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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLPP PROTEASE CATALYTIC DOMAIN FROM PLASMODIUM FALCIPARUM
 
Authors :  A. Mulichak, P. Loppnau, J. Bray, M. Amani, M. Vedadi, G. Wasney, P. Fine M. Sundstrom, J. Weigelt, A. Edwards, C. Arrowsmith, R. Hui, O. Plotni Structural Genomics Consortium (Sgc)
Date :  29 Nov 05  (Deposition) - 20 Dec 05  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A,B,C,D,E,F,G  (2x)
Keywords :  Clp Protease, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. El Bakkouri, A. Pow, A. Mulichak, K. L. Cheung, J. D. Artz, M. Amani, S. Fell, T. F. De Koning-Ward, C. D. Goodman, G. I. Mcfadden, J. Ortega R. Hui, W. A. Houry
The Clp Chaperones And Proteases Of The Human Malaria Parasite Plasmodium Falciparum.
J. Mol. Biol. V. 404 456 2010
PubMed-ID: 20887733  |  Reference-DOI: 10.1016/J.JMB.2010.09.051
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE, PUTATIVE
    Chains: A, B, C, D, E, F, G
    EC Number: 3.4.21.92
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A VECTOR CUSTOMIZED FOR THROMBIN CLEAVAGE AND LIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: MALARIA PARASITE P. FALCIPARUM
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (2x): ABCDEFG

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2F6I)

(-) Sites  (0, 0)

(no "Site" information available for 2F6I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F6I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F6I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F6I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F6I)

(-) Exons   (0, 0)

(no "Exon" information available for 2F6I)

(-) Sequences/Alignments

Asymmetric Unit
   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 O97252_PLAF7 | O97252 from UniProtKB/TrEMBL  Length:370

    Alignment length:190
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366
         O97252_PLAF7   177 NDDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAFGHPQDIEIQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYFN 366
               SCOP domains d2f6ia1 A:177-366 Clp protease, ClpP subunit                                                                                                                                                   SCOP domains
               CATH domains 2f6iA00 A:177-366 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhh.....eee....eee.........--------hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f6i A 177 HMDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAF--------QTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYFN 366
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366
                                                                                                                                                 296      305                                                             


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with O97252_PLAF7 | O97252 from UniProtKB/TrEMBL  Length:370

    Alignment length:189
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356         
         O97252_PLAF7   177 NDDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAFGHPQDIEIQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYF 365
               SCOP domains d2f6ib_ B: Clp protease, ClpP subunit                                                                                                                                                         SCOP domains
               CATH domains 2f6iB00 B:177-365 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhh.....eeeeeeeeeehhhhhhhhh......ee....eee..---------------hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f6i B 177 HMDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIH---------------QTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYF 365
                                   186       196       206       216       226       236       246       256       266       276       286  |      -       306       316       326       336       346       356         
                                                                                                                                          289             305                                                            


Chain C from PDB  Type:PROTEIN  Length:183
 aligned with O97252_PLAF7 | O97252 from UniProtKB/TrEMBL  Length:370

    Alignment length:189
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356         
         O97252_PLAF7   177 NDDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAFGHPQDIEIQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYF 365
               SCOP domains d2f6ic_ C: Clp protease, ClpP subunit                                                                                                                                                         SCOP domains
               CATH domains 2f6iC00 C:177-365 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhh.....eee....eee..........------.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f6i C 177 HMDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAFG------IQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYF 365
                                   186       196       206       216       226       236       246       256       266       276       286       296|      306       316       326       336       346       356         
                                                                                                                                                  297    304                                                             


Chain D from PDB  Type:PROTEIN  Length:182
 aligned with O97252_PLAF7 | O97252 from UniProtKB/TrEMBL  Length:370

    Alignment length:189
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356         
         O97252_PLAF7   177 NDDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAFGHPQDIEIQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYF 365
               SCOP domains d2f6id_ D: Clp protease, ClpP subunit                                                                                                                                                         SCOP domains
               CATH domains 2f6iD00 D:177-365 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhh......ee....ee..........-------.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...eehhhhhhhh...ee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f6i D 177 HMDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAF-------IQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYF 365
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356         
                                                                                                                                                 296     304                                                             


Chain E from PDB  Type:PROTEIN  Length:175
 aligned with O97252_PLAF7 | O97252 from UniProtKB/TrEMBL  Length:370

    Alignment length:189
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356         
         O97252_PLAF7   177 NDDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAFGHPQDIEIQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYF 365
               SCOP domains d2f6ie_ E: Clp protease, ClpP subunit                                                                                                                                                         SCOP domains
               CATH domains 2f6iE00 E:177-365 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh......ee....eee..--------------.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f6i E 177 HMDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIH--------------IQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYF 365
                                   186       196       206       216       226       236       246       256       266       276       286  |      -       306       316       326       336       346       356         
                                                                                                                                          289            304                                                             


Chain F from PDB  Type:PROTEIN  Length:181
 aligned with O97252_PLAF7 | O97252 from UniProtKB/TrEMBL  Length:370

    Alignment length:189
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356         
         O97252_PLAF7   177 NDDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAFGHPQDIEIQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYF 365
               SCOP domains d2f6if_ F: Clp protease, ClpP subunit                                                                                                                                                         SCOP domains
               CATH domains 2f6iF00 F:177-365 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh.....eeeee..eehhhhhhhhhh......ee....eee.........--------hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f6i F 177 HMDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAF--------QTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYF 365
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356         
                                                                                                                                                 296      305                                                            


Chain G from PDB  Type:PROTEIN  Length:178
 aligned with O97252_PLAF7 | O97252 from UniProtKB/TrEMBL  Length:370

    Alignment length:190
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366
         O97252_PLAF7   177 NDDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQPLGNAFGHPQDIEIQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYFN 366
               SCOP domains d2f6ig_ G: Clp protease, ClpP subunit                                                                                                                                                          SCOP domains
               CATH domains 2f6iG00 G:177-366 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh......ee....eee....------------.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhh....ee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f6i G 177 HMDIKDMKKDVKLFFFKKRIIYLTDEINKKTADELISQLLYLDNINHNDIKIYINSPGGSINEGLAILDIFNYIKSDIQTISFGLVASMASVILASGKKGKRKSLPNCRIMIHQP------------IQTKEILYLKKLLYHYLSSFTNQTVETIEKDSDRDYYMNALEAKQYGIIDEVIETKLPHPYFN 366
                                   186       196       206       216       226       236       246       256       266       276       286    |    -       306       316       326       336       346       356       366
                                                                                                                                            291          304
   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  (1, 7)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 7)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F6I)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G   (O97252_PLAF7 | O97252)
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).
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:0020011    apicoplast    The plastid organelle found in apicomplexans.

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 Related Entries

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