PDBsum entry: 2fu3

Biosynthetic protein/structural protein

PDB id: 2fu3

Contents

Protein chains

405 a.a. *

Waters ×66

* Residue conservation analysis

PDB id:

2fu3

Name:

Biosynthetic protein/structural protein

Title:

Crystal structure of gephyrin e-domain

Structure:

Gephyrin. Chain: a, b. Fragment: e-domain, residues 318-736 (np 074056). Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: rattus norvegicus (norway rat). Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.202 R-free: 0.273

Authors:

E.Y.Kim,H.Schindelin

Key ref:

E.Y.Kim et al. (2006). Deciphering the structural framework of glycine receptor anchoring by gephyrin. EMBO J, 25, 1385-1395. PubMed id: 16511563 DOI: 10.1038/sj.emboj.7601029

Date:

25-Jan-06 Release date: 14-Mar-06

Protein chains

Q03555  (GEPH_RAT) -  Gephyrin

Seq: 768 a.a.

Struc: 405 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.7601029

EMBO J 25:1385-1395 (2006)

PubMed id: 16511563

Deciphering the structural framework of glycine receptor anchoring by gephyrin.

E.Y.Kim, N.Schrader, B.Smolinsky, C.Bedet, C.Vannier, G.Schwarz, H.Schindelin.

ABSTRACT

Glycine is the major inhibitory neurotransmitter in the spinal cord and brain stem. Gephyrin is required to achieve a high concentration of glycine receptors (GlyRs) in the postsynaptic membrane, which is crucial for efficient glycinergic signal transduction. The interaction between gephyrin and the GlyR involves the E-domain of gephyrin and a cytoplasmic loop located between transmembrane segments three and four of the GlyR beta subunit. Here, we present crystal structures of the gephyrin E-domain with and without the GlyR beta-loop at 2.4 and 2.7 A resolutions, respectively. The GlyR beta-loop is bound in a symmetric 'key and lock' fashion to each E-domain monomer in a pocket adjacent to the dimer interface. Structure-guided mutagenesis followed by in vitro binding and in vivo colocalization assays demonstrate that a hydrophobic interaction formed by Phe 330 of gephyrin and Phe 398 and Ile 400 of the GlyR beta-loop is crucial for binding.

Selected figure(s)

Figure 4.
Figure 4 ITC experiments with Geph-E and GlyR -loop variants. Overlaid binding isotherms of (A) Geph-E variants (WT, F330A, P713E and PPAA (P713A/P714A) and P2 Y673F titrated with WT GlyR -loop and (B) WT Geph-E titrated with GlyR -loop variants (WT, F398A, S399A, I400A, FI ( F398A/I400A) and FIF ( F398A/I400A/F408A)). All experiments were performed under the same conditions and the measured binding enthalpies are plotted as a function of the molar ratio of GlyR -loop to Geph-E. The P713E measurement was terminated earlier as no binding enthalpy could be detected. The binding parameters determined are summarized in Supplementary Table I.

Figure 5.
Figure 5 Transient expression of GFP-tagged gephyrin variants and DsRed-tagged GlyR -loop variants in HEK 293 cells. HEK 293 cells were individually transfected with WT (A1), F330A (B1) and P713E gephyrin (C1) or WT (A2), F398A (D2) and F398A/I400A/F408A GlyR -loop variants (E2). Coexpression with WT GlyR -loop (A3–5, B3–5, C3–5) and WT gephyrin (A3–5, D3–5, E3–5) is shown in the corresponding panels with green gephyrin clusters (A3–E3), clustered or diffusely distributed GlyR -loop (A4–E4) and the overlay of both images (A5–E5).

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 1385-1395) copyright 2006.

Figures were selected by an automated process.