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(-) Description

Title :  PLASMEPSIN II COMPLEXED WITH A HIGHLY ACTIVE ACHIRAL INHIBITOR
 
Authors :  L. Prade, A. F. Jones, C. Boss, S. Richards-Bildstein, S. Meyer, C. Binkert, D. Bur
Date :  08 Feb 05  (Deposition) - 18 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A
Keywords :  Plasmepsin, Aspartic Proteinase, Drug Design, Malaria, Aspartyl Protease, Glycoprotein, Hydrolase, Signal, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Prade, A. F. Jones, C. Boss, S. Richard-Bildstein, S. Meyer, C. Binkert, D. Bur
X-Ray Structure Of Plasmepsin Ii Complexed With A Potent Achiral Inhibitor.
J. Biol. Chem. V. 280 23837 2005
PubMed-ID: 15840589  |  Reference-DOI: 10.1074/JBC.M501519200

(-) Compounds

Molecule 1 - PLASMEPSIN II
    Chains: A
    EC Number: 3.4.23.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Synonym: ASPARTIC HEMOGLOBINASE II, PFAPD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1IH42Ligand/IonN-(R-CARBOXY-ETHYL)-ALPHA-(S)-(2-PHENYLETHYL)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:14 , MET A:15 , ILE A:32 , ASP A:34 , MET A:75 , TYR A:77 , PHE A:111 , TYR A:115 , SER A:118 , ASP A:121 , TYR A:192 , ASP A:214 , GLY A:216 , THR A:217 , ILE A:300 , IH4 A:1331 , HOH A:2284 , HOH A:2377 , HOH A:2378 , HOH A:2379BINDING SITE FOR RESIDUE IH4 A1330
2AC2SOFTWAREILE A:14 , TYR A:77 , THR A:114 , GLY A:216 , THR A:217 , SER A:218 , PHE A:241 , PHE A:244 , LEU A:287 , ASN A:288 , ILE A:289 , LEU A:292 , IH4 A:1330 , HOH A:2186 , HOH A:2284 , HOH A:2379 , HOH A:2381BINDING SITE FOR RESIDUE IH4 A1331

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:47 -A:52
2A:249 -A:285

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:112 -Pro A:113
2Gln A:232 -Asn A:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PLM2_PLAFA140-447  1A:16-323
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PLM2_PLAFA155-166
335-346		  2A:31-42
A:211-222

(-) Exons   (0, 0)

(no "Exon" information available for 2BJU)

(-) 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:329
 aligned with PLM2_PLAFA | P46925 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:329
                                   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         
           PLM2_PLAFA   125 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 453
               SCOP domains d2bjua1 A:1-329 Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2bjuA01 A:1-175 Acid Proteases                                                                                                                                                 2bjuA02 A:176-329 Acid Proteases                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeee....eeeeeeee.....eeee.......hhhhh...hhhhh...eeeeeeeeee....eeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhh...........................hhh..............................................hhhhhhhhh.....ee......eeee....................hhhhheee.......eeee..............hhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------PEPTIDASE_A1  PDB: A:16-323 UniProt: 140-447                                                                                                                                                                                                                                                                        ------ PROSITE (1)
                PROSITE (2) ------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bju A   1 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 329
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLM2_PLAFA | P46925)
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: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.
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:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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  2bju
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  PLM2_PLAFA | P46925
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  3.4.23.39
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 Related Entries

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

UniProtKB/Swiss-Prot
        PLM2_PLAFA | P46925: 1j8j 1lee 1lf2 1lf3 1lf4 1m43 1me6 1pfz 1sme 1w6h 1w6i 1xdh 1xe5 1xe6 2bl3 2igx 2igy 2r9b 3f9q 4cku 4y6m 4ya8 4z22 5bwy

(-) Related Entries Specified in the PDB File

1j8j A NEW CLASS OF SMALL NON-PEPTIDYL COMPOUNDS BLOCKSPLASMODIUM FALCIPARUM DEVELOPMENT IN VITRO BY INHIBITINGPLASMEPSINS
1lee CRYSTAL STRUCTURE OF PLASMEPSIN FROM P. FALCIPARUM INCOMPLEX WITH INHIBITOR RS367
1lf2 CRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM INCOMPLEX WITH INHIBITOR RS370
1lf3 CRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM INCOMPLEX WITH INHIBITOR EH58
1lf4 STRUCTURE OF PLASMEPSIN II
1m43 CRYSTAL STRUCTURE OF PMII IN COMPLEX WITH PEPSTATIN A TO2.4 A
1me6 CRYSTAL STRUCTURE OF PLASMEPSIN II, AN ASPARTYL PROTEASEFROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH A STATINE-BASED INHIBITOR
1pfz PROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM
1sme PLASMEPSIN II, A HEMOGLOBIN-DEGRADING ENZYME FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH PEPSTATIN A
1w6h NOVEL PLASMEPSIN II-INHIBITOR COMPLEX
1w6i PLASMEPSIN II-PEPSTATIN A COMPLEX