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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPSTATIN A BOUND HISTO-ASPARTIC PROTEASE (HAP) FROM PLASMODIUM FALCIPARUM
 
Authors :  P. Bhaumik, A. Gustchina, A. Wlodawer
Date :  26 Dec 08  (Deposition) - 12 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,I
Biol. Unit 1:  A,I  (2x)
Biol. Unit 2:  A,I  (1x)
Keywords :  Histo-Aspartic Protease, Hap, Plasmepsin, Pepstatin A, Aspartic Protease, Hydrolase-Hydrolase Inhibitor Complex (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) Fro Plasmodium Falciparum.
J. Mol. Biol. V. 388 520 2009
PubMed-ID: 19285084  |  Reference-DOI: 10.1016/J.JMB.2009.03.011

(-) Compounds

Molecule 1 - HAP PROTEIN
    Chains: A
    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
    Organism Taxid: 36329
    Strain: 3D7
 
Molecule 2 - INHIBITOR, (IVA)VV(STA)A(STA)
    Chains: I
    Engineered: YES
    Other Details: UNSPECIFIED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AI
Biological Unit 1 (2x): AI
Biological Unit 2 (1x): AI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2IVA1Mod. Amino AcidISOVALERIC ACID
3STA2Mod. Amino AcidSTATINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2IVA2Mod. Amino AcidISOVALERIC ACID
3STA4Mod. Amino AcidSTATINE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2IVA1Mod. Amino AcidISOVALERIC ACID
3STA2Mod. Amino AcidSTATINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:3 , ASP A:127 , SER A:129 , SER A:132BINDING SITE FOR RESIDUE EDO A 501

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:45 -A:50
2A:249 -A:282

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FNT)

(-) 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:323
 aligned with Q8IM15_PLAF7 | Q8IM15 from UniProtKB/TrEMBL  Length:451

    Alignment length:323
                                   136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446   
        Q8IM15_PLAF7    127 DNVELKDLANVLSFGEAKLGDNGQKFNFLFHTASSNVWVPSIKCTSESCESKNHYDSSKSKTYEKDDTPVKLTSKAGTISGIFSKDLVTIGKLSVPYKFIEMTEIVGFEPFYSESDVDGVFGLGWKDLSIGSIDPYIVELKTQNKIEQAVYSIYLPPENKNKGYLTIGGIEERFFDGPLNYEKLNHDLMWQVDLDVHFGNVSSKKANVILDSATSVITVPTEFFNQFVESASVFKVPFLSLYVTTCGNTKLPTLEYRSPNKVYTLEPKQYLEPLENIFSALCMLNIVPIDLEKNTFVLGDPFMRKYFTVYDYDNHTVGFALAK  449
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fntA01 A:2-172 Acid Proteases                                                                                                                                              3fntA02 A:173-326 Acid Proteases                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........eeeee....eeeeeeee......eee.....hhhhhhh...........eeeeeeeeee....eeeeeeeeeeee......eeeeeeeeee....hhhhhh...eeee............hhhhh..........eeeee........eeeee.......................eeeeeee....eeeeeeeee......eeehhhhhhhhhh....eee..eeeeeee........eeee.....eeehhhh.eee.......eeee.eee......eeeehhhhhh..eeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3fnt A    2 DNVELKDLANVLSFGEAKLGDNGQKFNFLFHTASSNVWVPSIKCTSESCESKNHYDSSKSKTYEKDDTPVKLTSKAGTISGIFSKDLVTIGKLSVPYKFIEMTEIVGFEPFYSESDVDGVFGLGWKDLSIGSIDPYIVELKTQNKIEQAVYSIYLPPENKNKGYLTIGGIEERFFDGPLNYEKLNHDLMWQVDLDVHFGNVSSKKANVILDSATSVITVPTEFFNQFVESASVFKVPFLSLYVTTCGNTKLPTLEYRSPNKVYTLEPKQYLEPLENIFSALCMLNIVPIDLEKNTFVLGDPFMRKYFTVYDYDNHTVGFALAK  326
                                    11        21        31        41        51        61        71        81        91    || 102       110       120       130       140       150       160       170       180       190    || 203|      214       224       234      243A       254       264       274    | |280       290 ||    303       313       323   
                                                                                                                         96|        109A|                                                                                   195| ||||                                   243A     251|                      278A |||          292|                              
                                                                                                                          98         109B                                                                                    197 ||||                                             253                        279A||           296                              
                                                                                                                                                                                                                               199|||                                                                         279B|                                            
                                                                                                                                                                                                                                201||                                                                          279C                                            
                                                                                                                                                                                                                                 203|                                                                                                                          
                                                                                                                                                                                                                                  205                                                                                                                          


Chain I from PDB  Type:PROTEIN  Length:6
                                       
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                3fnt I    1 xVVxAx    6
                            |  | |
                            1-IVA|
                               4-STA
                                 6-STA
   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 3FNT)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (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)

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        Q8IM15_PLAF7 | Q8IM15: 3fns 3fnu

(-) Related Entries Specified in the PDB File

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