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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PEPTIDYLPROLYL ISOMERASE DOMAIN OF HUMAN PPWD1
 
Authors :  J. R. Walker, T. L. Davis, E. M. Newman, F. Mackenzie, M. Sundstrom, C. Ar A. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics Con (Sgc)
Date :  22 Jun 05  (Deposition) - 05 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Cis-Trans Isomerization, Protein-Folding, Peptidylprolyl Isomerase, Structural Genomics, Structural Genomics Consortium, Sgc, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. L. Davis, J. R. Walker, H. Ouyang, F. Mackenzie, C. Butler-Cole, E. M. Newman, E. Z. Eisenmesser, S. Dhe-Paganon
The Crystal Structure Of Human Wd40 Repeat-Containing Peptidylprolyl Isomerase (Ppwd1).
Febs J. V. 275 2283 2008
PubMed-ID: 18397323  |  Reference-DOI: 10.1111/J.1742-4658.2008.06381.X

(-) Compounds

Molecule 1 - PEPTIDYLPROLYL ISOMERASE DOMAIN AND WD REPEAT CONTAINING 1
    ChainsA, B, C
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28-LIC
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentPEPTIDYLPROLYL ISOMERASE DOMAIN, RESIDUES 482-646
    GenePPWD1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:489 , VAL A:521 , ASN A:525 , LYS C:538 , GLY C:539BINDING SITE FOR RESIDUE GOL C 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A2N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A2N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A2N)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.PPWD1_HUMAN490-645
 
 
  3A:490-645
B:490-645
C:490-645
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.PPWD1_HUMAN490-645
 
 
  1A:490-645
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.PPWD1_HUMAN490-645
 
 
  1-
B:490-645
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.PPWD1_HUMAN490-645
 
 
  1-
-
C:490-645

(-) Exons   (4, 12)

Asymmetric Unit (4, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002613081bENSE00002075273chr5:64859066-64859333268PPWD1_HUMAN1-66660--
1.4aENST000002613084aENSE00000748741chr5:64863340-64863442103PPWD1_HUMAN66-100350--
1.6bENST000002613086bENSE00000748743chr5:64865459-64865559101PPWD1_HUMAN100-134350--
1.7bENST000002613087bENSE00000748746chr5:64865705-64865825121PPWD1_HUMAN134-174410--
1.8dENST000002613088dENSE00000748749chr5:64867666-64868113448PPWD1_HUMAN174-3231500--
1.9bENST000002613089bENSE00000748752chr5:64872706-64872896191PPWD1_HUMAN324-387640--
1.10bENST0000026130810bENSE00000748755chr5:64875251-64875440190PPWD1_HUMAN387-450640--
1.11cENST0000026130811cENSE00000748758chr5:64878865-64879046182PPWD1_HUMAN451-511613A:483-511
B:483-511
C:482-511
29
29
30
1.12bENST0000026130812bENSE00000748761chr5:64880841-6488092282PPWD1_HUMAN511-538283A:511-538
B:511-538
C:511-538
28
28
28
1.13ENST0000026130813ENSE00001302837chr5:64881826-64882008183PPWD1_HUMAN539-599613A:539-599
B:539-599
C:539-599
61
61
61
1.14dENST0000026130814dENSE00001312083chr5:64883080-64883376297PPWD1_HUMAN600-646473A:600-646
B:600-646
C:600-646
47
47
47

(-) 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:164
 aligned with PPWD1_HUMAN | Q96BP3 from UniProtKB/Swiss-Prot  Length:646

    Alignment length:164
                                   492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642    
          PPWD1_HUMAN   483 QAEGPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGEFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITVK 646
               SCOP domains d2a2na1 A:483-646 Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain                                                       SCOP domains
               CATH domains 2a2nA00 A:483-646 Cyclophilin                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..eeeeeee....hhhhhhhhhhhhhh.........eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh...............eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------CSA_PPIASE_2  PDB: A:490-645 UniProt: 490-645                                                                                                               - PROSITE
           Transcript 1 (1) Exon 1.11c  PDB: A:483-511   ---------------------------Exon 1.13  PDB: A:539-599 UniProt: 539-599                   Exon 1.14d  PDB: A:600-646 UniProt: 600-646     Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.12b  PDB: A:511-538  ------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2a2n A 483 QAEGPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGEFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITVK 646
                                   492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642    

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with PPWD1_HUMAN | Q96BP3 from UniProtKB/Swiss-Prot  Length:646

    Alignment length:164
                                   492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642    
          PPWD1_HUMAN   483 QAEGPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGEFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITVK 646
               SCOP domains d2a2nb_ B: Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain                                                              SCOP domains
               CATH domains 2a2nB00 B:483-646 Cyclophilin                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee..eeeeeee....hhhhhhhhhhhhhh.........eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh...............eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------CSA_PPIASE_2  PDB: B:490-645 UniProt: 490-645                                                                                                               - PROSITE
           Transcript 1 (1) Exon 1.11c  PDB: B:483-511   ---------------------------Exon 1.13  PDB: B:539-599 UniProt: 539-599                   Exon 1.14d  PDB: B:600-646 UniProt: 600-646     Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.12b  PDB: B:511-538  ------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2a2n B 483 QAEGPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGEFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITVK 646
                                   492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642    

Chain C from PDB  Type:PROTEIN  Length:165
 aligned with PPWD1_HUMAN | Q96BP3 from UniProtKB/Swiss-Prot  Length:646

    Alignment length:165
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641     
          PPWD1_HUMAN   482 TQAEGPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGEFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITVK 646
               SCOP domains d2a2nc_ C: Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain                                                               SCOP domains
               CATH domains 2a2nC00 C:482-646 Cyclophilin                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee..eeeeeee....hhhhhhhhhhhhhhh........eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh...............eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------CSA_PPIASE_2  PDB: C:490-645 UniProt: 490-645                                                                                                               - PROSITE
           Transcript 1 (1) Exon 1.11c  PDB: C:482-511    ---------------------------Exon 1.13  PDB: C:539-599 UniProt: 539-599                   Exon 1.14d  PDB: C:600-646 UniProt: 600-646     Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.12b  PDB: C:511-538  ------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2a2n C 482 TQAEGPKRVSDSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGEFEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTPWLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITVK 646
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641     

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A2N)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PPWD1_HUMAN | Q96BP3)
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:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    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:0071013    catalytic step 2 spliceosome    A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
    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.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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