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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST CYCLOPHILIN A COMPLEXED WITH ACE-ALA-ALA-PRO-ALA-7-AMINO-4-METHYLCOUMARIN
 
Authors :  M. Konno, T. Shibano, K. Okudaira, N. Takahashi
Date :  24 Mar 04  (Deposition) - 28 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Barrel, Isomerase-Isomerase Inhibitor Complex, Rotamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Konno, T. Shibano, K. Okudaira, N. Takahashi
Crystal Structure Of Yeast Cyclophilin A Complexed With Ace-Ala-Ala-Pro-Ala-7-Amino-4-Methylcoumarin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYCLOPHILIN A
    Chains: A
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
 
Molecule 2 - (ACE)AAPA(MCM)
    Chains: B
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2MCM1Mod. Amino Acid7-AMINO-4-METHYL-CHROMEN-2-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:3 , VAL A:19 , ARG A:53 , ILE A:55 , ASP A:57 , PHE A:58 , GLN A:61 , ASP A:91 , ARG A:92 , ALA A:99 , ASN A:100 , PHE A:111 , PRO A:116 , LEU A:120 , HIS A:124 , PRO A:146 , HOH A:174 , HOH A:175 , HOH A:186 , HOH A:274 , HOH B:54 , HOH B:70 , HOH B:118BINDING SITE FOR CHAIN B OF (ACE)AAPA(MCM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala B:3 -Pro B:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.CYPH_YEAST5-161  1A:5-161
2CSA_PPIASE_1PS00170 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.CYPH_YEAST46-63  1A:46-63

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR155C1YDR155C.1IV:768998-768510489CYPH_YEAST1-1621621A:2-162161

(-) 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:161
 aligned with CYPH_YEAST | P14832 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
           CYPH_YEAST     2 SQVYFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGEKGFGYAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESLGSPSGATKARIVVAKSGEL 162
               SCOP domains d1vdna_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains 1vdnA00 A:2-162 Cyclophilin                                                                                                                                       CATH domains
               Pfam domains ---Pro_isomerase-1vdnA01 A:5-161                                                                                                                                - Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh............eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh...........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CSA_PPIASE_2  PDB: A:5-161 UniProt: 5-161                                                                                                                    - PROSITE (1)
                PROSITE (2) --------------------------------------------CSA_PPIASE_1      --------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:2-162 UniProt: 1-162 [INCOMPLETE]                                                                                                                Transcript 1
                 1vdn A   2 SQVYFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGEKGFGYAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESLGSPSGATKARIVVAKSGEL 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 


Chain B from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1vdn B   1 xAAPAx   6
                            |    |
                            1-ACE|
                                 6-MCM
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Cyclophil-like (65)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYPH_YEAST | P14832)
molecular function
    GO:0016018    cyclosporin A binding    Interacting selectively and non-covalently with cyclosporin A, a cyclic undecapeptide that contains several N-methylated and unusual amino acids.
    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:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
biological process
    GO:0030437    ascospore formation    The process in which cells that are products of meiosis acquire the specialized features of ascospores. Ascospores are generally found in clusters of four or eight spores within a single mother cell, the ascus, and are characteristic of the ascomycete fungi (phylum Ascomycota).
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    GO:0045836    positive regulation of meiotic nuclear division    Any process that activates or increases the frequency, rate or extent of meiosis.
    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.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0034967    Set3 complex    A histone deacetylase complex that is involved in transcriptional regulation. In S. cerevisiae, this complex consists of Set3p, Snt1p, Hos4p, Sif2p, Cpr1p, Hos2p, and Hst1p.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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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 Related Entries

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        CYPH_YEAST | P14832: 1ist

(-) Related Entries Specified in the PDB File

1ist FREE YEAST CYCLOPHILIN A