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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PYROGLUTAMYL PEPTIDASE I FROM BACILLUS AMYLOLIQUEFACIENS
 
Authors :  Y. Odagaki, A. Hayashi, K. Okada, K. Hirotsu, T. Kabashima, K. Ito, T. Yoshimoto, D. Tsuru, M. Sato, J. Clardy
Date :  26 Aug 97  (Deposition) - 23 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pyroglutamyl Peptidase, Cysteine Proteinase, Bacillus Amyloliquefaciens, Hydrolase, Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Odagaki, A. Hayashi, K. Okada, K. Hirotsu, T. Kabashima, K. Ito, T. Yoshimoto, D. Tsuru, M. Sato, J. Clardy
The Crystal Structure Of Pyroglutamyl Peptidase I From Bacillus Amyloliquefaciens Reveals A New Structure For A Cysteine Protease.
Structure Fold. Des. V. 7 399 1999
PubMed-ID: 10196127  |  Reference-DOI: 10.1016/S0969-2126(99)80053-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYROGLUTAMYL PEPTIDASE-1
    Chains: A, B, C, D
    EC Number: 3.4.19.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBPG 1
    Expression System Taxid: 562
    Organism Scientific: BACILLUS AMYLOLIQUEFACIENS
    Organism Taxid: 1390
    Synonym: PGP-1, PYRROLIDONE-CARBOXYLATE PEPTIDASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1AUG)

(-) Sites  (0, 0)

(no "Site" information available for 1AUG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRASE_GLUPS01333 Pyrrolidone-carboxylate peptidase glutamic acid active site.PCP_BACAM70-86
 
 
 		  4A:70-86
B:280-296
C:490-506
D:700-716
2PYRASE_CYSPS01334 Pyrrolidone-carboxylate peptidase cysteine active site.PCP_BACAM131-145
 
 
 		  4A:131-145
B:341-355
C:551-565
D:761-775

(-) Exons   (0, 0)

(no "Exon" information available for 1AUG)

(-) 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:210
 aligned with PCP_BACAM | P46107 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
            PCP_BACAM     1 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDIETG 210
               SCOP domains d1auga_ A: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                           SCOP domains
               CATH domains 1augA00 A:1-210  [code=3.40.630.20, no name defined]                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.........hhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhhh...eeeeeee...........eee..........................eee....hhhhhhhhhhh.............hhhhhhhhhhhhhhhh....eeeeeee...hhh..........hhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ----------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1aug A   1 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDIETG 210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210


Chain B from PDB  Type:PROTEIN  Length:210
 aligned with PCP_BACAM | P46107 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
            PCP_BACAM     1 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDIETG 210
               SCOP domains d1augb_ B: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                           SCOP domains
               CATH domains 1augB00 B:211-420  [code=3.40.630.20, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.........hhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhhh...eeeeeee...........eee..........................eee....hhhhhhhhhhh.............hhhhhhhhhhhhhhhh....eeeeeee...hhh..........hhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ----------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1aug B 211 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDIETG 420
                                   220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420


Chain C from PDB  Type:PROTEIN  Length:210
 aligned with PCP_BACAM | P46107 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
            PCP_BACAM     1 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDIETG 210
               SCOP domains d1augc_ C: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                           SCOP domains
               CATH domains 1augC00 C:421-630  [code=3.40.630.20, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.........hhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhhh...eeeeeee...........eee..........................eee....hhhhhhhhhhh.............hhhhhhhhhhhhhhhh....eeeeeee...hhh..........hhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ----------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1aug C 421 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDIETG 630
                                   430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630


Chain D from PDB  Type:PROTEIN  Length:210
 aligned with PCP_BACAM | P46107 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:210
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
            PCP_BACAM     1 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDIETG 210
               SCOP domains d1augd_ D: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                           SCOP domains
               CATH domains 1augD00 D:631-840  [code=3.40.630.20, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.........hhhhhhhhh.......eeeeeeee.....hhhhhhhhhhhhh...eeeeeee...........eee..........................eee....hhhhhhhhhhh.............hhhhhhhhhhhhhhhh....eeeeeee...hhh..........hhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ----------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1aug D 631 MEKKVLLTGFDPFGGETVNPSWEAVKRLNGAAEGPASIVSEQVPTVFYKSLAVLREAIKKHQPDIIICVGQAGGRMQITPERVAINLNEARIPDNEGNQPVGEDISQGGPAAYWTGLPIKRIVEEIKKEGIPAAVSYTAGTFVCNHLFYGLMDEISRHHPHIRGGFIHIPYIPEQTLQKSAPSLSLDHITKALKIAAVTAAVHEDDIETG 840
                                   640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AUG)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PCP_BACAM | P46107)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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:0016920    pyroglutamyl-peptidase activity    Catalysis of the release of the N-terminal pyroglutamyl group from a peptide or protein.
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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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        PCP_BACAM | P46107: 3rnz 3ro0

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