1R90 - JenaLib

Title :   3D STRUCTURE PREDICTION OF CLPP3 PROTEASE FROM ARABIDOPSIS THALIANA, USING THE CRYSTAL STRUCTURE OF E. COLI CLPP (1TYF)

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

Date :   28 Oct 03 (Deposition) - 18 Nov 03 (Release) - 10 Feb 04 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A

Keywords :   Serine Protease, Clp Protease, Arabidopsis Thaliana (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Peltier, D. R. Ripoll, G. Friso, A. Rudella, Y. Cai, J. Ytterberg, L. Giacomelli, J. Pillardy, K. J. Van Wijk
Clp Protease Complexes From Photosynthetic And Non-Photosynthetic Plastids And Mitochondria Of Plants, Their Predicted Three-Dimensional Structures, And Functional Implications.
J. Biol. Chem. V. 279 4768 2004
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Theoretical Model

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:214
 aligned with CLPP3_ARATH | Q9SXJ6 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:214
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287    
          CLPP3_ARATH    78 LPSFEELDTTNMLLRQRIVFLGSQVDDMTADLVISQLLLLDAEDSERDITLFINSPGGSITAGMGIYDAMKQCKADVSTVCLGLAASMGAFLLASGSKGKRYCMPNSKVMIHQPLGTAGGKATEMSIRIREMMYHKIKLNKIFSRITGKPESEIESDTDRDNFLNPWEAKEYGLIDAVIDDGKPGLIAPIGDGTPPPKTKVWDLWKVEGTKKDN 291
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..eeehhhhhhhhh...ee....hhhhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------CLP_PROTEASE----------CLP_PROTEASE_H---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r90 A  78 LPSFEELDTTNMLLRQRIVFLGSQVDDMTADLVISQLLLLDAEDSERDITLFINSPGGSITAGMGIYDAMKQCKADVSTVCLGLAASMGAFLLASGSKGKRYCMPNSKVMIHQPLGTAGGKATEMSIRIREMMYHKIKLNKIFSRITGKPESEIESDTDRDNFLNPWEAKEYGLIDAVIDDGKPGLIAPIGDGTPPPKTKVWDLWKVEGTKKDN 291
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Theoretical Model(hide GO term definitions)

Chain A (CLPP3_ARATH | Q9SXJ6)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009941	chloroplast envelope	The double lipid bilayer enclosing the chloroplast and separating its contents from the rest of the cytoplasm; includes the intermembrane space.
	GO:0009570	chloroplast stroma	The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
	GO:0009534	chloroplast thylakoid	Sac-like membranous structures (cisternae) in a chloroplast combined into stacks (grana) and present singly in the stroma (stroma thylakoids or frets) as interconnections between grana. An example of this component is found in Arabidopsis thaliana.
	GO:0009840	chloroplastic endopeptidase Clp complex	A Clp endopeptidase complex located in the chloroplast.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	GO:0009532	plastid stroma	The proteinaceous ground substance of plastids.

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	1r90
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