Sandbox Reserved 824: Difference between revisions

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==Structure==

Domaines N, G, M /

''(Domaines N, G, M / ''

Interaction N-G => Domaine NG pour activité GTPase / Mention du domaine NG très similaire de SR alpha

''Interaction N-G => Domaine NG pour activité GTPase / Mention du domaine NG très similaire de SR alpha''

Domaine M avec partie rigide en c-term, partie flexible en n-term et grossièrement leurs fonctions

''Domaine M avec partie rigide en c-term, partie flexible en n-term et grossièrement leurs fonctions)''

SRP54 is composed of 3 domains: N terminal domain with 4 alpha-helices; G domain, central, corresponding to a GTPase activity and the M domain (Methionin Rich). M domain corresponds to 1qb2 protein.

SRP54M is composed by 504 Amino Acids, forming 7 alpha helices (h1 to h7). The helices 2 to 7 from the core protein, stabilized by hydrophobic residues such as Met382 (invariant) and by hydrogen and salt bonds involving conserved amino acids: Glu386, Arg402, and Arg405. The helix 1 extends from the core protein.

The protein was difficult to crystalize, and it appears in the crystals dimeres of 1QB2 protein.

1QB2 contains 2 binding domains:

:* Peptide signal binding domain

:* SRP RNA binding domain

: Signal peptide binding domain

This domain involves h2 to h4 to generate the hydrophobic groove witch will recognise and bind the nascent protein. It also involves a highly structured loop between h2 and h3: 17 amino acids (349 to 365) with the Met-Ile-Pro-Gly motif (351 to 354) and two phenylalanins (355 and 359). In addition of the loop and the three helices, h1 is located near the hydrophobic groove and is an equivalent of the signal peptide. This similarity explains the dimerization of 1QB2 in the crystal. Each h1 take place in the groove of the opposite monomer. Because of this interaction, we are able to suppose that h1 in vivo is involved in protection of the hydrophobic groove against solvents.

: SRP RNA binding domain

The RNA is linked to the 1QB2 protein by electrostatic potential. This interaction involves helices 5 and 6, but also some small parts of helices 4 and 7. This proposal is confirmed by experiments of directed site mutation (Gowda et al., 1998). It appears that some basics residues are required (Arg402 and Arg405) to maintain the core structure and the interaction with the RNA.

==Remarks:==

It is important to note the linkage between M and G subunits of SRP54, GTP hydrolysis in the G subunit could provide conformational changes and modify interactions, especially for electrostatic bonds with the signal peptide (released after hydrolysis).

==Fonctions==

Lien avec la structure, explications des intéractions en fonction des structures etc ...

''Lien avec la structure, explications des intéractions en fonction des structures etc ...

''

<scene name='56/568022/Hsrp54m_dimer/1'>hSRP54M Dimer</scene>

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@@ Line 28: / Line 28: @@
 ==Structure==
-Domaines N, G, M /
+''(Domaines N, G, M / ''
-Interaction N-G => Domaine NG pour activité GTPase / Mention du domaine NG très similaire de SR alpha
+''Interaction N-G => Domaine NG pour activité GTPase / Mention du domaine NG très similaire de SR alpha''
-Domaine M avec partie rigide en c-term, partie flexible en n-term et grossièrement leurs fonctions
+''Domaine M avec partie rigide en c-term, partie flexible en n-term et grossièrement leurs fonctions)''
+SRP54 is composed of 3 domains: N terminal domain with 4 alpha-helices; G domain, central, corresponding to a GTPase activity and the M domain (Methionin Rich). M domain corresponds to 1qb2 protein.
+SRP54M is composed by 504 Amino Acids, forming 7 alpha helices (h1 to h7). The helices 2 to 7 from the core protein, stabilized by hydrophobic residues such as Met382 (invariant) and by hydrogen and salt bonds involving conserved amino acids: Glu386, Arg402, and Arg405. The helix 1 extends from the core protein.
+The protein was difficult to crystalize, and it appears in the crystals dimeres of 1QB2 protein.
+QB2 contains 2 binding domains:
+:* Peptide signal binding domain
+:* SRP RNA binding domain
+: Signal peptide binding domain
+This domain involves h2 to h4 to generate the hydrophobic groove witch will recognise and bind the nascent protein. It also involves a highly structured loop between h2 and h3: 17 amino acids (349 to 365) with the Met-Ile-Pro-Gly motif (351 to 354) and two phenylalanins (355 and 359). In addition of the loop and the three helices, h1 is located near the hydrophobic groove and is an equivalent of the signal peptide. This similarity explains the dimerization of 1QB2 in the crystal. Each h1 take place in the groove of the opposite monomer. Because of this interaction, we are able to suppose that h1 in vivo is involved in protection of the hydrophobic groove against solvents.
+: SRP RNA binding domain
+The RNA is linked to the 1QB2 protein by electrostatic potential. This interaction involves helices 5 and 6, but also some small parts of helices 4 and 7. This proposal is confirmed by experiments of directed site mutation (Gowda et al., 1998). It appears that some basics residues are required (Arg402 and Arg405) to maintain the core structure and the interaction with the RNA.
+==Remarks:==
+It is important to note the linkage between M and G subunits of SRP54, GTP hydrolysis in the G subunit could provide conformational changes and modify interactions, especially for electrostatic bonds with the signal peptide (released after hydrolysis).
 ==Fonctions==
-Lien avec la structure, explications des intéractions en fonction des structures etc ...
+''Lien avec la structure, explications des intéractions en fonction des structures etc ...
+''
 <scene name='56/568022/Hsrp54m_dimer/1'>hSRP54M Dimer</scene>