Neurofibromin: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 8: | Line 8: | ||
[[Image:Nfdomains2.png|800 px|thumb|Figure 1. Domains of Neurofibromin.]] | [[Image:Nfdomains2.png|800 px|thumb|Figure 1. Domains of Neurofibromin.]] | ||
==== GRD domain ==== | ==== GRD domain ==== | ||
The Gap-related domain, or GRD, is the catalytic domain of neurofibromin. This domain also contains a tubulin-binding domain. Its main catalytic mechanism is the hydrolysis of GTP-bound Ras into GDP-bound Ras, which converts Ras from its active form into its inactive form. The GRD provides an arginine residue, known as the arginine finger, to Ras. | The Gap-related domain, or GRD, is the catalytic domain of neurofibromin. This domain also contains a tubulin-binding domain. Its main catalytic mechanism is the hydrolysis of GTP-bound Ras into GDP-bound Ras, which converts Ras from its active form into its inactive form. The GRD provides an arginine residue, known as the arginine finger, to Ras. <scene name='90/904326/Grd_closed_conformation/3'>grd closed conformation</scene> <scene name='90/904326/Open_conformation_with_grd_hig/3'>grd open conformation</scene> | ||
==== SEC-PH ==== | ==== SEC-PH ==== | ||
The Sec-PH domain is the lipid-binding domain of neurofibromin. In the <scene name='90/904326/Sec14ph_and_grd_closed/ | The Sec-PH domain is the lipid-binding domain of neurofibromin. In the <scene name='90/904326/Sec14ph_and_grd_closed/4'>closed conformation</scene> of neurofibromin, the hydrophobic core is blocked by the Gap-related domain. The <scene name='90/904326/Sec15ph_and_grd_open/4'>open conformation</scene> allows the hydrophobic core in the Sec cavity to be accessible and exposed. | ||
==== CSRD and CTD ==== | ==== CSRD and CTD ==== | ||
The Cysteine-Serine-rich domain (CSRD) and C-terminal domain (CTD) contain phosphorylation sites. The CSRD is able to be phosphorylated by protein kinases A and C. Phosphorylation by protein kinase C is a positive regulator of neurofibromin activity. The CTD is phosphorylated primarily by protein kinase C. This domain is a negative regulator of neurofibromin activity if particular residues are phosphorylated. It also plays an important role in tubulin binding, as it helps in the transition from metaphase to anaphase. CTD contains a nuclear localization signal as well. | The Cysteine-Serine-rich domain (CSRD) and C-terminal domain (CTD) contain phosphorylation sites. The CSRD is able to be phosphorylated by protein kinases A and C. Phosphorylation by protein kinase C is a positive regulator of neurofibromin activity. The CTD is phosphorylated primarily by protein kinase C. This domain is a negative regulator of neurofibromin activity if particular residues are phosphorylated. It also plays an important role in tubulin binding, as it helps in the transition from metaphase to anaphase. CTD contains a nuclear localization signal as well. | ||
| Line 16: | Line 16: | ||
====Conformations==== | ====Conformations==== | ||
=====Closed Conformation===== | =====Closed Conformation===== | ||
The closed state of neurofibromin has both protomers in a closed conformation, which inhibits the binding of Ras to the GRD of neurofibromin due to the HEAT/ARM blocking the GRD. A metal binding site between the N-HEAT/ARM domain and the GRD-Sec14-PH linker stabilize the closed conformation. This site is coordinated by three residues, C1032, H1558, and H1576, and a water molecule. This binding site is preferential for zinc- Zinc has been found to stabilize the closed conformation of neurofibromin. ....... | The <scene name='90/904326/Closed_conformation/3'>closed state</scene> of neurofibromin has both protomers in a closed conformation, which inhibits the binding of Ras to the GRD of neurofibromin due to the HEAT/ARM blocking the GRD. A metal binding site between the N-HEAT/ARM domain and the GRD-Sec14-PH linker stabilize the closed conformation. This site is coordinated by three residues, C1032, H1558, and H1576, and a water molecule. This binding site is preferential for zinc- Zinc has been found to stabilize the closed conformation of neurofibromin. ....... | ||
=====Open Conformation===== | =====Open Conformation===== | ||
The open state of neurofibromin has one protomer in a open conformation and the other in a closed conformation. The protomer in the open conformation allows for the binding of Ras because of reorientation of the GRD and Sec14-PH domains. In the open conformation, the metal binding site found in the closed conformation is lost due to separation of the N-HEAT/ARM and the cysteine residue from the histidine residues founds in the GRD-Sec14-PH linker. | The <scene name='90/904326/Open_conformation/3'>open state</scene> of neurofibromin has one protomer in a open conformation and the other in a closed conformation. The protomer in the open conformation allows for the binding of Ras because of reorientation of the GRD and Sec14-PH domains. In the open conformation, the metal binding site found in the closed conformation is lost due to separation of the N-HEAT/ARM and the cysteine residue from the histidine residues founds in the GRD-Sec14-PH linker. | ||
=====Transition Between Open and Closed Conformation===== | =====Transition Between Open and Closed Conformation===== | ||
In the transition from the closed state to the open state, several of the domains of neurofibromin rotate to make the binding site of neurofibromin more accessible . This rotation is able to occur due to the rotation of three connective linkers, L1, L2, and L3. L1 is located between an alpha helix 48 in N-HEAT and an alpha helix 49 in GRD. G1190 is a potential hinge point when L1 rotates and pushes the alpha helixes outwards to move the Gap-related domain. L3 is located between the Sec14-PH domain and the C-HEAT/ARM and aids in the movement of the Sec14-PH domain. Without this rotation, the membrane binding sites are occluded and inaccessible. The proximity of L1 and L3 has to be close to facilitate the rotation of the domains. | In the transition from the closed state to the open state, several of the domains of neurofibromin rotate to make the binding site of neurofibromin more accessible . This rotation is able to occur due to the rotation of three connective linkers, L1, L2, and L3. L1 is located between an alpha helix 48 in N-HEAT and an alpha helix 49 in GRD. G1190 is a potential hinge point when L1 rotates and pushes the alpha helixes outwards to move the Gap-related domain. L3 is located between the Sec14-PH domain and the C-HEAT/ARM and aids in the movement of the Sec14-PH domain. Without this rotation, the membrane binding sites are occluded and inaccessible. The proximity of L1 and L3 has to be close to facilitate the rotation of the domains. | ||
| Line 25: | Line 25: | ||
====Ras binding site==== | ====Ras binding site==== | ||
Ras and Neurofibromin associate through an arginine residue, 1276, that comes from neurofibromin. This arginine is referred to as the [http://https://en.wikipedia.org/wiki/Arginine_finger “arginine finger”] and assists in the hydrolysis of GTP by binding to a backbone carbon atom of tyrosine 32 of Ras when neurofibromin is in the open conformation. It points into the GTP binding site of Ras when neurofibromin is in the open conformation. R1276 also helps stabilize the position of Glutamine 61, a key catalytic residue, through hydrogen bonds. [[Image:arginine_finger.png|400 px|right|thumb|Figure 2: The arginine finger of NF interacts with GTP in Ras and catalytic glutamine through H-bonding]] | Ras and Neurofibromin associate through an arginine residue, 1276, that comes from neurofibromin. This arginine is referred to as the [http://https://en.wikipedia.org/wiki/Arginine_finger “arginine finger”] and assists in the hydrolysis of GTP by binding to a backbone carbon atom of tyrosine 32 of Ras when neurofibromin is in the open conformation. It points into the <scene name='90/904326/Active_site_with_residues/7'>GTP binding site</scene> of Ras when neurofibromin is in the open conformation. R1276 also helps stabilize the position of Glutamine 61, a key catalytic residue, through hydrogen bonds. [[Image:arginine_finger.png|400 px|right|thumb|Figure 2: The arginine finger of NF interacts with GTP in Ras and catalytic glutamine through H-bonding]] | ||
Glutamine 61 of Ras is a residue that facilitates the conversion of GTP to GDP, turning Ras from its active state to inactive state. There is a catalytic water molecule that glutamine interacts with to position the molecule for a nucleophilic attack on the gamma phosphate of GTP. Mutations of this residue have been related to lower rates of hydrolysis. <ref name= ''Frech''>PMID:8136358</ref>. Tyrosine 32 makes water-mediated hydrogen bonds with the gamma phosphate of GTP. This position is also where Ras is phosphorylation to promote the activity of GTPase-activating proteins and GTP hydrolysis. <ref name= ''Bunda''>DOI:10.1038/ncomms9859</ref> | Glutamine 61 of Ras is a residue that facilitates the conversion of GTP to GDP, turning Ras from its active state to inactive state. There is a catalytic water molecule that glutamine interacts with to position the molecule for a nucleophilic attack on the gamma phosphate of GTP. Mutations of this residue have been related to lower rates of hydrolysis. <ref name= ''Frech''>PMID:8136358</ref>. Tyrosine 32 makes water-mediated hydrogen bonds with the gamma phosphate of GTP. This position is also where Ras is phosphorylation to promote the activity of GTPase-activating proteins and GTP hydrolysis. <ref name= ''Bunda''>DOI:10.1038/ncomms9859</ref> | ||
