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(-) Description

Title :  CRYSTAL STRUCTURE OF HISTO-ASPARTIC PROTEASE (HAP) FROM PLASMODIUM FALCIPARUM
 
Authors :  P. Bhaumik, A. Gustchina, A. Wlodawer
Date :  26 Dec 08  (Deposition) - 12 May 09  (Release) - 12 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Histo-Aspartic Protease, Hap, Plasmepsin, Aspartic Protease, Hormone, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Bhaumik, H. Xiao, C. L. Parr, Y. Kiso, A. Gustchina, R. Y. Yada, A. Wlodawer
Crystal Structures Of The Histo-Aspartic Protease (Hap) From Plasmodium Falciparum.
J. Mol. Biol. V. 388 520 2009
PubMed-ID: 19285084  |  Reference-DOI: 10.1016/J.JMB.2009.03.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HAP PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32B(+)
    Expression System Strain: ROSETTA-GAMI B (DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HISTO-ASPARTIC PROTEASE (HAP)
    Gene: HAP, PF14_0078
    Organism Scientific: PLASMODIUM FALCIPARUM 3D7
    Organism Taxid: 36329

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:32 , ASP A:215 , HOH A:374 , GLU B:278ABINDING SITE FOR RESIDUE ZN A 329
2AC2SOFTWAREASP A:195 , HIS A:198BINDING SITE FOR RESIDUE ZN A 330
3AC3SOFTWAREASP A:127 , HIS A:186 , ASP A:187BINDING SITE FOR RESIDUE ZN A 331
4AC4SOFTWAREGLU A:48 , GLU A:51 , GLU B:51 , HOH B:375BINDING SITE FOR RESIDUE ZN A 332
5AC5SOFTWAREGLU A:278A , HOH A:336 , HIS B:32 , ASP B:215BINDING SITE FOR RESIDUE ZN B 329
6AC6SOFTWAREASP B:195 , HIS B:198BINDING SITE FOR RESIDUE ZN B 330

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:45 -A:50
2A:249 -A:282
3B:45 -B:50
4B:249 -B:282

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:109B-Pro A:110
2Glu B:109B-Pro B:110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FNS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FNS)

(-) Exons   (0, 0)

(no "Exon" information available for 3FNS)

(-) Sequences/Alignments

Asymmetric/Biological 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:325
 aligned with Q8IM15_PLAF7 | Q8IM15 from UniProtKB/TrEMBL  Length:451

    Alignment length:325
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
        Q8IM15_PLAF7    125 EFDNVELKDLANVLSFGEAKLGDNGQKFNFLFHTASSNVWVPSIKCTSESCESKNHYDSSKSKTYEKDDTPVKLTSKAGTISGIFSKDLVTIGKLSVPYKFIEMTEIVGFEPFYSESDVDGVFGLGWKDLSIGSIDPYIVELKTQNKIEQAVYSIYLPPENKNKGYLTIGGIEERFFDGPLNYEKLNHDLMWQVDLDVHFGNVSSKKANVILDSATSVITVPTEFFNQFVESASVFKVPFLSLYVTTCGNTKLPTLEYRSPNKVYTLEPKQYLEPLENIFSALCMLNIVPIDLEKNTFVLGDPFMRKYFTVYDYDNHTVGFALAK  449
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fnsA01 A:0-172 Acid Proteases                                                                                                                                                3fnsA02 A:173-326 Acid Proteases                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeeee....eeeeeeee......eee.....hhhhh.....hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeeeeee...........eeee..hhhhh.....hhhhhhhhh......eeeee........eeeee...hhhhh....eeee.......eeeeeeee..eeeeeeeeee......eeehhhhhhhhhhhhhhh........eee........eeee....eeeehhhhheee.......eeee.eee......eeeehhhhhhheeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3fns A    0 EFDNVELKDLANVLSFGEAKLGDNGQKFNFLFHTASSNVWVPSIKCTSESCESKNHYDSSKSKTYEKDDTPVKLTSKAGTISGIFSKDLVTIGKLSVPYKFIEMTEIVGFEPFYSESDVDGVFGLGWKDLSIGSIDPYIVELKTQNKIEQAVYSIYLPPENKNKGYLTIGGIEERFFDGPLNYEKLNHDLMWQVDLDVHFGNVSSKKANVILDSATSVITVPTEFFNQFVESASVFKVPFLSLYVTTCGNTKLPTLEYRSPNKVYTLEPKQYLEPLENIFSALCMLNIVPIDLEKNTFVLGDPFMRKYFTVYDYDNHTVGFALAK  326
                                     9        19        29        39        49        59        69        79        89      |100      109A|      118       128       138       148       158       168       178       188      |199|||    212       222       232       242 |     251|      262       272      279B|      288   ||  301       311       321     
                                                                                                                           96|        109A|                                                                                   195| ||||                                   243A     251|                      278A |||          292|                              
                                                                                                                            98         109B                                                                                    197 ||||                                             253                        279A||           296                              
                                                                                                                                                                                                                                 199|||                                                                         279B|                                            
                                                                                                                                                                                                                                  201||                                                                          279C                                            
                                                                                                                                                                                                                                   203|                                                                                                                          
                                                                                                                                                                                                                                    205                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:325
 aligned with Q8IM15_PLAF7 | Q8IM15 from UniProtKB/TrEMBL  Length:451

    Alignment length:325
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
        Q8IM15_PLAF7    125 EFDNVELKDLANVLSFGEAKLGDNGQKFNFLFHTASSNVWVPSIKCTSESCESKNHYDSSKSKTYEKDDTPVKLTSKAGTISGIFSKDLVTIGKLSVPYKFIEMTEIVGFEPFYSESDVDGVFGLGWKDLSIGSIDPYIVELKTQNKIEQAVYSIYLPPENKNKGYLTIGGIEERFFDGPLNYEKLNHDLMWQVDLDVHFGNVSSKKANVILDSATSVITVPTEFFNQFVESASVFKVPFLSLYVTTCGNTKLPTLEYRSPNKVYTLEPKQYLEPLENIFSALCMLNIVPIDLEKNTFVLGDPFMRKYFTVYDYDNHTVGFALAK  449
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fnsB01 B:0-172 Acid Proteases                                                                                                                                                3fnsB02 B:173-326 Acid Proteases                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeeeeee....eeeeeeee......eee.....hhhhh.............eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeeee..hhhhhh...eeee..hhhhh.....hhhhhhhhh......eeeee........eeeee.......eeeeeeeeeeee....eeeeeeee..eeeeeeeeee......eeehhhhhhhhhhhhhhh........eee........eeee....eeeehhhhheee.......eeee.eee......eeeehhhhhh.eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3fns B    0 EFDNVELKDLANVLSFGEAKLGDNGQKFNFLFHTASSNVWVPSIKCTSESCESKNHYDSSKSKTYEKDDTPVKLTSKAGTISGIFSKDLVTIGKLSVPYKFIEMTEIVGFEPFYSESDVDGVFGLGWKDLSIGSIDPYIVELKTQNKIEQAVYSIYLPPENKNKGYLTIGGIEERFFDGPLNYEKLNHDLMWQVDLDVHFGNVSSKKANVILDSATSVITVPTEFFNQFVESASVFKVPFLSLYVTTCGNTKLPTLEYRSPNKVYTLEPKQYLEPLENIFSALCMLNIVPIDLEKNTFVLGDPFMRKYFTVYDYDNHTVGFALAK  326
                                     9        19        29        39        49        59        69        79        89      |100      109A|      118       128       138       148       158       168       178       188      |199|||    212       222       232       242 |     251|      262       272      279B|      288   ||  301       311       321     
                                                                                                                           96|        109A|                                                                                   195| ||||                                   243A     251|                      278A |||          292|                              
                                                                                                                            98         109B                                                                                    197 ||||                                             253                        279A||           296                              
                                                                                                                                                                                                                                 199|||                                                                         279B|                                            
                                                                                                                                                                                                                                  201||                                                                          279C                                            
                                                                                                                                                                                                                                   203|                                                                                                                          
                                                                                                                                                                                                                                    205
   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 3FNS)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FNS)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8IM15_PLAF7 | Q8IM15)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0020020    food vacuole    Vacuole within a parasite used for digestion of the host cell cytoplasm. An example of this component is found in the Apicomplexa.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8IM15_PLAF7 | Q8IM15: 3fnt 3fnu

(-) Related Entries Specified in the PDB File

3fnt CRYSTAL STRUCTURE OF PEPSTATIN A BOUND HISTO-ASPARTIC PROTEASE FROM PLASMODIUM FALCIPARUM
3fnu CRYSTAL STRUCTURE OF KNI-10006 BOUND HISTO-ASPARTIC PROTEASE (HAP) FROM PLASMODIUM FALCIPARUM