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(-) Description

Title :  PROLIDASE FROM PYROCOCCUS FURIOSUS
 
Authors :  M. J. Maher, M. Ghosh, A. M. Grunden, A. L. Menon, M. W. Adams, H. C. Freema J. M. Guss
Date :  27 Jun 03  (Deposition) - 23 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Prolidase, Peptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Maher, M. Ghosh, A. M. Grunden, A. L. Menon, M. W. Adams, H. C. Freeman, J. M. Guss
Structure Of The Prolidase From Pyrococcus Furiosus.
Biochemistry V. 43 2771 2004
PubMed-ID: 15005612  |  Reference-DOI: 10.1021/BI0356451
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - XAA-PRO DIPEPTIDASE
    Chains: A, B
    EC Number: 3.4.13.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-PROL
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET-21B
    Gene: PEPQ OR PF1343
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: X-PRO DIPEPTIDASE, PROLINE DIPEPTIDASE, PROLIDASE, IMIDODIPEPTIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:220 , HIS A:284 , GLU A:313 , GLU A:327 , ZN A:402 , HOH A:502BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREASP A:209 , ASP A:220 , THR A:222 , GLU A:327 , ZN A:401 , HOH A:502BINDING SITE FOR RESIDUE ZN A 402
3AC3SOFTWAREASP B:220 , HIS B:284 , THR B:311 , GLU B:313 , GLU B:327 , ZN B:402BINDING SITE FOR RESIDUE ZN B 401
4AC4SOFTWAREPHE B:178 , ASP B:209 , ASP B:220 , THR B:222 , GLU B:327 , ZN B:401BINDING SITE FOR RESIDUE ZN B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PV9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:293 -Pro A:294
2Trp B:293 -Pro B:294

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PV9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROLINE_PEPTIDASEPS00491 Aminopeptidase P and proline dipeptidase signature.PEPQ_PYRFU280-292
 		  2A:280-292
B:280-292

(-) Exons   (0, 0)

(no "Exon" information available for 1PV9)

(-) 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:337
 aligned with PEPQ_PYRFU | P81535 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:338
                                    17        27        37        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        
           PEPQ_PYRFU     8 LVKFMDENSIDRVFIAKPVNVYYFSGTSPLGGGYIIVDGDEATLYVPELEYEMAKEESKLPVVKFKKFDEIYEILKNTETLGIEGTLSYSMVENFKEKSNVKEFKKIDDVIKDLRIIKTKEEIEIIEKACEIADKAVMAAIEEITEGKREREVAAKVEYLMKMNGAEKPAFDTIIASGHRSALPHGVASDKRIERGDLVVIDLGALYNHYNSDITRTIVVGSPNEKQREIYEIVLEAQKRAVEAAKPGMTAKELDSIAREIIKEYGYGDYFIHSLGHGVGLEIHEWPRISQYDETVLKEGMVITIEPGIYIPKLGGVRIEDTVLITENGAKRLTKTER 345
               SCOP domains d1pv9a1 A:8-124 Aminopeptidase P                                                                                     d1pv9a2 A:125-345 Aminopeptidase P, C-terminal domain                                                                                                                                                                         SCOP domains
               CATH domains 1pv9A01 A:8-122 Creatine Amidinohydrolase, subunit A, domain 1                                                     1pv9A02 A:123-345 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh...eeee.....hhhhhh.......eeeee..eeeeeee..hhhhhhhhh...eeee...hhhhhhh....eeee....hhhhhhhhhhh.-..eeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...ee....eeee.hhhhh..............eeeeee.eee..ee..eeeeee....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhh....eee......eeeee............eeee..eeee...eeee..eeeee....eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROLINE_PEPTI----------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pv9 A   8 LVKFMDENSIDRVFIAKPVNVYYFSGTSPLGGGYIIVDGDEATLYVPELEYEMAKEESKLPVVKFKKFDEIYEILKNTETLGIEGTLSYSMVENFKEKS-VKEFKKIDDVIKDLRIIKTKEEIEIIEKACEIADKAVMAAIEEITEGKREREVAAKVEYLMKMNGAEKPAFDTIIASGHRSALPHGVASDKRIERGDLVVIDLGALYNHYNSDITRTIVVGSPNEKQREIYEIVLEAQKRAVEAAKPGMTAKELDSIAREIIKEYGYGDYFIHSLGHGVGLEIHEWPRISQYDETVLKEGMVITIEPGIYIPKLGGVRIEDTVLITENGAKRLTKTER 345
                                    17        27        37        47        57        67        77        87        97        |-|      117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337        
                                                                                                                            106 |                                                                                                                                                                                                                                             
                                                                                                                              108                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:318
 aligned with PEPQ_PYRFU | P81535 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:342
                                    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       323       333       343  
           PEPQ_PYRFU     4 RLEKLVKFMDENSIDRVFIAKPVNVYYFSGTSPLGGGYIIVDGDEATLYVPELEYEMAKEESKLPVVKFKKFDEIYEILKNTETLGIEGTLSYSMVENFKEKSNVKEFKKIDDVIKDLRIIKTKEEIEIIEKACEIADKAVMAAIEEITEGKREREVAAKVEYLMKMNGAEKPAFDTIIASGHRSALPHGVASDKRIERGDLVVIDLGALYNHYNSDITRTIVVGSPNEKQREIYEIVLEAQKRAVEAAKPGMTAKELDSIAREIIKEYGYGDYFIHSLGHGVGLEIHEWPRISQYDETVLKEGMVITIEPGIYIPKLGGVRIEDTVLITENGAKRLTKTER 345
               SCOP domains d1pv9b1 B:4-124 Aminopeptidase P                                                                                         d1pv9b2 B:125-345 Aminopeptidase P, C-terminal domain                                                                                                                                                                         SCOP domains
               CATH domains 1pv9B01 B:4-122 Creatine Amidinohydrolase, subunit A, domain 1                                                         1pv9B02 B:123-345 Creatinase/methionine aminopeptidase superfamily                                                                                                                                                              CATH domains
           Pfam domains (1) Creatinase_N-1pv9B01 B:4-124                                                                                             ------Peptidase_M24-1pv9B03 B:131-334                                                                                                                                                                             ----------- Pfam domains (1)
           Pfam domains (2) Creatinase_N-1pv9B02 B:4-124                                                                                             ------Peptidase_M24-1pv9B04 B:131-334                                                                                                                                                                             ----------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh...eeee.....hhhhhh.......eeeee..eeeeeee..hhhhhhh.....eeee.hhhhhhhhh....eeee....hhhhhhhhhhhh...eeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...ee....eeehhhhhhh...............eeeee.eee..ee..eeeee.-----------------hhhhhhhhh....hhhhhhhhhhhhhhhhh..-......eee......eeeee--..........eeee..ee.----..ee..eeeeee..eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROLINE_PEPTI----------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pv9 B   4 RLEKLVKFMDENSIDRVFIAKPVNVYYFSGTSPLGGGYIIVDGDEATLYVPELEYEMAKEESKLPVVKFKKFDEIYEILKNTETLGIEGTLSYSMVENFKEKSNVKEFKKIDDVIKDLRIIKTKEEIEIIEKACEIADKAVMAAIEEITEGKREREVAAKVEYLMKMNGAEKPAFDTIIASGHRSALPHGVASDKRIERGDLVVIDLGALYNHYNSDITRTIV-----------------AQKRAVEAAKPGMTAKELDSIAREIIKEYGYG-YFIHSLGHGVGLEIHEWPRI--YDETVLKEGMVITIEPGIY----GGVRIEDTVLITENGAKRLTKTER 345
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  |      -         -|      253       263       273 | |   283       293  |  | 303       313   |   323       333       343  
                                                                                                                                                                                                                                                        226               244                            275 |                296  |               317  322                       
                                                                                                                                                                                                                                                                                                           277                   299
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: AMP_N-like (22)
(-)
Clan: no clan defined [family: Peptidase_M24] (23)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PEPQ_PYRFU | P81535)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0102009    proline dipeptidase activity    Catalysis of the reaction: H2O + a dipeptide with proline at the C-terminal <=> L-proline + a standard alpha 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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