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(-) Description

Title :  X-RAY CRYSTALLINE STRUCTURES OF PYRROLIDONE CARBOXYL PEPTIDASE FROM A HYPERTHERMOPHILE, PYROCOCCUS FURIOSUS, AND ITS CYS-FREE MUTANT
 
Authors :  H. Tanaka, M. Chinami, M. Ota, T. Tsukihara, K. Yutani
Date :  09 Mar 01  (Deposition) - 21 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pgp-I, Pyroglutamyl-Peptidase I, Pcp, Protease, Pyrococcus Furiosus, Archaea, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Tanaka, M. Chinami, T. Mizushima, K. Ogasahara, M. Ota, T. Tsukihara, K. Yutani
X-Ray Crystalline Structures Of Pyrrolidone Carboxyl Peptidase From A Hyperthermophile, Pyrococcus Furiosus, And Its Cys-Free Mutant
J. Biochem. (Tokyo) V. 130 107 2001
PubMed-ID: 11432786
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRROLIDONE CARBOXYL PEPTIDASE
    Chains: A, B, C, D
    EC Number: 3.4.19.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPCP3
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261

 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 1IOF)

(-) Sites  (0, 0)

(no "Site" information available for 1IOF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:158 -Pro A:159
2Tyr B:158 -Pro B:159
3Tyr C:158 -Pro C:159
4Tyr D:158 -Pro D:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRASE_GLUPS01333 Pyrrolidone-carboxylate peptidase glutamic acid active site.PCP_PYRFU68-84
 
 
 		  4A:68-84
B:68-84
C:68-84
D:68-84
2PYRASE_CYSPS01334 Pyrrolidone-carboxylate peptidase cysteine active site.PCP_PYRFU129-143
 
 
 		  4A:129-143
B:129-143
C:129-143
D:129-143

(-) Exons   (0, 0)

(no "Exon" information available for 1IOF)

(-) 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:208
 aligned with PCP_PYRFU | O73944 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
            PCP_PYRFU     1 MKVLVTGFEPFGGEKINPTERIAKDLDGIKIGDAQVFGRVLPVVFGKAKEVLEKTLEEIKPDIAIHVGLAPGRSAISIERIAVNAIDARIPDNEGKKIEDEPIVPGAPTAYFSTLPIKKIMKKLHERGIPAYISNSAGLYLCNYVMYLSLHHSATKGYPKMSGFIHVPYIPEQIIDKIGKGQVPPSMCYEMELEAVKVAIEVALEELL 208
               SCOP domains d1iofa_ A: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                         SCOP domains
               CATH domains 1iofA00 A:1-208  [code=3.40.630.20, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhh..ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee......eeee.eee..........................eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh......eeee..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ----------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iof A   1 MKVLVTGFEPFGGEKINPTERIAKDLDGIKIGDAQVFGRVLPVVFGKAKEVLEKTLEEIKPDIAIHVGLAPGRSAISIERIAVNAIDARIPDNEGKKIEDEPIVPGAPTAYFSTLPIKKIMKKLHERGIPAYISNSAGLYLCNYVMYLSLHHSATKGYPKMSGFIHVPYIPEQIIDKIGKGQVPPSMCYEMELEAVKVAIEVALEELL 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with PCP_PYRFU | O73944 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
            PCP_PYRFU     1 MKVLVTGFEPFGGEKINPTERIAKDLDGIKIGDAQVFGRVLPVVFGKAKEVLEKTLEEIKPDIAIHVGLAPGRSAISIERIAVNAIDARIPDNEGKKIEDEPIVPGAPTAYFSTLPIKKIMKKLHERGIPAYISNSAGLYLCNYVMYLSLHHSATKGYPKMSGFIHVPYIPEQIIDKIGKGQVPPSMCYEMELEAVKVAIEVALEELL 208
               SCOP domains d1iofb_ B: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                         SCOP domains
               CATH domains 1iofB00 B:1-208  [code=3.40.630.20, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhh..ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee......eeee.eee..........................eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh......eeee..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ----------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iof B   1 MKVLVTGFEPFGGEKINPTERIAKDLDGIKIGDAQVFGRVLPVVFGKAKEVLEKTLEEIKPDIAIHVGLAPGRSAISIERIAVNAIDARIPDNEGKKIEDEPIVPGAPTAYFSTLPIKKIMKKLHERGIPAYISNSAGLYLCNYVMYLSLHHSATKGYPKMSGFIHVPYIPEQIIDKIGKGQVPPSMCYEMELEAVKVAIEVALEELL 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        


Chain C from PDB  Type:PROTEIN  Length:208
 aligned with PCP_PYRFU | O73944 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
            PCP_PYRFU     1 MKVLVTGFEPFGGEKINPTERIAKDLDGIKIGDAQVFGRVLPVVFGKAKEVLEKTLEEIKPDIAIHVGLAPGRSAISIERIAVNAIDARIPDNEGKKIEDEPIVPGAPTAYFSTLPIKKIMKKLHERGIPAYISNSAGLYLCNYVMYLSLHHSATKGYPKMSGFIHVPYIPEQIIDKIGKGQVPPSMCYEMELEAVKVAIEVALEELL 208
               SCOP domains d1iofc_ C: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                         SCOP domains
               CATH domains 1iofC00 C:1-208  [code=3.40.630.20, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhh..ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee......eeee.eee..........................eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh......eeee..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ----------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iof C   1 MKVLVTGFEPFGGEKINPTERIAKDLDGIKIGDAQVFGRVLPVVFGKAKEVLEKTLEEIKPDIAIHVGLAPGRSAISIERIAVNAIDARIPDNEGKKIEDEPIVPGAPTAYFSTLPIKKIMKKLHERGIPAYISNSAGLYLCNYVMYLSLHHSATKGYPKMSGFIHVPYIPEQIIDKIGKGQVPPSMCYEMELEAVKVAIEVALEELL 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        


Chain D from PDB  Type:PROTEIN  Length:208
 aligned with PCP_PYRFU | O73944 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
            PCP_PYRFU     1 MKVLVTGFEPFGGEKINPTERIAKDLDGIKIGDAQVFGRVLPVVFGKAKEVLEKTLEEIKPDIAIHVGLAPGRSAISIERIAVNAIDARIPDNEGKKIEDEPIVPGAPTAYFSTLPIKKIMKKLHERGIPAYISNSAGLYLCNYVMYLSLHHSATKGYPKMSGFIHVPYIPEQIIDKIGKGQVPPSMCYEMELEAVKVAIEVALEELL 208
               SCOP domains d1iofd_ D: Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)                                                                                                                                         SCOP domains
               CATH domains 1iofD00 D:1-208  [code=3.40.630.20, no name defined]                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhh..ee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee......eeee.eee..........................eee...hhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh......eeee..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------PYRASE_GLU       --------------------------------------------PYRASE_CYS     ----------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iof D   1 MKVLVTGFEPFGGEKINPTERIAKDLDGIKIGDAQVFGRVLPVVFGKAKEVLEKTLEEIKPDIAIHVGLAPGRSAISIERIAVNAIDARIPDNEGKKIEDEPIVPGAPTAYFSTLPIKKIMKKLHERGIPAYISNSAGLYLCNYVMYLSLHHSATKGYPKMSGFIHVPYIPEQIIDKIGKGQVPPSMCYEMELEAVKVAIEVALEELL 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 1IOF)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PCP_PYRFU | O73944)
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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  Cis Peptide Bonds
    Tyr A:158 - Pro A:159   [ RasMol ]  
    Tyr B:158 - Pro B:159   [ RasMol ]  
    Tyr C:158 - Pro C:159   [ RasMol ]  
    Tyr D:158 - Pro D:159   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCP_PYRFU | O73944: 1ioi 1x10 1x12 1z8t 1z8w 1z8x 2df5 2eo8

(-) Related Entries Specified in the PDB File

1ioi 1IOI CONTAINS THE SAME PROTEIN C142S/C188S MUTANT