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(-) Description

Title :  PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE
 
Authors :  V. Fulop
Date :  12 Apr 99  (Deposition) - 13 May 99  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Prolyl Oligopeptidase, Amnesia, Alpha/Beta-Hydrolase, Beta-Propeller, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Fulop, Z. Bocskei, L. Polgar
Prolyl Oligopeptidase: An Unusual Beta-Propeller Domain Regulates Proteolysis.
Cell(Cambridge, Mass. ) V. 94 161 1998
PubMed-ID: 9695945  |  Reference-DOI: 10.1016/S0092-8674(00)81416-6

(-) Compounds

Molecule 1 - PROTEIN (PROLYL OLIGOPEPTIDASE)
    Cellular Location: CYTOPLASM
    Chains: A
    EC Number: 3.4.21.26
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Other Details: PORCINE BRAIN SEQUENCE WAS USED FOR STRUCTURE DETERMINATION AND REFINEMENT
    Synonym: PROLYL ENDOPEPTIDASE, POST-PROLINE CLEAVING ENZYME
    Tissue: MUSCLE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1CSD2Mod. Amino Acid3-SULFINOALANINE
2CSX3Mod. Amino AcidS-OXY CYSTEINE
3GOL4Ligand/IonGLYCEROL
4SGL2Ligand/Ion1-HYDROXY-1-THIO-GLYCEROL
5SGM2Ligand/IonMONOTHIOGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:473 , SER A:554 , ASN A:555 , VAL A:580 , TRP A:595 , HIS A:680 , HOH A:838BINDING SITE FOR RESIDUE SGL A 781
2AC2SOFTWARECSX A:255 , ILE A:591 , TRP A:595 , ARG A:643 , HOH A:838 , HOH A:1473 , HOH A:1586BINDING SITE FOR RESIDUE SGL A 782
3AC3SOFTWARECYS A:78 , HIS A:79 , PHE A:80 , TYR A:385 , SER A:386 , HOH A:1212 , HOH A:1460BINDING SITE FOR RESIDUE SGM A 783
4AC4SOFTWAREPRO A:443 , CYS A:532 , GLU A:535BINDING SITE FOR RESIDUE SGM A 784
5AC5SOFTWAREILE A:118 , LEU A:119 , SER A:120 , ASP A:121 , ASP A:446 , ASN A:522 , ASN A:525 , HOH A:1163 , HOH A:1418BINDING SITE FOR RESIDUE GOL A 790
6AC6SOFTWAREALA A:226 , GLU A:227 , PHE A:228 , TRP A:262 , ILE A:276 , LYS A:281 , HOH A:1238 , HOH A:1529BINDING SITE FOR RESIDUE GOL A 791
7AC7SOFTWARETRP A:150 , VAL A:151 , GLU A:169 , ARG A:170 , VAL A:171 , SER A:197 , HOH A:1021BINDING SITE FOR RESIDUE GOL A 792
8AC8SOFTWAREPRO A:7 , ASP A:8 , VAL A:9 , TRP A:30 , GLN A:38 , ALA A:41 , PHE A:42 , HOH A:929 , HOH A:959 , HOH A:1412 , HOH A:1507BINDING SITE FOR RESIDUE GOL A 793

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_PPCE_PIG_001 *A29HPPCE_PIG  ---  ---AA29H
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PRO_ENDOPEP_SERPS00708 Prolyl endopeptidase family serine active site.PPCE_PIG529-559  1A:529-559

(-) Exons   (0, 0)

(no "Exon" information available for 1QFM)

(-) 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:710
 aligned with PPCE_PIG | P23687 from UniProtKB/Swiss-Prot  Length:710

    Alignment length:710
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710
             PPCE_PIG     1 MLSFQYPDVYRDETAIQDYHGHKVCDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNAYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESNGITGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRHSPNYRLINIDFTDPEESKWKVLVPEHEKDVLEWVACVRSNFLVLCYLHDVKNTLQLHDLATGALLKIFPLEVGSVVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGVLAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVATCANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLIKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQNNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNIDWIP 710
               SCOP domains d1qfma1 A:1-430 Prolyl oligopeptidase, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                      d1qfma2 A:431-710 Prolyl oligopeptidase, C-terminal domain                                                                                                                                                                                                                               SCOP domains
               CATH domains 1qfmA01 A:1-73,A:427-705  [code=3.40.50.1820, no name defined]           1qfmA02 A:74-426 Prolyl oligopeptidase, N-terminal domain                                                                                                                                                                                                                                                                                                        1qfmA01 A:1-73,A:427-705  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                         ----- CATH domains
               Pfam domains ------Peptidase_S9_N-1qfmA02 A:7-423                                                                                                                                                                                                                                                                                                                                                                                                   ----------------------------------------------------------Peptidase_S9-1qfmA01 A:482-707                                                                                                                                                                                                    --- Pfam domains
         Sec.struct. author ...............eeee..eeee...hhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........eee..eeeeee........eeeee......eeeee.hhhh.....eee..eee.....eeeeeeee......eeeeee..................eee.....eeeeee...................eeeeee....hhh.eeee........eeeeee.....eeeeeee.......eeeeeehhh.....................eeeeeee..eeeeee.......eeeeeehhh..hhh.eeee......eeeeeeee...eeeeeeee..eeeeeeee.....eeeee.....eeeeee......eeeeeee......eeeeee........eeeee.......hhheeeeeeeee.....eeeeeeeee..........eeee..............hhhhhhhhhh..eeeee........hhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhheeeeeehhhhhhhhhhhhh.hhh..eeeee........hhh...hhhhhhhh.....hhhhhhhhhh.hhh.............eeeeeee.......hhhhhhhhhhhhhh..........eeeeee..........hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------H--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PRO_ENDOPEP_SER  PDB: A:529-559------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qfm A   1 MLSFQYPDVYRDETAIQDYHGHKVcDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQcPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFScMAWTHDGKGMFYNAYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGcDPVNRLWYCDLQQESNGITGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRHSPNYRLINIDFTDPEESKWKVLVPEHEKDVLEWVACVRSNFLVLCYLHDVKNTLQLHDLATGALLKIFPLEVGSVVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGVLAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVATCANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGcSDSKQHFEWLIKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQNNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNIDWIP 710
                                    10        20    |   30        40        50      | 60        70        80        90       100       110       120       130       140       150       160       170    |  180       190       200       210       220       230       240       250    |  260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600|      610       620       630       640       650       660       670       680       690       700       710
                                                   25-CSX                          57-CSX                                                                                                               175-CSD                                                                         255-CSX                                                                                                                                                                                                                                                                                                                                                   601-CSD
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: AB_hydrolase (347)
(-)
Clan: Beta_propeller (192)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPCE_PIG | P23687)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0070008    serine-type exopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1qfm
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 Related Entries

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

UniProtKB/Swiss-Prot
        PPCE_PIG | P23687: 1e5t 1e8m 1e8n 1h2w 1h2x 1h2y 1h2z 1o6f 1o6g 1qfs 1uoo 1uop 1uoq 1vz2 1vz3 2xdw 3eq7 3eq8 3eq9 4amy 4amz 4an0 4an1 4ax4 4bcb 4bcc 4bcd

(-) Related Entries Specified in the PDB File

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