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(-) Description

Title :  STRUCTURAL AND MECHANISTIC ANALYSIS OF TWO PROLYL ENDOPEPTIDASES: ROLE OF INTER-DOMAIN DYNAMICS IN CATALYSIS AND SPECIFICITY
 
Authors :  L. Shan, I. I. Mathews, C. Khosla
Date :  02 Feb 05  (Deposition) - 15 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Prolyl Endopeptidase, Mechanistic Study, Celiac Sprue, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Shan, I. I. Mathews, C. Khosla
Structural And Mechanistic Analysis Of Two Prolyl Endopeptidases: Role Of Interdomain Dynamics In Catalysis And Specificity
Proc. Natl. Acad. Sci. Usa V. 102 3599 2005
PubMed-ID: 15738423  |  Reference-DOI: 10.1073/PNAS.0408286102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROLYL OLIGOPEPTIDASE
    Chains: A
    EC Number: 3.4.21.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET28B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: ATCC
    Organism Scientific: NOVOSPHINGOBIUM CAPSULATUM
    Organism Taxid: 13688
    Synonym: PROLYL ENDOPEPTIDASES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:589 , ASP A:590 , PHE A:592 , TYR A:647 , PRO A:648 , LYS A:681 , HOH A:1304 , HOH A:1310BINDING SITE FOR RESIDUE GOL A 750
2AC2SOFTWAREARG A:175 , ALA A:197 , GLY A:644 , VAL A:645 , ASP A:646 , ALA A:677 , HOH A:792 , HOH A:878 , HOH A:934BINDING SITE FOR RESIDUE GOL A 755

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YR2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YR2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YR2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YR2)

(-) Exons   (0, 0)

(no "Exon" information available for 1YR2)

(-) 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:680
 aligned with Q9ZNM8_9SPHN | Q9ZNM8 from UniProtKB/TrEMBL  Length:723

    Alignment length:701
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       723               
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717     |   -         - 
         Q9ZNM8_9SPHN    38 PPYPASPQVPLVEDHFGEKVSDPWRWLEADVRTDAKVAAWVQAQSAYTAAYLKQLPERAALEKRMKALIDYERFGLPQRRGASVFYSWNSGLMNQSQLLVRPADAPVGTKGRVLLDPNTWAKDGATALDAWAASDDGRLLAYSVQDGGSDWRTVKFVGVADGKPLADELKWVKFSGLAWLGNDALLYSRFAEPKEGQAFQALNYNQTVWLHRLGTPQSADQPVFATPELPKRGHGASVSSDGRWVVITSSEGTDPVNTVHVARVTNGKIGPVTALIPDLKAQWDFVDGVGDQLWFVSGDGAPLKKIVRVDLSGSTPRFDTVVPESKDNLESVGIAGNRLFASYIHDAKSQVLAFDLDGKPAGAVSLPGIGSASGLSGRPGDRHAYLSFSSFTQPATVLALDPATAKTTPWEPVHLTFDPADFRVEQVFYPSKDGTKVPMFIVRRKDAKGPLPTLLYGYGGFNVALTPWFSAGFMTWIDSGGAFALANLRGGGEYGDAWHDAGRRDKKQNVFDDFIAAGEWLIANGVTPRHGLAIEGGSNGGLLIGAVTNQRPDLFAAASPAVGVMDMLRFDQFTAGRYWVDDYGYPEKEADWRVLRRYSPYHNVRSGVDYPAILVTTADTDDRVVPGHSLKYTAALQTAAIGPKPHLIRIETRAGHGSGKPIDKQIEETADVQAFLAHFTGLTPRP---------------   -
               SCOP domains d1yr2a1 A:38-456 automated matches                                                                                                                                                                                                                                                                                                                                                                                                 d1yr2a2 A:457-738 automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------1yr2A01 A:48-108,A:452-738                                   -------------------------------------------------    ---------------------------------------------------------------------        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1yr2A01 A:48-108,A:452-738  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                CATH domains
               Pfam domains ---Peptidase_S9_N-1yr2A02 A:41-450                                                                                                                                                                                                                                                                                                                                                                                           -----------------------------------------------------Peptidase_S9-1yr2A01 A:504-720                                                                                                                                                                                           ------------------ Pfam domains
         Sec.struct. author ...........eeee..eeee..hhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...ee...eee..eeeeeee.......eeeeee.........eeeehhhhh----.eeeeeeee.....eeeeeeee....eeeeeeee.....eeeeeeeeee....ee....eeeeee....--------.....eeeeee...hhhhheeee........eeeeee.....eeeeeee.......eeeeeeee..ee...eeee......eeeeeee..eeeeee.......eeeeee......eeeeee.....eeeeeeee..eeeeeeee..eeeeeeee....eeee.......eeeeee.......eeeeeee..eeeeeeeee....eeee........hhh.eeeeeeeee.....eeeeeeeee........eeee.............hhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhh.eeeee.......hhhhh.hhhhhhhhhh...hhhhhhhhhh.hhhhh........eeeeeee.......hhhhhhhhhhhhhh......eeeeee---------hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yr2 A  38 PPYPASPQVPLVEDHFGEKVSDPWRWLEADVRTDAKVAAWVQAQSAYTAAYLKQLPERAALEKRMKALIDYERFGLPQRRGASVFYSWNSGLMNQSQLLVRPADAPVGTKGRVLLDPNTW----ATALDAWAASDDGRLLAYSVQDGGSDWRTVKFVGVADGKPLADELKWVKFSGLAWLGNDALLYSRFAEP--------LNYNQTVWLHRLGTPQSADQPVFATPELPKRGHGASVSSDGRWVVITSSEGTDPVNTVHVARVTNGKIGPVTALIPDLKAQWDFVDGVGDQLWFVSGDGAPLKKIVRVDLSGSTPRFDTVVPESKDNLESVGIAGNRLFASYIHDAKSQVLAFDLDGKPAGAVSLPGIGSASGLSGRPGDRHAYLSFSSFTQPATVLALDPATAKTTPWEPVHLTFDPADFRVEQVFYPSKDGTKVPMFIVRRKDAKGPLPTLLYGYGGFNVALTPWFSAGFMTWIDSGGAFALANLRGGGEYGDAWHDAGRRDKKQNVFDDFIAAGEWLIANGVTPRHGLAIEGGSNGGLLIGAVTNQRPDLFAAASPAVGVMDMLRFDQFTAGRYWVDDYGYPEKEADWRVLRRYSPYHNVRSGVDYPAILVTTADTDDRVVPGHSFKYTAALQTAAIGPKPHLIRIE---------PIDKQIEETADVQAFLAHFTGLTPRPWSSVDKLAAALEHHH 738
                                    47        57        67        77        87        97       107       117       127       137       147       157    |  167       177       187       197       207       217       227  |      - |     247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687|        -|      707       717       727       737 
                                                                                                                                                 157  162                                                                 230      239                                                                                                                                                                                                                                                                                                                                                                                                                                                              688       698
   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  (1, 1)

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

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9ZNM8_9SPHN | Q9ZNM8)
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: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.

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 Related Entries

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