PDBsum entry 2zle

Hydrolase

PDB id: 2zle

Contents

Protein chains

(+ 6 more) 396 a.a. *

346 a.a. *

* Residue conservation analysis

PDB id:

2zle

Name:

Hydrolase

Title:

Cryo-em structure of degp12/omp

Structure:

Protease do. Chain: a, b, c, e, f, g, h, i, j, k, l, m. Synonym: degp. Engineered: yes. Outer membrane protein c. Chain: d. Synonym: porin ompc, outer membrane protein 1b. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: degp, htra, ptd. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ompc, meoa, par. Expression_system_taxid: 562

Authors:

E.Schaefer,H.R.Saibil

Key ref:

T.Krojer et al. (2008). Structural basis for the regulated protease and chaperone function of DegP. Nature, 453, 885-890. PubMed id: 18496527 DOI: 10.1038/nature07004

Date:

09-Apr-08 Release date: 03-Jun-08

Protein chains

P0C0V0  (DEGP_ECOLI) -  Periplasmic serine endoprotease DegP from Escherichia coli (strain K12)

Seq: 474 a.a.

Struc: 396 a.a.

Protein chain

P06996  (OMPC_ECOLI) -  Outer membrane porin C from Escherichia coli (strain K12)

Seq: 367 a.a.

Struc: 346 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, B, C, E, F, G, H, I, J, K, L, M: E.C.3.4.21.107 - peptidase Do.
• Enzyme class 2: Chain D: E.C.?

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.

DOI no: 10.1038/nature07004

Nature 453:885-890 (2008)

PubMed id: 18496527

Structural basis for the regulated protease and chaperone function of DegP.

T.Krojer, J.Sawa, E.Schäfer, H.R.Saibil, M.Ehrmann, T.Clausen.

ABSTRACT

All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms underlying the regulated protease and chaperone function of DegP from Escherichia coli. We show that binding of misfolded proteins transforms hexameric DegP into large, catalytically active 12-meric and 24-meric multimers. A structural analysis of these particles revealed that DegP represents a protein packaging device whose central compartment is adaptable to the size and concentration of substrate. Moreover, the inner cavity serves antagonistic functions. Whereas the encapsulation of folded protomers of outer-membrane proteins is protective and might allow safe transit through the periplasm, misfolded proteins are eliminated in the molecular reaction chamber. Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases.

Selected figure(s)

Figure 2.
Figure 2: Regulation of protease activity by oligomer reassembly. a, Ribbon plot of the protease domain of DegP[6] (1kj9) and DegP[24], highlighting the mechanistically important loops LA*, LD, L1, L2 and L3. Residues of the catalytic triad (Asp 105, His 135 and Ala 210) are shown in stick mode and the loop nomenclature used^12, ^41 is indicated. b, Electron density of the active-site loops L1 and LD. The 2F[o] - F[c] simulated annealing omit map was calculated at 3.0 Å resolution (contoured at 1.1 ) after omitting loops L1 and LD from the refined model. The oxyanion hole (blue sphere) and the main-chain carbonyl group of Arg 207 are highlighted. The position of the latter oxygen is a distinctive feature of proteolytically active HtrA proteases. c, Denatured lysozyme and DegP[6] were incubated in different ratios and the resulting complexes were analysed by SEC. Left: incubation of different amounts of lysozyme (orange, 30 M; red, 300 M; blue, 600 M) with DegP[6] (15 M). Right: incubation of different amounts of DegP[6] (orange, 3 M; red, 15 M; blue, 65 M) with lysozyme (170 M). d, Brief incubation of wild-type DegP with casein (1 min, magenta line) resulted in the formation of the DegP[24]–casein complex (the pronounced low-molecular-mass peak represents unprocessed casein). After completion of degradation (30 min, green line), DegP recycled into its hexameric state. Composites of individual elution peaks are indicated on the SDS gel; the self-cleavage products of DegP are labelled DegP*.

Figure 5.
Figure 5: Cryo-electron microscopy structure of the DegP[12]–OMP complex. a, The asymmetric DegP[12]–OMP complex viewed along the approximate three-fold (top) and two-fold (bottom) axes. In the left panels the ribbon model of the DegP dodecamer is overlaid with the semi-transparent three-dimensional map. b, Central section of the DegP[12]–OMP electron microscopy map with an OmpC monomer (blue) modelled in the central density. The adjacent PDZ1 domains from neighbouring trimers are coloured in cyan and magenta. Three catalytic triads are coloured in red, green and blue and are shown magnified in the lower panel. Scale bar, 100 Å.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 453, 885-890) copyright 2008.

Figures were selected by an automated process.