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Title :  3D STRUCTURE PREDICTION OF CLPP1 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

Molecule 1 - ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
    Chains: A
    EC Number: 3.4.21.92
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Other Details: ECOTYPE: COLUMBIA 0
    Synonym: ENDOPEPTIDASE CLP

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1R8Z)

(-) Sites  (0, 0)

(no "Site" information available for 1R8Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R8Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R8Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R8Z)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLP_PROTEASE_HISPS00382 Endopeptidase Clp histidine active site.CLPP1_ARATH115-128  1A:115-128

(-) Exons   (0, 0)

(no "Exon" information available for 1R8Z)

(-) 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:182
 aligned with CLPP1_ARATH | P56772 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:182
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  
          CLPP1_ARATH    15 EGDTSWVDIYNRLYRERLFFLGQEVDTEISNQLISLMIYLSIEKDTKDLYLFINSPGGWVISGMAIYDTMQFVRPDVQTICMGLAASIASFILVGGAITKRIAFPHARVMIHQPASSFYEAQTGEFILEAEELLKLRETITRVYVQRTGKPIWVISEDMERDVFMSATEAQAYGIVDLVAVQ 196
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhhh.....eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...eeehhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------CLP_PROTEASE_H-------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8z A  15 EGDTSWVDIYNRLYRERLFFLGQEVDTEISNQLISLMIYLSIEKDTKDLYLFINSPGGWVISGMAIYDTMQFVRPDVQTICMGLAASIASFILVGGAITKRIAFPHARVMIHQPASSFYEAQTGEFILEAEELLKLRETITRVYVQRTGKPIWVISEDMERDVFMSATEAQAHGIVDLVAVQ 196
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1R8Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R8Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1R8Z)

(-) Gene Ontology  (8, 8)

Theoretical Model(hide GO term definitions)
Chain A   (CLPP1_ARATH | P56772)
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: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: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.

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  1r8z
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