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(-) Description

Title :  CRYSTAL STRUCTURE OF PROPLASMEPSIN FROM THE HUMAN MALARIAL PATHOGEN PLASMODIUM VIVAX
 
Authors :  N. K. Bernstein, M. M. Cherney, C. A. Yowell, J. B. Dame, M. N. James
Date :  23 Aug 02  (Deposition) - 18 Sep 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Aspartic Proteinase Zymogen, Domain Opening, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Bernstein, M. M. Cherney, C. A. Yowell, J. B. Dame, M. N. James
Structural Insights Into The Activation Of P. Vivax Plasmepsin.
J. Mol. Biol. V. 329 505 2003
PubMed-ID: 12767832  |  Reference-DOI: 10.1016/S0022-2836(03)00444-3

(-) Compounds

Molecule 1 - PLASMEPSIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: MALARIA PARASITE P. VIVAX
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 5855
    Other Details: THE 122-RESIDUE PROSEGMENT HAS BEEN TRUNCATED TO 48 RESIDUES
    Synonym: ASPARTIC PROTEINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1MIQ)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:47 -A:52
2A:249 -A:285
3B:47 -B:52
4B:249 -B:285

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:112 -Pro A:113
2Glu B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MIQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1MIQ)

(-) 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:373
 aligned with O60989_PLAVI | O60989 from UniProtKB/TrEMBL  Length:450

    Alignment length:373
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447   
        O60989_PLAVI     78 HLTLAFKIERPYDKVLKTISKKNLKNYIKETFNFFKSGYMKQNYLGSENDVIELDDVANIMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSSGCSIKNLYDSSKSKSYEKDGTKVDITYGSGTVKGFFSKDLVTLGHLSMPYKFIEVTDTDDLEPIYSSVEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDNALFTFYLPVHDVHAGYLTIGGIEEKFYEGNITYEKLNHDLYWQIDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFTVFDYDKESVGFAIAKN  450
               SCOP domains d1miqa_ A: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------1miqA01 A:1-175 Acid Proteases                                                                                                                                                 1miqA02 A:176-327 Acid Proteases                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhh..eeee...ee....ee..eeee.....eeee......hhhhhh...hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee............hhhhhhhhh......eeeee.......eeeeee...hhh.eeeeeeeee.......eeeeeeee..eeeeeeeeee......eeehhhhhhhhhhhhh.ee......eeee........eeee....eeeehhhh.eee.......eeee.eee......eeeehhhhhhheeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1miq A  78P HLTLAFKIERPYDKVLKTISKKNLKNYIKETFNFFKSGYMKQNYLGSENDVIELDDVANIMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSSGCSIKNLYDSSKSKSYEKDGTKVDITYGSGTVKGFFSKDLVTLGHLSMPYKFIEVTDTDDLEPIYSSVEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDNALFTFYLPVHDVHAGYLTIGGIEEKFYEGNITYEKLNHDLYWQIDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFTVFDYDKESVGFAIAKN  327
                            |||||||87P|||||||97P||||||107P||||||117P|||||||  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324   
                            ||||||86P||||||95P|||||104P|||||113P|||||122P||                                                                                                                                                                                                                                                                                                                                      
                          78P||||||87P||||||96P|||||105P|||||114P|||||123P|                                                                                                                                                                                                                                                                                                                                      
                           79P||||||88P||||||97P|||||106P|||||115P||||||  1                                                                                                                                                                                                                                                                                                                                      
                            80P||||| 89P||||| 98P|||||107P|||||116P|||||                                                                                                                                                                                                                                                                                                                                         
                             81P||||  90P||||  99P|||| 108P|||| 117P||||                                                                                                                                                                                                                                                                                                                                         
                              82P|||   91P|||  100P|||  109P|||  118P|||                                                                                                                                                                                                                                                                                                                                         
                               83P||    92P||   101P||   110P||   119P||                                                                                                                                                                                                                                                                                                                                         
                                84P|     93P|    102P|    111P|    120P|                                                                                                                                                                                                                                                                                                                                         
                                 85P      94P     103P     112P     121P                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:375
 aligned with O60989_PLAVI | O60989 from UniProtKB/TrEMBL  Length:450

    Alignment length:375
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445     
        O60989_PLAVI     76 TEHLTLAFKIERPYDKVLKTISKKNLKNYIKETFNFFKSGYMKQNYLGSENDVIELDDVANIMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSSGCSIKNLYDSSKSKSYEKDGTKVDITYGSGTVKGFFSKDLVTLGHLSMPYKFIEVTDTDDLEPIYSSVEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDNALFTFYLPVHDVHAGYLTIGGIEEKFYEGNITYEKLNHDLYWQIDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFTVFDYDKESVGFAIAKN  450
               SCOP domains d1miqb_ B: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------1miqB01 B:1-175 Acid Proteases                                                                                                                                                 1miqB02 B:176-327 Acid Proteases                                                                                                                         CATH domains
           Pfam domains (1) --------------------------------------------------------------Asp-1miqB01 B:15-325                                                                                                                                                                                                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------Asp-1miqB02 B:15-325                                                                                                                                                                                                                                                                                                   -- Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhh..hhhhhhhhhhhhhhhh...............hhhhh..eeee...ee........eeee.....eeee......hhhhhh...hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee............hhhhhhhhh......eeeee.......eeeeee...hhh.eeeeeeeee.......eeeeeeee..eeeeeeeeee......eeehhhhhhhhhhhh..ee......eeee........eeee....eeeehhhhheeee...eeeeeee.eee......eeeehhhhhhheeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1miq B  76P TEHLTLAFKIERPYDKVLKTISKKNLKNYIKETFNFFKSGYMKQNYLGSENDVIELDDVANIMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSSGCSIKNLYDSSKSKSYEKDGTKVDITYGSGTVKGFFSKDLVTLGHLSMPYKFIEVTDTDDLEPIYSSVEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDNALFTFYLPVHDVHAGYLTIGGIEEKFYEGNITYEKLNHDLYWQIDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFTVFDYDKESVGFAIAKN  327
                            |||||||85P|||||||95P||||||105P||||||115P|||||||||2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322     
                          76P||||||85P||||||94P|||||103P|||||112P|||||121P|||                                                                                                                                                                                                                                                                                                                                      
                           77P||||||86P||||||95P|||||104P|||||113P|||||122P||                                                                                                                                                                                                                                                                                                                                      
                            78P||||||87P||||||96P|||||105P|||||114P|||||123P|                                                                                                                                                                                                                                                                                                                                      
                             79P||||| 88P||||| 97P|||||106P|||||115P|||||   1                                                                                                                                                                                                                                                                                                                                      
                              80P||||  89P||||  98P|||| 107P|||| 116P||||                                                                                                                                                                                                                                                                                                                                          
                               81P|||   90P|||   99P|||  108P|||  117P|||                                                                                                                                                                                                                                                                                                                                          
                                82P||    91P||   100P||   109P||   118P||                                                                                                                                                                                                                                                                                                                                          
                                 83P|     92P|    101P|    110P|    119P|                                                                                                                                                                                                                                                                                                                                          
                                  84P      93P     102P     111P     120P
   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, 2)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Peptidase_AA (368)
(-)
Family: Asp (155)
(-)
Plasmodium vivax (1)
1aAsp-1miqB01B:15-325
1bAsp-1miqB02B:15-325

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O60989_PLAVI | O60989)
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: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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    Glu A:112 - Pro A:113   [ RasMol ]  
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  1miq
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 Related Entries

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

UniProtKB/TrEMBL
        O60989_PLAVI | O60989: 1qs8

(-) Related Entries Specified in the PDB File

1ls5 P. FALCIPARUM PLASMEPSIN IV
1pfz P. FALCIPARUM PROPLASMEPSIN II
1qs8 P. VIVAX PLASMEPSIN
1sme P. FALCIPARUM PLASMEPSIN II