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(-) Description

Title :  CRYSTAL STRUCTURE OF PROLYL AMINOPEPTIDASE, COMPLEX WITH PRO-TBODA
 
Authors :  Y. Nakajima, T. Inoue, K. Ito, T. Tozaka, S. Hatakeyama, N. Tanaka, K. T. Nakamura, T. Yoshimoto
Date :  01 Jul 04  (Deposition) - 20 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Proline Iminopeptidase, Complex With Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Inoue, K. Ito, T. Tozaka, S. Hatakeyama, N. Tanaka, K. T. Nakamura, T. Yoshimoto
Novel Inhibitor For Prolyl Aminopeptidase From Serratia Marcescens And Studies On The Mechanism Of Substrate Recognition Of The Enzyme Using The Inhibitor
Arch. Biochem. Biophys. V. 416 147 2003
PubMed-ID: 12893291  |  Reference-DOI: 10.1016/S0003-9861(03)00293-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROLINE IMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
    Synonym: PIP, PROLYL AMINOPEPTIDASE, PAP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PTB1Ligand/Ion(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)[(2R)-PYRROLIDIN-2-YL]METHANONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:45 , GLY A:46 , GLY A:112 , SER A:113 , TRP A:114 , ARG A:136 , TYR A:150 , GLU A:204 , GLU A:232 , PHE A:236 , HIS A:296 , HOH A:408BINDING SITE FOR RESIDUE PTB A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WM1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:46 -Pro A:47
2Arg A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WM1)

(-) Exons   (0, 0)

(no "Exon" information available for 1WM1)

(-) 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:313
 aligned with PIP_SERMA | O32449 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:313
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313   
            PIP_SERMA     4 LRGLYPPLAAYDSGWLDTGDGHRIYWELSGNPNGKPAVFIHGGPGGGISPHHRQLFDPERYKVLLFDQRGCGRSRPHASLDNNTTWHLVADIERLREMAGVEQWLVFGGSWGSTLALAYAQTHPERVSEMVLRGIFTLRKQRLHWYYQDGASRFFPEKWERVLSILSDDERKDVIAAYRQRLTSADPQVQLEAAKLWSVWEGETVTLLPSRESASFGEDDFALAFARIENHYFTHLGFLESDDQLLRNVPLIRHIPAVIVHGRYDMACQVQNAWDLAKAWPEAELHIVEGAGHSYDEPGILHQLMIATDRFAG 316
               SCOP domains d1wm1a_ A: Proline aminopeptidase                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1wm1A00 A:4-316  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------Abhydrolase_1-1wm1A01 A:64-300                                                                                                                                                                                                               ---------------- Pfam domains
         Sec.struct. author ...........eeeeee.....eeeeeeee....eeeeee........hhhhhhhh....eeeeee.................hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh....eeeeee......hhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wm1 A   4 LRGLYPPLAAYDSGWLDTGDGHRIYWELSGNPNGKPAVFIHGGPGGGISPHHRQLFDPERYKVLLFDQRGCGRSRPHASLDNNTTWHLVADIERLREMAGVEQWLVFGGSWGSTLALAYAQTHPERVSEMVLRGIFTLRKQRLHWYYQDGASRFFPEKWERVLSILSDDERKDVIAAYRQRLTSADPQVQLEAAKLWSVWEGETVTLLPSRESASFGEDDFALAFARIENHYFTHLGFLESDDQLLRNVPLIRHIPAVIVHGRYDMACQVQNAWDLAKAWPEAELHIVEGAGHSYDEPGILHQLMIATDRFAG 316
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PIP_SERMA | O32449)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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.
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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  1wm1
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  3.4.11.5
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 Related Entries

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

UniProtKB/Swiss-Prot
        PIP_SERMA | O32449: 1qtr 1x2b 1x2e

(-) Related Entries Specified in the PDB File

1qtr THE SAME PROTEIN