PDBsum entry 1r8v

Hydrolase

PDB id: 1r8v

Contents

Protein chain

201 a.a.

Theoretical model

PDB id:

1r8v

Name:

Hydrolase

Title:

3d structure prediction of clpp2 protease from arabidopsis thaliana, using the crystal structure of e. Coli clpp (1tyf)

Structure:

Atp-dependent clp protease proteolytic subunit (clpp2). Chain: a. Ec: 3.4.21.92

Source:

Arabidopsis thaliana. Mouse-ear cress. Other_details: ecotype: columbia 0

Authors:

J.B.Peltier,D.R.Ripoll,G.Friso,A.Rudella,Y.Cai,J.Ytterberg, L.Giacomelli,J.Pillardy,K.J.Van Wijk

Key ref:

J.B.Peltier et al. (2004). Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications. J Biol Chem, 279, 4768-4781. PubMed id: 14593120 DOI: 10.1074/jbc.M309212200

Date:

28-Oct-03 Release date: 18-Nov-03

Protein chain

No UniProt id for this chain

Struc: 201 a.a.

DOI no: 10.1074/jbc.M309212200

J Biol Chem 279:4768-4781 (2004)

PubMed id: 14593120

Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications.

J.B.Peltier, D.R.Ripoll, G.Friso, A.Rudella, Y.Cai, J.Ytterberg, L.Giacomelli, J.Pillardy, K.J.van Wijk.

ABSTRACT

Tetradecameric Clp protease core complexes in non-photosynthetic plastids of roots, flower petals, and in chloroplasts of leaves of Arabidopsis thaliana were purified based on native mass and isoelectric point and identified by mass spectrometry. The stoichiometry between the subunits was determined. The protease complex consisted of one to three copies of five different serine-type protease Clp proteins (ClpP1,3-6) and four non-proteolytic ClpR proteins (ClpR1-4). Three-dimensional homology modeling showed that the ClpP/R proteins fit well together in a tetradecameric complex and also indicated unique contributions for each protein. Lateral exit gates for proteolysis products are proposed. In addition, ClpS1,2, unique to land plants, tightly interacted with this core complex, with one copy of each per complex. The three-dimensional modeling show that they do fit well on the axial sites of the ClpPR cores. In contrast to plastids, plant mitochondria contained a single approximately 320-kDa homo-tetradecameric ClpP2 complex, without association of ClpR or ClpS proteins. It is surprising that the Clp core composition appears identical in all three plastid types, despite the remarkable differences in plastid proteome composition. This suggests that regulation of plastid proteolysis by the Clp machinery is not through differential regulation of ClpP/R/S gene expression, but rather through substrate recognition mechanisms and regulated interaction of chaperone-like molecules (ClpS1,2 and others) to the ClpP/R core.

Selected figure(s)

Figure 6.
FIG. 6. Structure alignment of the models for the ClpP/R monomers with 1TYF [PDB] , 1NZY [PDB] , and 1HNO [PDB] . The alignments are based on the structure alignment between the 1TYF [PDB] monomer and its structural neighbors.a, 1TYF [PDB] eClpP;b, ConsRes indicates conserved residues in all the ClpP/R sequences;c, Cat.Site indicates residues forming the catalytic site;d, Put_Open indicates residues that are involved in the putative opening in the Clp core;e, SS indicates the secondary structure information of the specified molecule: E, extended; H, helix; T, turn.

Figure 9.
FIG. 9. Alignment of the ClpS sequences with the N-terminal domain of eClpA. NT-eClpA denotes the N-terminal domain of eClpA (PDB code 1K6K [PDB] ); COG542-eClpA indicates the consensus N-terminal domain of eClpA structures found by BLAST (NCBI CD, COG0542.1,ClpA; PSSM-Idm 10413); N domain denotes the Clp N-terminal domain found in one or two copies at the N terminus of ClpA and ClpB proteins from bacteria or eukaryotes. Color code: positions with polar residue conservation in blue; charge conservation in red, and hydrophobicity conservation in green. Conserved residues are shown in boldface. The magenta (LL1) and orange (LL2) rectangles indicate residues from two loop regions on ClpS1,2. The equivalent loops in NT-eClpA possibly provide most of the interacting surface when bound to eClpS.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 4768-4781) copyright 2004.

Figures were selected by an automated process.