PDBsum entry 2ng1

Signal recognition

PDB id: 2ng1

Contents

Protein chain

293 a.a.

Ligands

GDP

DIO

EDO ×2

Waters ×72

References listed in PDB file

Key reference

Title

Functional changes in the structure of the srp gtpase on binding gdp and mg2+gdp.

Authors

D.M.Freymann, R.J.Keenan, R.M.Stroud, P.Walter.

Ref.

Nat Struct Biol, 1999, 6, 793-801. [DOI no: 10.1038/11572]

PubMed id

10426959

Abstract

Ffh is a component of a bacterial ribonucleoprotein complex homologous to the signal recognition particle (SRP) of eukaryotes. It comprises three domains that mediate both binding to the hydrophobic 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 Mg2+GDP and GDP have been determined at 2.0 A 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.

Figure 3.
Figure 3. Comparison of the GDP-binding interactions in Ffh (G2) with those in Ras (4q21). a, In Ffh, the 'closing loop' wraps around Lys 117 and forms van der Waals contacts with the guanine base. Lys 117 and Thr 114 are bridged by a buried water molecule that forms the floor of the binding site and provides a hydrogen bond to the guanine N7. Motifs I and IV are coupled by interactions of Lys 246 and Thr 245 with carbonyl oxygens of the motif I backbone. b, In Ras, Asn 116 bridges the binding site by hydrogen-bonding the carbonyl oxygen of motif I Val 14 and the hydroxyl of Thr 144 of the G-5 loop. The G-5 loop provides a hydrogen bond from Ala 146 to the guanine O6; similar O6 hydrogen bonding is present in other GTPases, but is absent in Ffh. The hydrophobic character of the floor of the binding site is also typical of most other GTPases (but not the Rho subfamily of GTPases, which includes buried water molecules^46, ^47). A packing interaction structurally analogous to the 'closing loop' in Ffh is provided by Phe 28 from the 1-helix in Ras; in other GTPases, it is provided by elements of the 4 loop.

Figure 5.
Figure 5. Cartoon summarizing the structural consequences of binding of Mg^2+GDP and GDP to NG. The three structures suggest a pathway for stepwise release of Mg^2+ and GDP. GTPase sequence motifs I, II and III interact with the magnesium and phosphate groups. On release of Mg^2+ (or perhaps Mg^2+P[i]) they can form a network of hydrogen bonding interactions that stabilizes the nucleotide-free protein. Gln 144 is adjacent to the active site and can hydrogen bond the -phosphate of the product GDP, thereby opening up the active site for product release. The closing loop, depicted at the bottom of the active site, packs against the bound nucleotide but on nucleotide release moves away and becomes disordered. The position of motif IV, which provides recognition of the guanine base, is coupled to the position of the N domain. The concerted action of the four elements presumably allows regulation of binding and release, and can explain the low nucleotide affinity of the SRP GTPase.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1999, 6, 793-801) copyright 1999.

Secondary reference #1

Title

Crystal structure of the signal sequence binding subunit of the signal recognition particle.

Authors

R.J.Keenan, D.M.Freymann, P.Walter, R.M.Stroud.

Ref.

Cell, 1998, 94, 181-191. [DOI no: 10.1016/S0092-8674(00)81418-X]

PubMed id

9695947

Figure 6.
Figure 6. The Hydrophobic Groove of the M Domain Is Not Empty in the CrystalThe flexible finger loop of one M domain (magenta; residues 337–355 shown) inserts into the proposed signal sequence binding groove of another M domain (white, molecular surface representation), forming a hydrophobic cavity in the center of the groove that may contain detergent from the crystallization solution. This protein–protein interaction may represent an example of the extent to which the M domain has evolved to accommodate a wide variety of hydrophobic sequences.

Figure 7.
Figure 7. The Arginine-Rich, Helix-Turn-Helix Motif of the M Domain(A) Stereo view of the HTH motif (αM3 to αM4) and a third helix (αM2) of the M domain (green) superimposed onto the corresponding region from the lac repressor (blue) ([9]). The least-squares overlap of α carbons was performed using LSQMAN ( [24]). Conserved residues contributing to the compact hydrophobic core of the lac repressor are indicated, along with their counterparts in the M domain. Helix αM4 extends beyond helix α2 of the lac repressor by vert, similar 3 additional turns and contains basic residues at an extended C terminus; these characteristics are similar to the recognition helix of homeodomain DNA-binding proteins ([14]).(B) Stereo view of the conserved SRP RNA-binding motif of Ffh. This view is rotated vert, similar 90° about the vertical axis with respect to the orientation in Figure 7A. Positively charged side chains located in helix αM3 are likely to mediate the specific interaction of the M domain with SRP RNA. Arg-387 and Arg-361 form well-ordered salt bridges with the conserved residues Glu-373 and Glu-398, respectively.

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #2

Title

Structure of the conserved gtpase domain of the signal recognition particle.

Authors

D.M.Freymann, R.J.Keenan, R.M.Stroud, P.Walter.

Ref.

Nature, 1997, 385, 361-364.

PubMed id

9002524