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(-) Description

Title :  PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A NON-COVALENTLY BOUND P2-SUBSTITUTED N-ACYL-PROLYLPYRROLIDINE INHIBITOR
 
Authors :  P. Vanderveken, V. Fulop, D. Rea, M. Gerard, R. Vanelzen, J. Joossens, J V. Baekelandt, I. Demeester, A. M. Lambeir, K. Augustyns
Date :  01 Oct 12  (Deposition) - 13 Mar 13  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta-Hydrolase, Amnesia, Hydrolase, Parkinsons Disease, Alzheimers Disease, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Van Der Veken, V. Fulop, D. Rea, M. Gerard, R. Van Elzen, J. Joossens, J. D. Cheng, V. Baekelandt, I. De Meester, A. M. Lambeir, K. Augustyns
P2-Substituted N-Acylprolylpyrrolidine Inhibitors Of Prolyl Oligopeptidase: Biochemical Evaluation, Binding Mode Determination, And Assessment In A Cellular Model Of Synucleinopathy.
J. Med. Chem. V. 55 9856 2012
PubMed-ID: 23121075  |  Reference-DOI: 10.1021/JM301060G

(-) Compounds

Molecule 1 - PROLYL ENDOPEPTIDASE
    Chains: A
    EC Number: 3.4.21.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JM105
    Expression System Taxid: 562
    Organ: BRAIN
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: PE, POST-PROLINE CLEAVING ENZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE
3TDV1Ligand/Ion1-[(2S,4S)-4-[4-(4-FLUOROPHENYL)-1,2,3-TRIAZOL-1-YL]-2-PYRROLIDIN-1-YLCARBONYL-PYRROLIDIN-1-YL]-4-PHENYL-BUTAN-1-ONE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:173 , GLY A:254 , PHE A:476 , ILE A:478 , SER A:554 , VAL A:580 , ILE A:591 , TRP A:595 , ARG A:643 , VAL A:644BINDING SITE FOR RESIDUE TDV A 791
02AC2SOFTWAREILE A:118 , LEU A:119 , SER A:120 , ASP A:121 , LYS A:445 , ASP A:446 , ASN A:522 , ASN A:525 , HOH A:2118 , HOH A:2291 , HOH A:2757 , HOH A:2814 , HOH A:2956BINDING SITE FOR RESIDUE TAM A1711
03AC3SOFTWARELYS A:48 , GLU A:323 , SER A:324 , TRP A:326 , HOH A:2623 , HOH A:2640BINDING SITE FOR RESIDUE GOL A1712
04AC4SOFTWAREALA A:226 , GLU A:227 , PHE A:228 , ILE A:276 , LYS A:281 , HOH A:2957 , HOH A:2958BINDING SITE FOR RESIDUE GOL A1713
05AC5SOFTWAREGLY A:553 , HIS A:680 , HOH A:2959BINDING SITE FOR RESIDUE GOL A1714
06AC6SOFTWAREPRO A:568 , ASP A:569 , PHE A:571 , ILE A:628 , GLN A:629 , PRO A:631 , ASN A:668 , HOH A:2831 , HOH A:2917BINDING SITE FOR RESIDUE GOL A1715
07AC7SOFTWAREGLU A:239 , ASP A:291 , TYR A:292 , HOH A:2511 , HOH A:2518 , HOH A:2532 , HOH A:2593 , HOH A:2594 , HOH A:2596BINDING SITE FOR RESIDUE GOL A1716
08AC8SOFTWAREVAL A:341 , HOH A:2594 , HOH A:2595 , HOH A:2596 , HOH A:2961BINDING SITE FOR RESIDUE GOL A1717
09AC9SOFTWAREASP A:8 , VAL A:9 , TRP A:30 , GLN A:38 , ALA A:41 , PHE A:42 , HOH A:2033 , HOH A:2417 , HOH A:2963BINDING SITE FOR RESIDUE GOL A1718
10BC1SOFTWAREGLU A:287 , ASN A:305 , GLU A:512 , LYS A:516 , HOH A:2545 , HOH A:2584 , HOH A:2608 , HOH A:2609BINDING SITE FOR RESIDUE GOL A1719
11BC2SOFTWAREGLN A:193 , THR A:204 , ASN A:205 , LEU A:206BINDING SITE FOR RESIDUE GOL A1720

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BCD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BCD)

 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 4BCD)

(-) 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 d4bcda1 A:1-430 Prolyl oligopeptidase, N-terminal domain                                                                                                                                                                                                                                                                                                                                                                                      d4bcda2 A:431-710 Prolyl oligopeptidase, C-terminal domain                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeee..eeee..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee...eee..eeeeeee.......eeeee.......eeeehhhhhh....eeeeeeee.....eeeeeeee.....eeeeeee....eeeeeeeeee....eee.....eeeeee...................eeeeee...hhhhheeee........eeeeee.....eeeeeee.......eeeeee.hhh..........eeee......eeeeeee..eeeeee.......eeeeee....hhhhheeee......eeeeeeee...eeeeeeee..eeeeeeee.....eeeee.....eeeeee......eeeeeee......eeeeee........eeeee......hhh.eeeeeeeee.....eeeeeeeee..........eeee.............hhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeeehhhhhhhhhhhhhhhhhh.eeeee.......hhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhhh............eeeeeee.......hhhhhhhhhhhhhhh.........eeeeee.........hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------H--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PRO_ENDOPEP_SER  PDB: A:529-559------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bcd 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
   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  (0, 0)

(no "CATH Domain" information available for 4BCD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BCD)

(-) 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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  PPCE_PIG | P23687
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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 1qfm 1qfs 1uoo 1uop 1uoq 1vz2 1vz3 2xdw 3eq7 3eq8 3eq9 4amy 4amz 4an0 4an1 4ax4 4bcb 4bcc

(-) Related Entries Specified in the PDB File

1e5t PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT
1e8m PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT, COMPLEXED WITH INHIBITOR
1e8n PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, MUTANT, COMPLEXED WITH PEPTIDE
1h2w PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN
1h2x PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y473F MUTANT
1h2y PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y473F MUTANT WITH COVALENTLY BOUND INHIBITOR Z-PRO-PROLINAL
1h2z PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND PEPTIDE LIGAND SUC-GLY-PRO
1o6f PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, D641A MUTANT WITH BOUND PEPTIDE LIGAND SUC-GLY-PRO
1o6g PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, D641N MUTANT WITH BOUND PEPTIDE LIGAND SUC-GLY-PRO
1qfm PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE
1qfs PROLYL OLIGOPEPTIDASE FROM PORCINE MUSCLE WITH COVALENTLY BOUND INHIBITOR Z-PRO-PROLINAL
1uoo PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND PEPTIDE LIGAND GLY-PHE-ARG-PRO
1uop PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND PEPTIDE LIGAND GLY-PHE-GLU-PRO
1uoq PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, S554A MUTANT WITH BOUND PEPTIDE LIGAND GLU-PHE-SER-PRO
1vz2 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, Y73C/V427C/ C255T MUTANT
1vz3 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, T597C MUTANT
2xdw INHIBITION OF PROLYL OLIGOPEPTIDASE WITH A SYNTHETIC UNNATURAL DIPEPTIDE
4amy PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND INHIBITOR IC-1
4amz PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND INHIBITOR IC-2
4an0 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND INHIBITOR IC-3
4an1 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND INHIBITOR IC-4
4ax4 PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN, H680A MUTANT
4bcb PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND P2-SUBSTITUTED N-ACYL-PROLYLPYRROLIDINE INHIBITOR
4bcc PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND P2-SUBSTITUTED N-ACYL-PROLYLPYRROLIDINE INHIBITOR