PDBsum entry: 1t3e

Structural protein/signaling protein

PDB id: 1t3e

Contents

Protein chains

412 a.a. *

Ligands

ASN-ALA-ALA-LYS-LYS

SO4 ×8

* Residue conservation analysis

PDB id:

1t3e

Name:

Structural protein/signaling protein

Title:

Structural basis of dynamic glycine receptor clustering

Structure:

Gephyrin. Chain: a, b. Fragment: c-terminal domain. Synonym: putative glycine receptor-tubulin linker protein. Engineered: yes. 49-mer fragment of glycine receptor beta chain. Chain: p. Fragment: gephyrin binding region (residues 378-426). Synonym: glycine receptor 58 kda subunit.

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: gphn,gph. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: glrb. Other_details: modified with a tev site

Biol. unit:

Trimer (from PQS)

Resolution:

3.25Å R-factor: 0.246 R-free: 0.303

Authors:

M.Sola,V.N.Bavro,J.Timmins,T.Franz,S.Ricard-Blum,G.Schoehn, R.W.H.Ruigrok,I.Paarmann,T.Saiyed,G.A.O'Sullivan

Key ref:

M.Sola et al. (2004). Structural basis of dynamic glycine receptor clustering by gephyrin. EMBO J, 23, 2510-2519. PubMed id: 15201864 DOI: 10.1038/sj.emboj.7600256

Date:

26-Apr-04 Release date: 27-Jul-04

Protein chains

Q03555  (GEPH_RAT) -  Gephyrin

Seq: 768 a.a.

Struc: 412 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.10.1.1 - Molybdopterin molybdotransferase.
• Reaction: Adenylyl-molybdopterin + molybdate = molybdenum cofactor + AMP
• Cofactor: Zinc or magnesium
• Enzyme class 3: E.C.2.7.7.75 - Molybdopterin adenylyltransferase.
• Reaction: ATP + molybdopterin = diphosphate + adenylyl-molybdopterin
• Cofactor: Manganese or magnesium

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

 Gene Ontology (GO) functional annotation 

• Biological process: molybdopterin cofactor biosynthetic process (2 terms)

reference

DOI no: 10.1038/sj.emboj.7600256

EMBO J 23:2510-2519 (2004)

PubMed id: 15201864

Structural basis of dynamic glycine receptor clustering by gephyrin.

M.Sola, V.N.Bavro, J.Timmins, T.Franz, S.Ricard-Blum, G.Schoehn, R.W.Ruigrok, I.Paarmann, T.Saiyed, G.A.O'Sullivan, B.Schmitt, H.Betz, W.Weissenhorn.

ABSTRACT

Gephyrin is a bi-functional modular protein involved in molybdenum cofactor biosynthesis and in postsynaptic clustering of inhibitory glycine receptors (GlyRs). Here, we show that full-length gephyrin is a trimer and that its proteolysis in vitro causes the spontaneous dimerization of its C-terminal region (gephyrin-E), which binds a GlyR beta-subunit-derived peptide with high and low affinity. The crystal structure of the tetra-domain gephyrin-E in complex with the beta-peptide bound to domain IV indicates how membrane-embedded GlyRs may interact with subsynaptic gephyrin. In vitro, trimeric full-length gephyrin forms a network upon lowering the pH, and this process can be reversed to produce stable full-length dimeric gephyrin. Our data suggest a mechanism by which induced conformational transitions of trimeric gephyrin may generate a reversible postsynaptic scaffold for GlyR recruitment, which allows for dynamic receptor movement in and out of postsynaptic GlyR clusters, and thus for synaptic plasticity.

Selected figure(s)

Figure 2.
Figure 2 Negative staining EM of 'activated' gephyrin-300. (A) Proteoliposomes decorated with complexes formed by His -GST -GlyR (HR378 -426) and gephyrin-300 (see arrows) (scale bar, 100 nm). (B) Control proteoliposomes containing only the His -GST -GlyR (HR378 -426) fusion protein only. (C) Proteoliposomes containing GlyR -gephyrin-300 complexes (as seen in A) were dialyzed against ammonium acetate and liposomes were briefly 'solubilized' in 1% -octyl glucopyranoside prior to staining with uranylacetate. Network formation is schematically indicated for two areas highlighted by white squares next to panel C. (D) Soluble full-length gephyrin-200 shows single irregular particles. Some are indicated by black squares. Panels B -D are shown in the same magnification as indicated in panel A.

Figure 7.
Figure 7 Comparision of gephyrin-E and the E. coli MoeA structure. (A) Superposition of C-alpha atoms of one gephyrin-E monomer and one MoeA monomer (Xiang et al, 2001). The r.m.s.d. between the two monomers is 4.2 Å. (B, C) The movement of domain II leads to a more closed conformation of gephyrin-E with respect to the putative active site when compared to MoeA. This positions MPT binding residues Gly414 closer to Asp549 (B) than the corresponding residues Gly101 and Asp228 from MoeA (C). The corresponding monomers in panels B and C are shown as ribbon diagrams in different colors and the residues implicated in catalysis are shown as a ball and stick model.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 2510-2519) copyright 2004.

Figures were selected by the author.