2C03

GDP COMPLEX OF SRP GTPASE FFH NG DOMAIN

Summary for 2C03

• Entry DOI: 10.2210/pdb2c03/pdb
• Related: 1FFH 1JPJ 1JPN 1LS1 1NG1 1O87 1OKK 1RJ9 1RY1 2BQS 2BQT 2C04 2FFH 2NG1 3NG1
• Descriptor: SIGNAL RECOGNITION PARTICLE PROTEIN, GUANOSINE-5'-DIPHOSPHATE, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: ffh, gmppnp, gtp-binding, ng domain, rna-binding, signaling protein, srp54 nucleotide-binding, signal protein
• Biological source: THERMUS AQUATICUS
• Total number of polymer chains: 2
• Total formula weight: 67509.40

Authors

Ramirez, U.D.,Preininger, A.M.,Freymann, D.M. (deposition date: 2005-08-25, release date: 2007-02-13, Last modification date: 2023-12-13)

Primary citation

Ramirez, U.D.,Focia, P.J.,Freymann, D.M.
Nucleotide-Binding Flexibility in Ultrahigh-Resolution Structures of the Srp Gtpase Ffh
Acta Crystallogr.,Sect.D, 64:1043-, 2008

PubMed Abstract: Two structures of the nucleotide-bound NG domain of Ffh, the GTPase subunit of the bacterial signal recognition particle (SRP), have been determined at ultrahigh resolution in similar crystal forms. One is GDP-bound and one is GMPPCP-bound. The asymmetric unit of each structure contains two protein monomers, each of which exhibits differences in nucleotide-binding conformation and occupancy. The GDP-bound Ffh NG exhibits two binding conformations in one monomer but not the other and the GMPPCP-bound protein exhibits full occupancy of the nucleotide in one monomer but only partial occupancy in the other. Thus, under the same solution conditions, each crystal reveals multiple binding states that suggest that even when nucleotide is bound its position in the Ffh NG active site is dynamic. Some differences in the positioning of the bound nucleotide may arise from differences in the crystal-packing environment and specific factors that have been identified include the relative positions of the N and G domains, small conformational changes in the P-loop, the positions of waters buried within the active site and shifts in the closing loop that packs against the guanine base. However, ;loose' binding may have biological significance in promoting facile nucleotide exchange and providing a mechanism for priming the SRP GTPase prior to its activation in its complex with the SRP receptor.

PubMed: 18931411
DOI: 10.1107/S090744490802444X

Experimental method

X-RAY DIFFRACTION (1.24 Å)