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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FK506-BINDING DOMAIN OF PLASMODIUM FALCIPARUM FKBP35 IN COMPLEX WITH FK506
 
Authors :  M. Kotaka, R. Alag, H. Ye, P. R. Preiser, H. S. Yoon, J. Lescar
Date :  30 Jan 08  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Fkbp, Fk506, Isomerase, Tpr Repeat, Plasmodium Falciparum (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kotaka, H. Ye, R. Alag, G. Hu, Z. Bozdech, P. R. Preiser, H. S. Yoon, J. Lescar
Crystal Structure Of The Fk506 Binding Domain Of Plasmodium Falciparum Fkbp35 In Complex With Fk506.
Biochemistry V. 47 5951 2008
PubMed-ID: 18465874  |  Reference-DOI: 10.1021/BI800004U

(-) Compounds

Molecule 1 - 70 KDA PEPTIDYLPROLYL ISOMERASE
    Chains: A, B
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: FK506-BINDING DOMAIN, RESIDUES 1-127
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7
    Synonym: PLASMODIUM FALCIPARUM FKBP35

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FK52Ligand/Ion8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FK51Ligand/Ion8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FK51Ligand/Ion8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:44 , PHE A:55 , ASP A:56 , ARG A:61 , PHE A:65 , GLU A:73 , VAL A:74 , ILE A:75 , TRP A:78 , TYR A:101 , ILE A:110 , PHE A:118 , HOH A:2062 , HOH A:2063 , HOH A:2064 , HOH A:2065 , HOH A:2066 , HIS B:43 , SER B:57 , PHE B:59 , ASP B:60 , LYS B:90 , GLU B:119BINDING SITE FOR RESIDUE FK5 A 501
2AC2SOFTWAREHIS A:43 , SER A:57 , PHE A:59 , ASP A:60 , LYS A:90 , GLU A:119 , TYR B:44 , PHE B:55 , ASP B:56 , ARG B:61 , PHE B:65 , GLU B:73 , VAL B:74 , ILE B:75 , TRP B:78 , GLY B:100 , TYR B:101 , PHE B:118 , HOH B:2094 , HOH B:2095 , HOH B:2096BINDING SITE FOR RESIDUE FK5 B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VN1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VN1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VN1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VN1)

(-) Exons   (0, 0)

(no "Exon" information available for 2VN1)

(-) 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:123
 aligned with Q8I4V8_PLAF7 | Q8I4V8 from UniProtKB/TrEMBL  Length:304

    Alignment length:123
                                    16        26        36        46        56        66        76        86        96       106       116       126   
         Q8I4V8_PLAF7     7 FEKVELTADGGVIKTILKKGDEGEENIPKKGNEVTVHYVGKLESTGKVFDSSFDRNVPFKFHLEQGEVIKGWDICVSSMRKNEKCLVRIESMYGYGDEGCGESIPGNSVLLFEIELLSFREAK 129
               SCOP domains d2vn1a_ A: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeeeeee....hhhhh.....eeeeeeeeee.....eeee.......eeee......hhhhhhhhh......eeeeee.hhhh...............eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vn1 A   7 FEKVELTADGGVIKTILKKGDEGEENIPKKGNEVTVHYVGKLESTGKVFDSSFDRNVPFKFHLEQGEVIKGWDICVSSMRKNEKCLVRIESMYGYGDEGCGESIPGNSVLLFEIELLSFRELE 129
                                    16        26        36        46        56        66        76        86        96       106       116       126   


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with Q8I4V8_PLAF7 | Q8I4V8 from UniProtKB/TrEMBL  Length:304

    Alignment length:124
                                    15        25        35        45        55        65        75        85        95       105       115       125    
         Q8I4V8_PLAF7     6 EFEKVELTADGGVIKTILKKGDEGEENIPKKGNEVTVHYVGKLESTGKVFDSSFDRNVPFKFHLEQGEVIKGWDICVSSMRKNEKCLVRIESMYGYGDEGCGESIPGNSVLLFEIELLSFREAK 129
               SCOP domains d2vn1b_ B: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------FKBP_C-2vn1B01 B:30-123                                                                       ------ Pfam domains (1)
           Pfam domains (2) ------------------------FKBP_C-2vn1B02 B:30-123                                                                       ------ Pfam domains (2)
         Sec.struct. author ...eee......eeeeeee....hhhhh.....eeeeeeeeee.....eeee.......eeee......hhhhhhhhh......eeeeee.hhhh...............eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vn1 B   6 EFEKVELTADGGVIKTILKKGDEGEENIPKKGNEVTVHYVGKLESTGKVFDSSFDRNVPFKFHLEQGEVIKGWDICVSSMRKNEKCLVRIESMYGYGDEGCGESIPGNSVLLFEIELLSFRELE 129
                                    15        25        35        45        55        65        75        85        95       105       115       125
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VN1)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: FKBP_C] (58)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8I4V8_PLAF7 | Q8I4V8)
molecular function
    GO:0005528    FK506 binding    Interacting selectively and non-covalently with the 23-membered macrolide lactone FK506.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0061077    chaperone-mediated protein folding    The process of inhibiting aggregation and assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that is dependent on interaction with a chaperone.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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        Q8I4V8_PLAF7 | Q8I4V8: 2fbn 2ofn 4j4n 4qt2 4qt3

(-) Related Entries Specified in the PDB File

2fbn PLASMODIUM FALCIPARUM PUTATIVE FK506-BINDING PROTEINPFL2275C, C-TERMINAL TPR-CONTAINING DOMAIN