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(-) Description

Title :  APPEP_WTX OPENED STATE
 
Authors :  T. K. Chiu
Date :  31 Aug 09  (Deposition) - 05 May 10  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Prolyl Endopeptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Li, C. Chen, D. R. Davies, T. K. Chiu
Induced-Fit Mechanism For Prolyl Endopeptidase
J. Biol. Chem. V. 285 21487 2010
PubMed-ID: 20444688  |  Reference-DOI: 10.1074/JBC.M109.092692

(-) Compounds

Molecule 1 - PROLYL ENDOPEPTIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PROLYL ENDOPEPTIDASE
    Organism Common: AEROMONAS CAVIAE
    Organism Scientific: AEROMONAS PUNCTATA
    Organism Taxid: 648

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:77 , PHE A:91 , GOL A:702BINDING SITE FOR RESIDUE GOL A 701
2AC2SOFTWAREPHE A:91 , GOL A:701 , HOH A:1006BINDING SITE FOR RESIDUE GOL A 702
3AC3SOFTWAREPHE A:91 , GOL A:704 , HOH A:1131BINDING SITE FOR RESIDUE GOL A 703
4AC4SOFTWARESER A:332 , ASN A:374 , GLY A:375 , GOL A:703 , HOH A:1035BINDING SITE FOR RESIDUE GOL A 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IUM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IUM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IUM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IUM)

(-) Exons   (0, 0)

(no "Exon" information available for 3IUM)

(-) 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:668
 aligned with Q9X6R4_AERCA | Q9X6R4 from UniProtKB/TrEMBL  Length:690

    Alignment length:684
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686    
         Q9X6R4_AERCA     7 LHYPVTRQGEQVDHYFGQAVADPYRWLEDDRSPETEAWVKAQNAVTQDYLAQIPYRAAIKEKLAASWNYAKEGAPFREGRYHYFFKNDGLQNQNVLWRQKEGKPAEVFLDPNTLSPDGTTALDQLSFSRDGRILAYSLSLAGSDWREIHLMDVESKQPLETPLKDVKFSGISWLGNEGFFYSSYDKPDGSELSARTDQHKVYFHRLGTAQEDDRLVFGAIPAQHHRYVGATVTEDDRFLLISAANSTSGNRLYVKDLSQENAPLLTVQGDLDADVSLVDNKGSTLYLLTNRDAPNRRLVTVDAANPGPAHWRDLIPERHRVLTVHSGTAYLFAEYMVDATAPVEQFDYEGKRVREVALPGLGSVSGFNGKHDDPALYFGFENYAQPPTLYRFEPKSGAISLYRASAAPFKPEDYVSEQRFYQSKDGTRVPLIISYRKGLKLDGSNPTILYGYGGFDVSLTPSFSVSVANWLDLGGVYAVANLRGGGEYGQAWHLAGTQQNKQNVFDDFIAAAEYLKAEGYTRTDRLAIRGGSNGGLLVGAVMTQRPDLMRVALPAVGVLDMLRYHTFTAGAGWAYDYGTSADSEAMFDYLKGYSPLHNVRPGVSYPSTMVTTADHDDRVVPAHSFKFAATLQADNAGPHPQLIRIETNAGHGAGTPVAKLIEQSADIYAFTLYEMGYRELPRQP 690
               SCOP domains d3iuma1 A:7-417 automated matches                                                                                                                                                                                                                                                                                                                                                                                          d3iuma2 A:418-690 automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3iumA01 A:7-75,A:413-690  [code=3.40.50.1820, no name defined]       ----------------------------------------------------------------------------------------------------------------------        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3iumA01 A:7-75,A:413-690  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eee..eee....hhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...ee...eee..eeeeeee.......eeeee......eeeehhhhhh.....eeeeeee.....eeeeeee.....eeeeeeee....eeeeeeeeeee....eee...eeeeee....--------....eeeeee...hhhhheeee..hhhhh..eeeeee.....eeeeeee......eeeeee........eeee......eeeeeee..eeeeee.......eeeeee....hhhhheeee.......eeeee..eeeeeeee..eeeeeee.....eeee.......eeee.........eeeeeee..eeeeeeee......eeeee......hhh.eeeeeeeee.....eeeeeeeee..........eeee.............hhhhhhhhhh..eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeeehhhhhhhhhhhhhh.....eeeee....hhhhh..hhhhhhhhhhhh....hhhhhhhhhhhh............eeeeeee.......hhhhhhhhhhhhh.......eeeeee.--------hhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ium A   7 LHYPVTRQGEQVDHYFGQAVADPYRWLEDDRSPETEAWVKAQNAVTQDYLAQIPYRAAIKEKLAASWNYAKEGAPFREGRYHYFFKNDGLQNQNVLWRQQEGKPAEVFLDPNTLSPDGTTALDQLSFSRDGRILAYSLSLAGSDWREIHLmDVESKQPLETPLKDVKFSGISWLGNEGFFYSSYDKP--------TDQHKVYFHRLGTAQEDDRLVFGAIPAQHHRYVGATVTEDDRFLLISAANSTSGNRLYVKDLSQENAPLLTVQGDLDADVSLVDNKGSTLYLLTNRDAPNRRLVTVDAANPGPAHWRDLIPERQQVLTVHSGSGYLFAEYmVDATARVEQFDYEGKRVREVALPGLGSVSGFNGKHDDPALYFGFENYAQPPTLYRFEPKSGAISLYRASAAPFKPEDYVSEQRFYQSKDGTRVPLIISYRKGLKLDGSNPTILYGYGGFDVSLTPSFSVSVANWLDLGGVYAVANLRGGGEYGQAWHLAGTQQNKQNVFDDFIAAAEYLKAEGYTRTDRLAIRGGSNGGLLVGAVmTQRPDLmRVALPAVGVLDmLRYHTFTAGTGWAYDYGTSADSEAmFDYLKGYSPLHNVRPGVSYPSTmVTTADHDDRVVPAHSFKFAATLQADNAGPHPQLIRIET--------PVAKLIEQSADIYAFTLYEmGYRELPRQP 690
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156|      166       176       186      |  -     | 206       216       226       236       246       256       266       276       286       296       306       316       326       336     | 346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546 |     556       566|      576       586     | 596       606       616       626       636       646      |  -     | 666       676    |  686    
                                                                                                                                                                                157-MSE                             193      202                                                                                                                                         342-MSE                                                                                                                                                                                                       548-MSE  |         567-MSE                  592-MSE                615-MSE                               653      662                681-MSE     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              555-MSE
   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  (0, 0)

(no "Pfam Domain" information available for 3IUM)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9X6R4_AERCA | Q9X6R4)
molecular function
    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

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

UniProtKB/TrEMBL
        Q9X6R4_AERCA | Q9X6R4: 3iuj 3iul 3iun 3iuq 3iur 3ivm 3mun 3muo

(-) Related Entries Specified in the PDB File

3iuj APPEP_WT2 OPENED STATE
3iul APPEP_WT1 OPENED STATE
3iun APPEP_D622N OPENED STATE
3iuq APPEP_D622N+PP CLOSED STATE
3iur APPEP_D266NX+H2H3 OPENED STATE
3ivm APPEP_WT+PP CLOSED STATE