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(-) Description

Title :  CRYSTAL STRUCTURE OF HISTO-ASPARTIC PROTEASE (HAP) ZYMOGEN FROM PLASMODIUM FALCIPARUM
 
Authors :  P. Bhaumik, A. Gustchina, A. Wlodawer
Date :  25 Feb 11  (Deposition) - 12 Oct 11  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Histo-Aspartic Protease, Hap, Plasmepsin, Aspartic Protease, Malaria, Zymogen, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Bhaumik, H. Xiao, K. Hidaka, A. Gustchina, Y. Kiso, R. Y. Yada, A. Wlodawer
Structural Insights Into The Activation And Inhibition Of Histo-Aspartic Protease From Plasmodium Falciparum.
Biochemistry V. 50 8862 2011
PubMed-ID: 21928835  |  Reference-DOI: 10.1021/BI201118Z

(-) Compounds

Molecule 1 - HISTO-ASPARTIC PROTEASE
    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
    Gene: HAP
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Synonym: HAP PROTEIN, PUTATIVE ASPARTIC PROTEINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:67 , PHE A:84 , LYS A:102P , SER A:129 , GLY A:131 , ILE A:133 , HOH A:477BINDING SITE FOR RESIDUE EDO A 329
2AC2SOFTWAREGLU A:172 , PHE A:175 , LYS A:326 , HOH A:365 , HOH A:468 , HOH A:503BINDING SITE FOR RESIDUE EDO A 330
3AC3SOFTWAREVAL A:109P , PHE A:112P , ASN A:113P , PHE A:279B , LEU A:281 , HOH A:509BINDING SITE FOR RESIDUE EDO A 331
4AC4SOFTWAREASP A:2 , ASN A:229 , TYR A:245 , PRO A:288BINDING SITE FOR RESIDUE EDO A 332
5AC5SOFTWARELYS A:97P , TRP A:125 , LYS A:126 , ASP A:127 , LEU A:188BINDING SITE FOR RESIDUE EDO A 333

(-) 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
1Lys A:118P-Lys A:119P

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QVC)

(-) 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:368
 aligned with Q9Y006_PLAFA | Q9Y006 from UniProtKB/TrEMBL  Length:451

    Alignment length:375
                                    86        96       106       116       126       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     
        Q9Y006_PLAFA     77 KYSTVGFNIENSYDRLMKTIKEHKLKNYIKESVKLFNKGLTKKSYLGSEFDNVELKDLANVLSFGEAKLGDNGQKFNFLFHTASSNVWVPSIKCTSESCESKNHYDSSKSKTYEKDDTPVKLTSKAGTISGIFSKDLVTIGKLSVPYKFIEMTEIVGFEPFYSESDVDGVFGLGWKDLSIGSIDPYIVELKTQNKIEQAVYSIYLPPENKNKGYLTIGGIEERFFDGPLNYEKLNHDLMWQVDLDVHFGNVSSKKANVILDSATSVITVPTEFFNQFVESASVFKVPFLSLYVTTCGNTKLPTLEYRSPNKVYTLEPKQYLEPLENIFSALCMLNIVPIDLEKNTFVLGDPFMRKYFTVYDYDNHTVGFALAKNL  451
               SCOP domains d3qvca_ A: automated matches                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhh.....-------...hhhhhh.eeeeeeeee....eeeeeeee.....eeee.....hhhhh.....hhhhh...eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeeee..hhhhhh...eeee............hhhhhhhhh......eeeee.......eeeeee...hhh.eeeeeeeee.......eeeeeeee..eeeeeeeeee......eeehhhhhhhhhh....ee......eeee........eeeee..eeeeehhhhheee.......eeee.eee......eeeehhhhhhheeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3qvc A  77P KYSTVGFNIENSYDRLMKTIKEHKLKNYIKESVKLFNKGLTKK-------DNVELKDLANVLSFGEAKLGDNGQKFNFLFHTASSNVWVPSIKCTSESCESKNHYDSSKSKTYEKDDTPVKLTSKAGTISGIFSKDLVTIGKLSVPYKFIEMTEIVGFEPFYSESDVDGVFGLGWKDLSIGSIDPYIVELKTQNKIEQAVYSIYLPPENKNKGYLTIGGIEERFFDGPLNYEKLNHDLMWQVDLDVHFGNVSSKKANVILDSATSVITVPTEFFNQFVESASVFKVPFLSLYVTTCGNTKLPTLEYRSPNKVYTLEPKQYLEPLENIFSALCMLNIVPIDLEKNTFVLGDPFMRKYFTVYDYDNHTVGFALAKNL  328
                            |||||||86P|||||||96P||||||106P||||||116P|||      -|       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     
                            ||||||85P||||||94P|||||103P|||||112P|||||||       2                                                                                            96|        109A|                                                                                   195| ||||                                   243A     251|                      278A |||          292|                                
                          77P||||||86P||||||95P|||||104P|||||113P||||||                                                                                                     98         109B                                                                                    197 ||||                                             253                        279A||           296                                
                           78P||||||87P||||||96P|||||105P|||||114P|||||                                                                                                                                                                                                          199|||                                                                         279B|                                              
                            79P||||| 88P||||| 97P|||||106P|||||115P||||                                                                                                                                                                                                           201||                                                                          279C                                              
                             80P||||  89P||||  98P|||| 107P|||| 116P|||                                                                                                                                                                                                            203|                                                                                                                            
                              81P|||   90P|||   99P|||  108P|||  117P||                                                                                                                                                                                                             205                                                                                                                            
                               82P||    91P||   100P||   109P||   118P|                                                                                                                                                                                                                                                                                                                                            
                                83P|     92P|    101P|    110P|    119P                                                                                                                                                                                                                                                                                                                                            
                                 84P      93P     102P     111P
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QVC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9Y006_PLAFA | Q9Y006)
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: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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  3qvc
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9Y006_PLAFA | Q9Y006: 1qyj
UniProtKB/TrEMBL
        Q9Y006_PLAFA | Q9Y006: 3qvi

(-) Related Entries Specified in the PDB File

3qvi