PDBsum entry 2ng1

Signal recognition

PDB id: 2ng1

Contents

Protein chain

293 a.a. *

Ligands

GDP

DIO

EDO ×2

Waters ×72

* Residue conservation analysis

PDB id:

2ng1

Name:

Signal recognition

Title:

N and gtpase domains of the signal sequence recognition protein ffh from thermus aquaticus

Structure:

Signal sequence recognition protein ffh. Chain: a. Fragment: ng gtpase fragment. Synonym: ffh. Engineered: yes. Mutation: yes

Source:

Thermus aquaticus. Organism_taxid: 271. Gene: ffh. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.02Å R-factor: 0.200 R-free: 0.290

Authors:

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

Key ref:

D.M.Freymann et al. (1999). Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+GDP. Nat Struct Biol, 6, 793-801. PubMed id: 10426959 DOI: 10.1038/11572

Date:

11-Sep-98 Release date: 30-Jul-99

Protein chain

O07347  (SRP54_THEAQ) -  Signal recognition particle protein from Thermus aquaticus

Seq: 430 a.a.

Struc: 293 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.6.5.4 - signal-recognition-particle GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

GTP + H2O = GDP (Bound ligand (Het Group name = GDP) corresponds exactly) + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/11572

Nat Struct Biol 6:793-801 (1999)

PubMed id: 10426959

Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+GDP.

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

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.

Selected figure(s)

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.

Figures were selected by an automated process.