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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA CYCLOPHILIN 38 (ATCYP38)
 
Authors :  D. Vasudevan, K. Swaminathan
Date :  07 Apr 11  (Deposition) - 13 Jun 12  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Cyclophilin, Cyp38, Peptidyl Prolyl Isomerase, Ppiase, Tlp, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Vasudevan, A. Fu, S. Luan, K. Swaminathan
Crystal Structure Of Arabidopsis Cyclophilin38 Reveals A Previously Uncharacterized Immunophilin Fold And A Possible Autoinhibitory Mechanism.
Plant Cell V. 24 2666 2012
PubMed-ID: 22706283  |  Reference-DOI: 10.1105/TPC.111.093781

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE CYP38, CHLOROPLASTIC
    Chains: A
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-KG
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AT3G01480, CYP38, F4P13.3
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PPIASE CYP38, ROTAMASE CYP38, THYLAKOID LUMEN PPIASE

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3RFY)

(-) Sites  (0, 0)

(no "Site" information available for 3RFY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RFY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RFY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.CYP38_ARATH260-437  1A:260-433
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.CYP38_ARATH260-437  1A:260-433
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.CYP38_ARATH260-437  2A:260-433

(-) Exons   (0, 0)

(no "Exon" information available for 3RFY)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:356
 aligned with CYP38_ARATH | Q9SSA5 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:385
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428     
          CYP38_ARATH    49 GAFTSLKECAISLALSVGLMVSVPSIALPPNAHAVANPVIPDVSVLISGPPIKDPEALLRYALPIDNKAIREVQKPLEDITDSLKIAGVKALDSVERNVRQASRTLQQGKSIIVAGFAESKKDHGNEMIEKLEAGMQDMLKIVEDRKRDAVAPKQKEILKYVGGIEEDMVDGFPYEVPEEYRNMPLLKGRASVDMKVKIKDNPNIEDCVFRIVLDGYNAPVTAGNFVDLVERHFYDGMEIQRSDGFVVQTGDPEGPAEGFIDPSTEKTRTVPLEIMVTGEKTPFYGSTLEELGLYKAQVVIPFNAFGTMAMAREEFENDSGSSQVFWLLKESELTPSNSNILDGRYAVFGYVTDNEDFLADLKVGDVIESIQVVSGLENLANPSY 433
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----------------.eee-------------ee........eeee.....hhhhhhhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh................ee..eeeeeeeee........eeeeeeeee...hhhhhhhhhhhhhh.....ee.eeeeeeee........................................hhhh.eeeeeeee............................eeeee...........eeeeeeeee..hhhhhh....eeeeeeeeehhh.ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CSA_PPIASE_2  PDB: A:260-433 UniProt: 260-437                                                                                                                                  PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rfy A  78 G----------------GILL-------------VANPVIPDVSVLISGPPIKDPEALLRYALPIDNKAIREVQKPLEDITDSLKIAGVKALDSVERNVRQASRTLQQGKSIIVAGFAESKKDHGNEMIEKLEAGMQDMLKIVEDRKRDAVAPKQKEILKYVGGIEEDMVDGFPYEVPEEYRNMPLLKGRASVDMKVKIKDNPNIEDCVFRIVLDGYNAPVTAGNFVDLVERHFYDGMEIQRSDGFVVQTGDPEGPAEGFIDPSTEKTRTVPLEIMVTGEKTPFYGSTLEELGLYKAQVVIPFNAFGTMAMAREEFENDSGSSQVFWLLKESELTPSNSNILDGRYAVFGYVTDNEDFLADLKVGDVIESIQVVSGLENLANPSY 433
                            |        -       |81|        -    |   88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428     
                            |               79 82            83                                                                                                                                                                                                                                                                                                                                                              
                           78
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3RFY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (CYP38_ARATH | Q9SSA5)
molecular function
    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).
biological process
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    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:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009570    chloroplast stroma    The space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes and some temporary products of photosynthesis.
    GO:0009534    chloroplast thylakoid    Sac-like membranous structures (cisternae) in a chloroplast combined into stacks (grana) and present singly in the stroma (stroma thylakoids or frets) as interconnections between grana. An example of this component is found in Arabidopsis thaliana.
    GO:0009543    chloroplast thylakoid lumen    The cavity enclosed within the chloroplast thylakoid membrane. An example of this component is found in Arabidopsis thaliana.
    GO:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
    GO:0031977    thylakoid lumen    The volume enclosed by a thylakoid membrane.

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