID 27543052. S2CID 35346837.
  8. Hu SH, Peek JA, Rattigan E, Taylor RK, Martin JL (April 1997). "Structure of TcpG, the DsbA protein folding catalyst from Vibrio cholerae". Journal of Molecular Biology. 268 (1): 137–46. doi:10.1006/jmbi.1997.0940. PMID 9149147.
  9. Manganas P, MacPherson L, Tokatlidis K (January 2017). "Oxidative protein biogenesis and redox regulation in the mitochondrial intermembrane space". Cell and Tissue Research. 367 (1): 43–57. doi:10.1007/s00441-016-2488-5. PMC 5203823. PMID 27632163.
  10. Oka OB, Yeoh HY, Bulleid NJ (July 2015). "Thiol-disulfide exchange between the PDI family of oxidoreductases negates the requirement for an oxidase or reductase for each enzyme". The Biochemical Journal. 469 (2): 279–88. doi:10.1042/bj20141423. PMC 4613490. PMID 25989104.
  11. Hatahet F, Ruddock LW (October 2007). "Substrate recognition by the protein disulfide isomerases". The FEBS Journal. 274 (20): 5223–34. doi:10.1111/j.1742-4658.2007.06058.x. PMID 17892489. S2CID 9455925.
  12. Wittenberg G, Danon A (2008). "Disulfide bond formation in chloroplasts". Plant Science. 175 (4): 459–466. doi:10.1016/j.plantsci.2008.05.011.
  13. Ryser HJ, Flückiger R (August 2005). "Progress in targeting HIV-1 entry". Drug Discovery Today. 10 (16): 1085–94. doi:10.1016/S1359-6446(05)03550-6. PMID 16182193.
  14. McBean GJ, López MG, Wallner FK (June 2017). "Redox-based therapeutics in neurodegenerative disease". British Journal of Pharmacology. 174 (12): 1750–1770. doi:10.1111/bph.13551. PMC 5446580. PMID 27477685.
  15. Lundström J, Holmgren A (June 1990). "Protein disulfide-isomerase is a substrate for thioredoxin reductase and has thioredoxin-like activity". The Journal of Biological Chemistry. 265 (16): 9114–20. PMID 2188973.
  16. Lyles MM, Gilbert HF (January 1991). "Catalysis of the oxidative folding of ribonuclease A by protein disulfide isomerase: dependence of the rate on the composition of the redox buffer". Biochemistry. 30 (3): 613–9. doi:10.1021/bi00217a004. PMID 1988050.
  17. Raturi A, Mutus B (July 2007). "Characterization of redox state and reductase activity of protein disulfide isomerase under different redox environments using a sensitive fluorescent assay". Free Radical Biology & Medicine. 43 (1): 62–70. doi:10.1016/j.freeradbiomed.2007.03.025. PMID 17561094.
  18. Hoffstrom BG, Kaplan A, Letso R, Schmid RS, Turmel GJ, Lo DC, Stockwell BR (December 2010). "Inhibitors of protein disulfide isomerase suppress apoptosis induced by misfolded proteins". Nature Chemical Biology. 6 (12): 900–6. doi:10.1038/nchembio.467. PMC 3018711. PMID 21079601.
  19. Kaplan A, Gaschler MM, Dunn DE, Colligan R, Brown LM, Palmer AG, Lo DC, Stockwell BR (April 2015). "Small molecule-induced oxidation of protein disulfide isomerase is neuroprotective". Proceedings of the National Academy of Sciences of the United States of America. 112 (17): E2245-52. Bibcode:2015PNAS..112E2245K. doi:10.1073/pnas.1500439112. PMC 4418888. PMID 25848045.
  20. Galinski CN, Zwicker JI, Kennedy DR (January 2016). "Revisiting the mechanistic basis of the French Paradox: Red wine inhibits the activity of protein disulfide isomerase in vitro". Thrombosis Research. 137: 169–173. doi:10.1016/j.thromres.2015.11.003. PMC 4706467. PMID 26585763.
  21. Ellgaard L, Ruddock LW (January 2005). "The human protein disulphide isomerase family: substrate interactions and functional properties". EMBO Reports. 6 (1): 28–32. doi:10.1038/sj.embor.7400311. PMC 1299221. PMID 15643448.
  22. Appenzeller-Herzog C, Ellgaard L (April 2008). "The human PDI family: versatility packed into a single fold". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1783 (4): 535–48. doi:10.1016/j.bbamcr.2007.11.010. PMID 18093543.
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