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Title :  3D STRUCTURE PREDICTION OF CLPP2 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) - 17 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 (CLPP2)
    Chains: A
    EC Number: 3.4.21.92
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Other Details: ECOTYPE: 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 1R8V)

(-) Sites  (0, 0)

(no "Site" information available for 1R8V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R8V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R8V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R8V)

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLP_PROTEASE_SERPS00381 Endopeptidase Clp serine active site.CLPP2_ARATH119-130  1A:119-130
2CLP_PROTEASE_HISPS00382 Endopeptidase Clp histidine active site.CLPP2_ARATH141-154  1A:141-154

(-) Exons   (0, 0)

(no "Exon" information available for 1R8V)

(-) 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:201
 aligned with CLPP2_ARATH | Q9FN42 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:201
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
          CLPP2_ARATH    41 SRGERAYDIFSRLLKERIICINGPINDDTSHVVVAQLLYLESENPSKPIHMYLNSPGGHVTAGLAIYDTMQYIRSPISTICLGQAASMASLLLAAGAKGQRRSLPNATVMIHQPSGGYSGQAKDITIHTKQIVRVWDALNELYVKHTGQPLDVVANNMDRDHFMTPEEAKAFGIIDEVIDERPLELVKDAVGNESKDKSSS 241
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhh........eeeeeeeeeehhhhhhhhh.....eee....eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhh..........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------CLP_PROTEASE----------CLP_PROTEASE_H--------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r8v A  41 SRGERAYDIFSRLLKERIICINGPINDDTSHVVVAQLLYLESENPSKPIHMYLNSPGGHVTAGLAIYDTMQYIRSPISTICLGQAASMASLLLAAGAKGQRRSLPNATVMIHQPSGGYSGQAKDITIHTKQIVRVWDALNELYVKHTGQPLDVVANNMDRDHFMTPEEAKAFGIIDEVIDERPLELVKDAVGNESKDKSSS 241
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 1R8V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R8V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1R8V)

(-) Gene Ontology  (11, 11)

Theoretical Model(hide GO term definitions)
Chain A   (CLPP2_ARATH | Q9FN42)
molecular function
    GO:0050897    cobalt ion binding    Interacting selectively and non-covalently with a cobalt (Co) ion.
    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).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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: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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0009532    plastid stroma    The proteinaceous ground substance of plastids.

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