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Abstract
Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+ GDP.
Freyman, DM; Keenan, RJ; Stroud, RM; and Walter, P.
Nature Structural Biology 6, 793-801, August 1999
Brookhaven Protein Data Bank Accession Nos. 1NG1, 2NG1 , 3NG1
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Ffh is a component of a bacterial ribonucleoprotein complex homologous to the signal recognition particle (SRP) of eukaryotes. It consists of three domains that mediate both binding to the hydro- phobic signal sequence of the nascent polypeptide and the GTP-dependent interaction of Ffh with a structurally homologous GTPase of the SRP receptor. The X-ray structures of the two-domain 'NG' GTPase of Ffh in complex with MgÉ2;+GDP and GDP have been determined at 2.0 Å resolution.
The structures explain the low nucleotide affinity of Ffh and locate two regions of structural mobility at opposite sides of the nucleotide-binding site. One of these regions includes highly conserved sequence motifs that presumably contribute to the structural trigger signaling the GTP- bound state. The other includes the highly conserved interface between the N and G domains, and supports the hypothesis that the N domain regulates or signals the nucleotide occupancy of the G domain. Diagrams below show the functionally important flexibility in the structures of the NG domain.
The motif II corner of the IBD is destabilized upon binding MgÉ2;+GDP. Crystallographic temperature factors are mapped onto the Ca backbone of G2, with color ranging from blue (B-factor = 10 ÅÉ2;), to yellow (70 ÅÉ2;). The main chain atoms of motif II (residues Thr 136-Ala 140) show substantial disorder, as do the amino-terminal residues of helix a 2 that follow motif III. |
The interface between N and G domains is flexible. Four structures of the Ffh NG (A1, G1, A2, G2) are superimposed over the core of the G domain. The magnitude of the shift relative to the apo (A1) structure is mapped onto the Ca backbone of each, using a color gradient that ranges from blue (<0.01 Å shift) to yellow (2.5 Å). The G domain, particularly the 50 residues of the IBD ( at the right of the figure), is fairly rigid. The shift in the position of the N domain accompanies movement of the motif IV and the 'closing' loops toward the bound nucleotide. |
Disruption of three hydrogen bonds of the Arg 191 side chain frees Gly 190 in the MgÉ2;+GDP complex. Backbone atoms of motifs I, II and III in the apo and MgÉ2;+GDP complex structures are superimposed, along with the hydrogen bonded conformation of the Arg 191 and Asp 135 side chains seen in the apo structure. The hydrogen bond (upper left) between main chain atoms of motifs I and III is maintained in each structure and may help position the two motifs. |
Transition of helix a 3 between a- and 310-conformations. The main chain atoms of helix a 3 in its 'GDP' 310/a conformation are shown superimposed on a Ca diagram of the shorter 'apo' a-helical conformation. The N-terminal 310 hydrogen bonding pattern is indicated, as are the two water molecules that interject into the helix. Several highly conserved side chains are shown; Asp 42 of the ALLEADV motif forms a hydrogen bond with the backbone amide of Gln 224. Brookhaven Protein Data Bank Accession Nos. 1NG1, 2NG1 & 3NG1 |
