Protein arginine phosphatase

Last updated
Stained B.Subtilis, a gram-positive bacteria, under a microscope. Image by Farida125 / CC By B. subtilis.jpg
Stained B.Subtilis, a gram-positive bacteria, under a microscope. Image by Farida125 / CC By

Protein Arginine Phosphatase (PAPs), also known as Phosphoarginine Phosphatase, is an enzyme that catalyzes the dephosphorylation of phosphoarginine residues in proteins. [1] Protein phosphatases (PPs) are "obligatory heteromers [2] " made up of two maximum catalytic subunits attached to a non-catalytic subunit. Arginine modification is a post-translational protein modification in gram-positive bacteria. McsB and YwIE were recently identified as phosphorylating enzymes in Bacillus Subtilis (B.Subtilis). [3] YwIE was thought to be a protein-tyrosine-phosphatase, and McsB a tyrosine-kinase, [4] however in 2012 Elsholz et al. [3] showed that McsB is a protein-arginine-kinase (PAK) and YwlE is a phosphatase-arginine-phosphatase (PAP).

Contents

Many proteins rely on protein phosphatase activity for regulating their stability, localization, and interaction with other proteins. [3] Arginine modification is a post-translational protein modification in gram-positive bacteria, and protein arginine phosphorylation regulates transcription factors, in addition to tagging rogue proteins for degradation in gram-positive bacteria. [5] Like phosphorylation, dephosphorylation is a reversible post-translational event. It is reversible through the action of kinases (enzymes that adds a phosphate group to a protein via phosphorylation), and this antagonist activity of phosphorylation and dephosphorylation of proteins controls all aspect of prokaryotic and eukaryotic life. [5] In general, protein phosphatases play a crucial role in cell signaling regulation in both eukaryotes and prokaryotes. They act by removing a phosphate group from proteins, and their activity counteracts that of protein kinases. [6]

Function

YwIE is a member of the low-molecular-weight protein tyrosine phosphatase (LMW-PTP). [7] It is the only active PAP present in B.subtilis, and PAPs exhibits almost no activity against Protein Serine, Protein Tyrosine, and Protein Threonine peptides. [3] Also, YwIE has been shown to play a role in B.Subtilis's resistance to stress. Elsholz et al. [3] (2012), reported in their paper that protein arginine phosphorylation likely plays a critical physiological and regulatory role in bacteria. They showed that protein arginine phosphorylation is involved in the regulation of homeostasis, biofilm formation, motility, competence, stress, and stringent responses by regulating gene expression and protein activity in Bacillus Subtilis. [3] Their results suggested that the combined action of protein arginine phosphatase and kinase allows for rapid and reversible regulation of protein activity. Also, that protein-arginine-phosphatases reverse the effect of protein arginine kinases (PAKs) in living organisms. [3] In B.Subtilis, YwIE, a PAP, counteracts the action of McsB, a protein arginine kinase (PAK). McsB phosphorylates arginine residues in the winged helix-turn-helix domain of CtsR4, preventing it from binding to DNA, allowing for the expression of the repressed gene. However, YwIE is capable of restoring the DNA-binding ability of the CtsR repressor, a stress response & heat shock regulator in B.Subtilis, by reversing the McsB-mediated phosphorylation4. It accomplishes this by dephosphorylating the CtsR Protein. Additionally, McsB and YwIE are capable of differentiating between phosphoarginine and other amino acid residues [5] [8]

Known PAPs

As of 2020, YwIE is the only known active PAP in B.Subtilis, although Fuhrmann et al. (2013). [9] identified a YwIE homolog in Drosophila, but its role in the specie is still unknown. In contrast, Suzuki et al. (2013) identified the presence of McsB in over 150 bacteria species [5]

Mechanism

The specific molecular mechanism of action of the ywIE protein is currently unknown. [1] However, YwIE is believed to dephosphorylate phosphoarginine residues using a concerted, 2-step process via SN2 reactions. [1] Step 1 involves a nucleophilic attack of Cys7 on the phosphorus atom of the phosphoric group. [1] Then a thiophosphate intermediate is formed. In the second step, a phosphorylation-enzyme intermediate is hydrolyzed following the deprotonation of a water molecule by Asp118. [1] Fuhrmann et al. [1] (2016) believe that Asp118 likely promotes the reaction through the stabilization of the positive charge of the amino group via electrostatic interaction.

Sample general dephosphorylation reaction equation:

History

2005: YwIE was classified as a tyrosine phosphatase and McsB was identified as a tyrosine Kinase

In 2005, Suskiewicz et al. [1] classified the enzyme YwIE as a tyrosine phosphatase. And Kirstein et al. [4] (2005) found that McsB is a tyrosine kinase that needs McsA to become activated. They also found that the interaction of McsA and McsB with CtsR results in the formation of a 3-protein complex that stops the binding of CtsR to its target DNA and leads to subsequent phosphorylation of McsB, McsA, and CtsR.

2009: McsB was unequivocally identified as a protein arginine kinase

In their study, Fuhrmann et al. [10] (2009), performed a biochemical and structural analysis of the bacterial transcriptional regulators CtsR/McsB stress response. They sort to clarify and outline the exact function of CtsR and McsB in bacterial stress response. So, they screened proteins from various gram-negative bacteria for recombinant production and succeeded in reconstituting the Bacillus stearothermophilus CtsR/McsB system in vitro. Subsequently, they identified McsB as a protein kinase that targets arginine.

2012: YwlE was identified as a protein arginine phosphatase (PAP) in vivo & McsB was identified as a protein arginine kinase (PAK)

Elsholz et al. [3] (2012), showed that McsB and YwlE are a protein arginine kinase and phosphatase, rather than a tyrosine kinase and phosphatase because they observed only an McsB/YwlE-dependent detection of protein arginine phosphorylation or dephosphorylation in vivo. Specifically, they suggested that YwIE acts as a PAP in vivo.

McsB and YwlE were thought to be tyrosine kinases and phosphatases. [4] However,  in 2012, Elsholz et al. [3] detected 121 arginine phosphorylation sites in 87 proteins in living Bacillus Subtilis (B.subtillis), a gram-positive bacterium present in soil and human gastrointestinal tract. Their observations led them to believe that protein arginine phosphorylation exists in vivo as a posttranslational modification in bacteria. The arginine-phosphorylated proteins they detected were distributed among "distinct physiological classes of proteins" such as regulators, metabolic enzymes, stress, and ribosomal proteins. This result suggested that YwlE acts as a protein arginine phosphatase that explicitly dephosphorylates arginine residues both in vitro and in vivo [3]

Secondly, Elsholz et al. [3] (2012) were only able to detect protein arginine phosphorylation in a YwIE mutant gene and not the wild-type strain. But protein phosphorylates on either serine, threonine, or tyrosine were detected in both wild-type and a YwIE mutant strain in equal amounts. Therefore, they thought that YwIE might solely act as a protein arginine phosphatase. That is, the detection of protein arginine phosphorylation depended on the presence of YwIE. They confirmed this hypothesis after failing to detect protein arginine phosphorylation after (1) analyzing a mutant extract treated in vitro with purified YwIE protein before conducting mass spectroscopy analysis; and (2) overexpressing the YwIE in trans in a YwIE mutant in-vivo. The close interaction of the arginine phosphorylated proteins with YwIE suggested that the stability of the modifications was indeed influenced by the YwIE protein.

Related Research Articles

<span class="mw-page-title-main">Protein kinase</span> Enzyme that adds phosphate groups to other proteins

A protein kinase is a kinase which selectively modifies other proteins by covalently adding phosphates to them (phosphorylation) as opposed to kinases which modify lipids, carbohydrates, or other molecules. Phosphorylation usually results in a functional change of the target protein (substrate) by changing enzyme activity, cellular location, or association with other proteins. The human genome contains about 500 protein kinase genes and they constitute about 2% of all human genes. There are two main types of protein kinase. The great majority are serine/threonine kinases, which phosphorylate the hydroxyl groups of serines and threonines in their targets. Most of the others are tyrosine kinases, although additional types exist. Protein kinases are also found in bacteria and plants. Up to 30% of all human proteins may be modified by kinase activity, and kinases are known to regulate the majority of cellular pathways, especially those involved in signal transduction.

A protein phosphatase is a phosphatase enzyme that removes a phosphate group from the phosphorylated amino acid residue of its substrate protein. Protein phosphorylation is one of the most common forms of reversible protein posttranslational modification (PTM), with up to 30% of all proteins being phosphorylated at any given time. Protein kinases (PKs) are the effectors of phosphorylation and catalyse the transfer of a γ-phosphate from ATP to specific amino acids on proteins. Several hundred PKs exist in mammals and are classified into distinct super-families. Proteins are phosphorylated predominantly on Ser, Thr and Tyr residues, which account for 79.3, 16.9 and 3.8% respectively of the phosphoproteome, at least in mammals. In contrast, protein phosphatases (PPs) are the primary effectors of dephosphorylation and can be grouped into three main classes based on sequence, structure and catalytic function. The largest class of PPs is the phosphoprotein phosphatase (PPP) family comprising PP1, PP2A, PP2B, PP4, PP5, PP6 and PP7, and the protein phosphatase Mg2+- or Mn2+-dependent (PPM) family, composed primarily of PP2C. The protein Tyr phosphatase (PTP) super-family forms the second group, and the aspartate-based protein phosphatases the third. The protein pseudophosphatases form part of the larger phosphatase family, and in most cases are thought to be catalytically inert, instead functioning as phosphate-binding proteins, integrators of signalling or subcellular traps. Examples of membrane-spanning protein phosphatases containing both active (phosphatase) and inactive (pseudophosphatase) domains linked in tandem are known, conceptually similar to the kinase and pseudokinase domain polypeptide structure of the JAK pseudokinases. A complete comparative analysis of human phosphatases and pseudophosphatases has been completed by Manning and colleagues, forming a companion piece to the ground-breaking analysis of the human kinome, which encodes the complete set of ~536 human protein kinases.

<span class="mw-page-title-main">Kinase</span> Enzyme catalyzing transfer of phosphate groups onto specific substrates

In biochemistry, a kinase is an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates. This process is known as phosphorylation, where the high-energy ATP molecule donates a phosphate group to the substrate molecule. This transesterification produces a phosphorylated substrate and ADP. Conversely, it is referred to as dephosphorylation when the phosphorylated substrate donates a phosphate group and ADP gains a phosphate group. These two processes, phosphorylation and dephosphorylation, occur four times during glycolysis.

<span class="mw-page-title-main">Phosphatase</span> Enzyme which catalyzes the removal of a phosphate group from a molecule

In biochemistry, a phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester into a phosphate ion and an alcohol. Because a phosphatase enzyme catalyzes the hydrolysis of its substrate, it is a subcategory of hydrolases. Phosphatase enzymes are essential to many biological functions, because phosphorylation and dephosphorylation serve diverse roles in cellular regulation and signaling. Whereas phosphatases remove phosphate groups from molecules, kinases catalyze the transfer of phosphate groups to molecules from ATP. Together, kinases and phosphatases direct a form of post-translational modification that is essential to the cell's regulatory network.

In biochemistry, dephosphorylation is the removal of a phosphate (PO43−) group from an organic compound by hydrolysis. It is a reversible post-translational modification. Dephosphorylation and its counterpart, phosphorylation, activate and deactivate enzymes by detaching or attaching phosphoric esters and anhydrides. A notable occurrence of dephosphorylation is the conversion of ATP to ADP and inorganic phosphate.

<span class="mw-page-title-main">Receptor tyrosine kinase</span> Class of enzymes

Receptor tyrosine kinases (RTKs) are the high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. Of the 90 unique tyrosine kinase genes identified in the human genome, 58 encode receptor tyrosine kinase proteins. Receptor tyrosine kinases have been shown not only to be key regulators of normal cellular processes but also to have a critical role in the development and progression of many types of cancer. Mutations in receptor tyrosine kinases lead to activation of a series of signalling cascades which have numerous effects on protein expression. Receptor tyrosine kinases are part of the larger family of protein tyrosine kinases, encompassing the receptor tyrosine kinase proteins which contain a transmembrane domain, as well as the non-receptor tyrosine kinases which do not possess transmembrane domains.

<span class="mw-page-title-main">Phosphorylation cascade</span>

A phosphorylation cascade is a sequence of signaling pathway events where one enzyme phosphorylates another, causing a chain reaction leading to the phosphorylation of thousands of proteins. This can be seen in signal transduction of hormone messages. A signaling pathway begins at the cell surface where a hormone or protein binds to a receptor at the extracellular matrix. The interactions between the molecule and receptor cause a conformational change at the receptor, which activates multiple enzymes or proteins. These enzymes activate secondary messengers, which leads to the phosphorylation of thousands of proteins. The end product of a phosphorylation cascade is the changes occurring inside the cell.

<span class="mw-page-title-main">PTPN1</span> Protein-coding gene in the species Homo sapiens

Tyrosine-protein phosphatase non-receptor type 1 also known as protein-tyrosine phosphatase 1B (PTP1B) is an enzyme that is the founding member of the protein tyrosine phosphatase (PTP) family. In humans it is encoded by the PTPN1 gene. PTP1B is a negative regulator of the insulin signaling pathway and is considered a promising potential therapeutic target, in particular for treatment of type 2 diabetes. It has also been implicated in the development of breast cancer and has been explored as a potential therapeutic target in that avenue as well.

In enzymology, arginine kinase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Histidine kinase</span>

Histidine kinases (HK) are multifunctional, and in non-animal kingdoms, typically transmembrane, proteins of the transferase class of enzymes that play a role in signal transduction across the cellular membrane. The vast majority of HKs are homodimers that exhibit autokinase, phosphotransfer, and phosphatase activity. HKs can act as cellular receptors for signaling molecules in a way analogous to tyrosine kinase receptors (RTK). Multifunctional receptor molecules such as HKs and RTKs typically have portions on the outside of the cell that bind to hormone- or growth factor-like molecules, portions that span the cell membrane, and portions within the cell that contain the enzymatic activity. In addition to kinase activity, the intracellular domains typically have regions that bind to a secondary effector molecule or complex of molecules that further propagate signal transduction within the cell. Distinct from other classes of protein kinases, HKs are usually parts of a two-component signal transduction mechanisms in which HK transfers a phosphate group from ATP to a histidine residue within the kinase, and then to an aspartate residue on the receiver domain of a response regulator protein. More recently, the widespread existence of protein histidine phosphorylation distinct from that of two-component histidine kinases has been recognised in human cells. In marked contrast to Ser, Thr and Tyr phosphorylation, the analysis of phosphorylated Histidine using standard biochemical and mass spectrometric approaches is much more challenging, and special procedures and separation techniques are required for their preservation alongside classical Ser, Thr and Tyr phosphorylation on proteins isolated from human cells.

In enzymology, a [isocitrate dehydrogenase (NADP+)] kinase (EC 2.7.11.5) is an enzyme that catalyzes the chemical reaction:

<span class="mw-page-title-main">Protein phosphorylation</span> Process of introducing a phosphate group on to a protein

Protein phosphorylation is a reversible post-translational modification of proteins in which an amino acid residue is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Phosphorylation alters the structural conformation of a protein, causing it to become activated, deactivated, or otherwise modifying its function. Approximately 13000 human proteins have sites that are phosphorylated.

<span class="mw-page-title-main">PTPN18</span> Protein-coding gene in the species Homo sapiens

Tyrosine-protein phosphatase non-receptor type 18 is an enzyme that in humans is encoded by the PTPN18 gene.

<span class="mw-page-title-main">Tyrosine phosphorylation</span> Phosphorylation of peptidyl-tyrosine

Tyrosine phosphorylation is the addition of a phosphate (PO43−) group to the amino acid tyrosine on a protein. It is one of the main types of protein phosphorylation. This transfer is made possible through enzymes called tyrosine kinases. Tyrosine phosphorylation is a key step in signal transduction and the regulation of enzymatic activity.

Non-catalytic tyrosine-phosphorylated receptors (NTRs), also called immunoreceptors or Src-family kinase-dependent receptors, are a group of cell surface receptors expressed by leukocytes that are important for cell migration and the recognition of abnormal cells or structures and the initiation of an immune response. These transmembrane receptors are not grouped into the NTR family based on sequence homology, but because they share a conserved signalling pathway utilizing the same signalling motifs. A signaling cascade is initiated when the receptors bind their respective ligand resulting in cell activation. For that tyrosine residues in the cytoplasmic tail of the receptors have to be phosphorylated, hence the receptors are referred to as tyrosine-phosphorylated receptors. They are called non-catalytic receptors, as the receptors have no intrinsic tyrosine kinase activity and cannot phosphorylate their own tyrosine residues. Phosphorylation is mediated by additionally recruited kinases. A prominent member of this receptor family is the T-cell receptor.

H3S10P is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the phosphorylation the 10th serine residue of the histone H3 protein.

H3S28P is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the phosphorylation the 28th serine residue of the histone H3 protein.

H3Y41P is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the phosphorylation the 41st tyrosine residue of the histone H3 protein.

H3T11P is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the phosphorylation the 11th threonine residue of the histone H3 protein.

H3T6P is an epigenetic modification to the DNA packaging protein histone H3. It is a mark that indicates the phosphorylation of the 6th threonine residue of the histone H3 protein.

References

  1. 1 2 3 4 5 6 7 Fuhrmann, Jakob; Subramanian, Venkataraman; Kojetin, Douglas J.; Thompson, Paul R. (2016-08-18). "Activity-based profiling reveals a regulatory link between oxidative stress and protein arginine phosphorylation". Cell Chemical Biology. 23 (8): 967–977. doi:10.1016/j.chembiol.2016.07.008. ISSN   2451-9456. PMC   5157131 . PMID   27524296.
  2. ↑ Bertolotti, Anne (2018-12-12). "The split protein phosphatase system". Biochemical Journal. 475 (23): 3707–3723. doi:10.1042/BCJ20170726. ISSN   0264-6021. PMC   6282683 . PMID   30523060.
  3. 1 2 3 4 5 6 7 8 9 10 11 Elsholz, A. K. W.; Turgay, K.; Michalik, S.; Hessling, B.; Gronau, K.; Oertel, D.; Mader, U.; Bernhardt, J.; Becher, D.; Hecker, M.; Gerth, U. (2012-05-08). "Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis". Proceedings of the National Academy of Sciences. 109 (19): 7451–7456. doi: 10.1073/pnas.1117483109 . ISSN   0027-8424. PMC   3358850 . PMID   22517742.
  4. 1 2 3 Kirstein, Janine; Zühlke, Daniela; Gerth, Ulf; Turgay, Kürşad; Hecker, Michael (2005-10-05). "A tyrosine kinase and its activator control the activity of the CtsR heat shock repressor in B. subtilis". The EMBO Journal. 24 (19): 3435–3445. doi:10.1038/sj.emboj.7600780. ISSN   0261-4189. PMC   1276163 . PMID   16163393.
  5. 1 2 3 4 Suskiewicz, M.J.; Heuck, A.; Vu, L.D.; Clausen, T. (2019-02-06). "Protein arginine kinase McsB in the apo state". doi:10.2210/pdb6fh1/pdb. S2CID   145933241 . Retrieved 2020-12-07.{{cite journal}}: Cite journal requires |journal= (help)
  6. ↑ Elsholz, A. K. W.; Turgay, K.; Michalik, S.; Hessling, B.; Gronau, K.; Oertel, D.; Mader, U.; Bernhardt, J.; Becher, D.; Hecker, M.; Gerth, U. (2012-05-08). "Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis". Proceedings of the National Academy of Sciences. 109 (19): 7451–7456. doi: 10.1073/pnas.1117483109 . ISSN   0027-8424. PMC   3358850 . PMID   22517742.
  7. ↑ Musumeci, Lucia; Bongiorni, Cristina; Tautz, Lutz; Edwards, Robert A.; Osterman, Andrei; Perego, Marta; Mustelin, Tomas; Bottini, Nunzio (2005-07-01). "Low-Molecular-Weight Protein Tyrosine Phosphatases of Bacillus subtilis". Journal of Bacteriology. 187 (14): 4945–4956. doi: 10.1128/JB.187.14.4945-4956.2005 . ISSN   0021-9193. PMC   1169535 . PMID   15995210.
  8. ↑ Sarmiento, M.; Puius, Y. A.; Vetter, S. W.; Keng, Y. F.; Wu, L.; Zhao, Y.; Lawrence, D. S.; Almo, S. C.; Zhang, Z. Y. (2000-07-18). "Structural basis of plasticity in protein tyrosine phosphatase 1B substrate recognition". Biochemistry. 39 (28): 8171–8179. doi:10.1021/bi000319w. ISSN   0006-2960. PMID   10889023.
  9. ↑ Fuhrmann, Jakob; Mierzwa, Beata; Trentini, Débora B.; Spiess, Silvia; Lehner, Anita; Charpentier, Emmanuelle; Clausen, Tim (2013-06-27). "Structural basis for recognizing phosphoarginine and evolving residue-specific protein phosphatases in gram-positive bacteria". Cell Reports. 3 (6): 1832–1839. doi: 10.1016/j.celrep.2013.05.023 . ISSN   2211-1247. PMID   23770242.
  10. ↑ Fuhrmann, Jakob; Subramanian, Venkataraman; Thompson, Paul R. (2013-09-20). "Targeting the Arginine Phosphatase YwlE with a Catalytic Redox-Based Inhibitor". ACS Chemical Biology. 8 (9): 2024–2032. doi:10.1021/cb4001469. ISSN   1554-8929. PMID   23838530.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.