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(-) Description

Title :  STRUCTURE OF PLASMEPSIN II
 
Authors :  O. A. Asojo, S. V. Gulnik, E. Afonina, B. Yu, J. A. Ellman, T. S. Haque, A. M. Silva
Date :  10 Apr 02  (Deposition) - 10 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. A. Asojo, S. V. Gulnik, E. Afonina, B. Yu, J. A. Ellman, T. S. Haque, A. M. Silva
Novel Uncomplexed And Complexed Structures Of Plasmepsin Ii, An Aspartic Protease From Plasmodium Falciparum.
J. Mol. Biol. V. 327 173 2003
PubMed-ID: 12614616  |  Reference-DOI: 10.1016/S0022-2836(03)00036-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASMEPSIN 2
    Chains: A
    EC Number: 3.4.23.39
    Organism Common: MALARIA PARASITE P. FALCIPARUM
    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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LF4)

(-) Sites  (0, 0)

(no "Site" information available for 1LF4)

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:112 -Pro A:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LF4)

(-) 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 1LF4)

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

    Alignment length:331
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452 
           PLM2_PLAFA   123 LGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 453
               SCOP domains d1lf4a_ A: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains --1lf4A01 A:1-175 Acid Proteases                                                                                                                                                 1lf4A02 A:176-328 Acid Proteases                                                                                                                         - CATH domains
               Pfam domains ----------------Asp-1lf4A01 A:15-325                                                                                                                                                                                                                                                                                                   ---- Pfam domains
         Sec.struct. author .....eeeeeeee...eeeeeeee....eeeeeeee.....eeee.....hhhhhhh...hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhh......eeeee........eeeee...hhh.eeeeeeeee.......eeeeeee....eeeeeeeee......eeehhhhhhhhh......------..eee........eeee....eeeehhhhheee.......eeee.eee......eeeehhhhhhheeeeee....eeeeeee.... 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
                 1lf4 A  -1 LGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVI------FYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 329
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228        |-     | 248       258       268       278       288       298       308       318       328 
                                                                                                                                                                                                                                                                        237    244
   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, 1)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_AA (368)

(-) 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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  Cis Peptide Bonds
    Glu A:112 - Pro A:113   [ RasMol ]  
 

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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 1m43 1me6 1pfz 1sme 1w6h 1w6i 1xdh 1xe5 1xe6 2bju 2bl3 2igx 2igy 2r9b 3f9q 4cku 4y6m 4ya8 4z22 5bwy

(-) Related Entries Specified in the PDB File

1lee CRYSTAL STRUCTURE OF PLASMEPSIN FROM P. FALCIPARUM IN COMPLEX WITH INHIBITOR RS367
1lf2 CRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM IN COMPLEX WITH INHIBITOR RS370
1lf3 CRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM IN COMPLEX WITH INHIBITOR EH58
1sme PLASMEPSIN II, A HEMOGLOBIN-DEGRADING ENZYME FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH PEPSTATIN A