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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF SERA5E FROM PLASMODIUM FALCIPARUM WITH LOOP 690-700 ORDERED
 
Authors :  B. J. Smith, R. L. Malby, P. M. Colman, O. B. Clarke
Date :  27 Feb 09  (Deposition) - 31 Mar 09  (Release) - 31 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  X
Keywords :  Serine Repeat Antigen, Sera, Malaria, Vacuole, Protease, Cathepsin, Hydrolase, Plasmodium, Glycoprotein, Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. N. Hodder, J. E. Mccoubrie, R. L. Malby, P. R. Gilson, O. B. Clarke, W. D Fairlie, P. M. Colman, B. J. Smith, B. S Crabb
Structural And Functional Insights Into The Protease-Like Antigen Plasmodium Falciparum Sera5 And Its Non-Canonical Active-Site Serine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SERINE-REPEAT ANTIGEN PROTEIN
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: SERINE-PROTEASE DOMAIN, RESIDUES 555-819
    Organism Common: MALARIA PARASITE
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Synonym: 111 KDA ANTIGEN, P126, SERA5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3DMS6Ligand/IonDIMETHYL SULFOXIDE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP X:589 , SER X:641 , TYR X:663 , ASN X:664 , TYR X:665 , TYR X:703 , HOH X:2245BINDING SITE FOR RESIDUE DMS X1828
02AC2SOFTWAREGLU X:739 , ASN X:740 , ASP X:757 , GLY X:777 , HOH X:2165 , HOH X:2167BINDING SITE FOR RESIDUE CA X1829
03AC3SOFTWARESER X:640 , LYS X:667 , TYR X:735 , HOH X:2037BINDING SITE FOR RESIDUE CL X1830
04AC4SOFTWAREASP X:634 , ARG X:635 , CYS X:636 , ASP X:637BINDING SITE FOR RESIDUE CL X1831
05AC5SOFTWAREGLU X:588 , ASP X:589 , TYR X:663 , HOH X:2246BINDING SITE FOR RESIDUE DMS X1832
06AC6SOFTWARELYS X:701 , TRP X:789 , GLY X:790 , PRO X:791 , TYR X:792 , TRP X:793 , HOH X:2028BINDING SITE FOR RESIDUE CL X1833
07AC7SOFTWARECYS X:809 , HIS X:810 , ASN X:812 , HOH X:2247 , HOH X:2248BINDING SITE FOR RESIDUE DMS X1834
08AC8SOFTWAREASN X:580BINDING SITE FOR RESIDUE CL X1835
09AC9SOFTWAREGLU X:709 , ASP X:758 , HOH X:2087 , HOH X:2129 , HOH X:2234BINDING SITE FOR RESIDUE CA X1836
10BC1SOFTWAREASN X:626 , TYR X:628 , TYR X:652 , CYS X:672 , HOH X:2076BINDING SITE FOR RESIDUE DMS X1837
11BC2SOFTWAREARG X:710 , ASN X:714 , HOH X:2133BINDING SITE FOR RESIDUE DMS X1838
12BC3SOFTWARESER X:747 , GLY X:748 , LYS X:749 , GLY X:794 , ASP X:795 , HOH X:2207BINDING SITE FOR RESIDUE DMS X1839

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1X:567 -X:572
2X:581 -X:610
3X:593 -X:636
4X:627 -X:672
5X:755 -X:809

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WBF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.SERA_PLAFD752-762  1X:760-770
2THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.SERA_PLAFD774-793  1X:782-801

(-) Exons   (0, 0)

(no "Exon" information available for 2WBF)

(-) 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 X from PDB  Type:PROTEIN  Length:265
 aligned with SERA_PLAFD | P69193 from UniProtKB/Swiss-Prot  Length:989

    Alignment length:265
                                   564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814     
           SERA_PLAFD   555 DNMFCNKEYCNRLKDENNCISNLQVEDQGNCDTSWIFASKYHLETIRCMKGYEPTKISALYVANCYKGEHKDRCDEGSSPMEFLQIIEDYGFLPAESNYPYNYVKVGEQCPKVEDHWMNLWDNGKILHNKNEPNSLDGKGYTAYESERFHDNMDAFVKIIKTEVMNKGSVIAYIKAENVMGYEFSGKKVQNLCGDDTADHAVNIVGYGNYVNSEGEKKSYWIVRNSWGPYWGDEGYFKVDMYGPTHCHFNFIHSVVIFNVDLPMN 819
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wbfX00 X:563-827 Cysteine proteinases                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------Peptidase_C1-2wbfX01 X:573-819                                                                                                                                                                                                                         -------- Pfam domains
         Sec.struct. author ..........hhhhh...hhhhh.........hhhhhhhhhhhhhhhhhh.......hhhhhhhh.............hhhhhhhhhhhhh..........hhhhh..................ee..............eeeee.hhhh.hhhhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhh..ee.........eeeeeeeeeeee.....eeeeeeee...........eeeee.............eeeee.ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE-----------THIOL_PROTEASE_ASN  -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wbf X 563 DNMFCNKEYCNRLKDENNCISNLQVEDQGNCDTSWIFASKYHLETIRCMKGYEPTKISALYVANCYKGEHKDRCDEGSSPMEFLQIIEDYGFLPAESNYPYNYVKVGEQCPKVEDHWMNLWDNGKILHNKNEPNSLDGKGYTAYESERFHDNMDAFVKIIKTEVMNKGSVIAYIKAENVMGYEFSGKKVKNLCGDDTADHAVNIVGYGNYVNSEGEKKSYWIVRNSWGPYWGDEGYFKVDMYGPTHCHFNFIHSVVIFNVDLPMN 827
                                   572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822
   Legend:   → Mismatch (orange background)
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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 2WBF)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_CA (169)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (SERA_PLAFD | P69193)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue 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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