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(-) Description

Title :  STRUCTURE OF E. COLI CYCLOPHILIN B K163T MUTANT
 
Authors :  M. Konno, Y. Sano, K. Okudaira, Y. Kawaguchi, Y. Yamagishi-Ohmori, S. Fushinobu, H. Matsuzawa
Date :  26 Dec 02  (Deposition) - 10 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Konno, Y. Sano, K. Okudaira, Y. Kawaguchi, Y. Yamagishi-Ohmori, S. Fushinobu, H. Matsuzawa
Escherichia Coli Cyclophilin B Binds A Highly Distorted Form Of Trans-Prolyl Peptide Isomer
Eur. J. Biochem. V. 271 3794 2004
PubMed-ID: 15355356  |  Reference-DOI: 10.1111/J.1432-1033.2004.04321.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYCLOPHILIN B
    Chains: A
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PATRP EPPIA
    Expression System Strain: HB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1J2A)

(-) Sites  (0, 0)

(no "Site" information available for 1J2A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J2A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J2A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J2A)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.PPIA_ECO5735-188  1A:11-164
PPIA_ECOL635-188  1A:11-164
PPIA_ECOLI35-188  1A:11-164
2CSA_PPIASE_1PS00170 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.PPIA_ECO5765-82  1A:41-58
PPIA_ECOL665-82  1A:41-58
PPIA_ECOLI65-82  1A:41-58

(-) Exons   (0, 0)

(no "Exon" information available for 1J2A)

(-) 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 A from PDB  Type:PROTEIN  Length:166
 aligned with PPIA_ECO57 | P0AFL5 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:166
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184      
           PPIA_ECO57    25 AKGDPHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQKKPNPPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSAKVLP 190
               SCOP domains d1j2aa_ A: Peptidyl-prolyl cis-trans isomerase A, PpiA                                                                                                                 SCOP domains
               CATH domains 1j2aA00 A:1-166 Cyclophilin                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeee....hhhhhhhhhhhhhh.....ee..eee...eeee..................hhhhh......eeee............eeee...hhhhh.........eeeeeeehhhhhhhhhh.................eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------CSA_PPIASE_2  PDB: A:11-164 UniProt: 35-188                                                                                                               -- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ----------------------------------------CSA_PPIASE_1      ------------------------------------------------------------------------------------------------------------ PROSITE (5)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j2a A   1 AKGDPHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQKKPNPPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSATVLP 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      


Chain A from PDB  Type:PROTEIN  Length:166
 aligned with PPIA_ECOL6 | P0AFL4 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:166
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184      
           PPIA_ECOL6    25 AKGDPHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQKKPNPPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSAKVLP 190
               SCOP domains d1j2aa_ A: Peptidyl-prolyl cis-trans isomerase A, PpiA                                                                                                                 SCOP domains
               CATH domains 1j2aA00 A:1-166 Cyclophilin                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeee....hhhhhhhhhhhhhh.....ee..eee...eeee..................hhhhh......eeee............eeee...hhhhh.........eeeeeeehhhhhhhhhh.................eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ----------CSA_PPIASE_2  PDB: A:11-164 UniProt: 35-188                                                                                                               -- PROSITE (3)
                PROSITE (4) ----------------------------------------CSA_PPIASE_1      ------------------------------------------------------------------------------------------------------------ PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j2a A   1 AKGDPHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQKKPNPPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSATVLP 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      


Chain A from PDB  Type:PROTEIN  Length:166
 aligned with PPIA_ECOLI | P0AFL3 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:166
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184      
           PPIA_ECOLI    25 AKGDPHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQKKPNPPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSAKVLP 190
               SCOP domains d1j2aa_ A: Peptidyl-prolyl cis-trans isomerase A, PpiA                                                                                                                 SCOP domains
               CATH domains 1j2aA00 A:1-166 Cyclophilin                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeee....hhhhhhhhhhhhhh.....ee..eee...eeee..................hhhhh......eeee............eeee...hhhhh.........eeeeeeehhhhhhhhhh.................eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------CSA_PPIASE_2  PDB: A:11-164 UniProt: 35-188                                                                                                               -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                PROSITE (5) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                PROSITE (6) ----------------------------------------CSA_PPIASE_1      ------------------------------------------------------------------------------------------------------------ PROSITE (6)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j2a A   1 AKGDPHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQKKPNPPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSATVLP 166
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J2A)

(-) Gene Ontology  (6, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPIA_ECOL6 | P0AFL4)
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: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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain A   (PPIA_ECO57 | P0AFL5)
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: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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain A   (PPIA_ECOLI | P0AFL3)
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: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:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPIA_ECO57 | P0AFL5: 1clh 1v9t 1vai
        PPIA_ECOL6 | P0AFL4: 1clh 1v9t 1vai
        PPIA_ECOLI | P0AFL3: 1clh 1v9t 1vai

(-) Related Entries Specified in the PDB File

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1j29 THE SAME PROTEIN BOUNDED TO N-ACETYL-ALA-ALA-PRO-ALA- 4METHYL-COUMARYL-7-AMIDE