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Title :  3D STRUCTURE PREDICTION OF CLPP4 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 (CLPP4)
    ChainsA
    EC Number3.4.21.92
    Organism CommonMOUSE-EAR CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Other DetailsECOTYPE: COLUMBIA 0

 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 1R91)

(-) Sites  (0, 0)

(no "Site" information available for 1R91)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R91)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R91)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R91)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLP_PROTEASE_HISPS00382 Endopeptidase Clp histidine active site.CLPP4_ARATH172-185  1A:172-185

(-) Exons   (0, 0)

(no "Exon" information available for 1R91)

(-) 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:221
 aligned with CLPP4_ARATH | Q94B60 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:221
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291 
          CLPP4_ARATH    72 AIRGAESDVMGLLLRERIVFLGSSIDDFVADAIMSQLLLLDAKDPKKDIKLFINSPGGSLSATMAIYDVVQLVRADVSTIALGIAASTASIILGAGTKGKRFAMPNTRIMIHQPLGGASGQAIDVEIQAKEVMHNKNNVTSIIAGCTSRSFEQVLKDIDRDRYMSPIEAVEYGLIDGVIDGDSIIPLEPVPDRVKPRVNYEEISKDPMKFLTPEIPDDEIY 292
               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....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------CLP_PROTEASE_H----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r91 A  72 AIRGAESDVMGLLLRERIVFLGSSIDDFVADAIMSQLLLLDAKDPKKDIKLFINSPGGSLSATMAIYDVVQLVRADVSTIALGIAASTASIILGAGTKGKRFAMPNTRIMIHQPLGGASGQAIDVEIQAKEVMHNKNNVTSIIAGCTSRSFEQVLKDIDRDRYMSPIEAVEYGLIDGVIDGDSIIPLEPVPDRVKPRVNYEEISKDPMKFLTPEIPDDEIY 292
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 1R91)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R91)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1R91)

(-) Gene Ontology  (16, 16)

Theoretical Model(hide GO term definitions)
Chain A   (CLPP4_ARATH | Q94B60)
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:0009658    chloroplast organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the chloroplast.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0048510    regulation of timing of transition from vegetative to reproductive phase    The process controlling the point in time during development when a vegetative meristem will change its identity to become an inflorescence or floral meristem, and/or the rate at which the change occurs.
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:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. 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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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