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(-) Description

Title :  CRYSTAL STRUCTURE OF PROLYL TRIPEPTIDYL AMINOPEPTIDASE FROM PORPHYROMONAS GINGIVALIS
 
Authors :  Y. Nakajima, K. Ito, Y. Xu, N. Yamada, Y. Onohara, T. Yoshimoto
Date :  02 Nov 05  (Deposition) - 19 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Peptidase Family S9, Serine Peptidase, Prolyl Oligopeptidase Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ito, Y. Nakajima, Y. Xu, N. Yamada, Y. Onohara, T. Ito, F. Matsubara, T. Kabashima, K. Nakayama, T. Yoshimoto
Crystal Structure And Mechanism Of Tripeptidyl Activity Of Prolyl Tripeptidyl Aminopeptidase From Porphyromonas Gingivalis
J. Mol. Biol. V. 362 228 2006
PubMed-ID: 16914159  |  Reference-DOI: 10.1016/J.JMB.2006.06.083

(-) Compounds

Molecule 1 - DIPEPTIDYL AMINOPEPTIDASE IV, PUTATIVE
    Chains: A
    EC Number: 3.4.14.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 39-732
    Gene: PG1361
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619
    Strain: W83
    Synonym: PROLYL TRIPEPTIDYL AMINOPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:321 , SER A:347 , ASN A:349 , GLN A:350 , HOH A:1156BINDING SITE FOR RESIDUE SO4 A 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D5L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:280 -Pro A:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D5L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D5L)

(-) Exons   (0, 0)

(no "Exon" information available for 2D5L)

(-) Sequences/Alignments

Asymmetric 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:665
 aligned with PTP_PORGI | Q7MUW6 from UniProtKB/Swiss-Prot  Length:732

    Alignment length:688
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724        
            PTP_PORGI    45 EFYNFYPEYVVGLQWMGDNYVFIEGDDLVFNKANGKSAQTTRFSAADLNALMPEGCKFQTTDAFPSFRTLDAGRGLVVLFTQGGLVGFDMLARKVTYLFDTNEETASLDFSPVGDRVAYVRNHNLYIARGGKLGEGMSRAIAVTIDGTETLVYGQAVHQREFGIEKGTFWSPKGSCLAFYRMDQSMVKPTPIVDYHPLEAESKPLYYPMAGTPSHHVTVGIYHLATGKTVYLQTGEPKEKFLTNLSWSPDENILYVAEVNRAQNECKVNAYDAETGRFVRTLFVETDKHYVEPLHPLTFLPGSNNQFIWQSRRDGWNHLYLYDTTGRLIRQVTKGEWEVTNFAGFDPKGTRLYFESTEASPLERHFYCIDIKGGKTKDLTPESGMHRTQLSPDGSAIIDIFQSPTVPRKVTVTNIGKGSHTLLEAKNPDTGYAMPEIRTGTIMAADGQTPLYYKLTMPLHFDPAKKYPVIVYVYGGPHAQLVTKTWRSSVGGWDIYMAQKGYAVFTVDSRGSANRGAAFEQVIHRRLGQTEMADQMCGVDFLKSQSWVDADRIGVHGWSYGGFMTTNLMLTHGDVFKVGVAGGPVIDWNRYEIMYGERYFDAPQENPEGYDAANLLKRAGDLKGRLMLIHGAIDPVVVWQHSLLFLDACVKARTYPDYYVYPSHEHNVMGPDRVHLYETITRYFTDHL 732
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........--...eee..eeeeee..eeeee.-------....hhhhhhh...-----------..eeeee....eeeeee..eeeeee....eeeeee.........ee.....eeeeee..eeeeee...........ee........eee...hhhhh......eee.....eeeeeeee......eeeee......eeeee..........eeeeeeee....eeee.........eeeeeee.....eeeeeee.....eeeeeeee.....eeeeeeeee...........ee......eeeeee......eeeeee....eeee.......eeeeeee.....eeeeee........eeeeee.....eee......eeeeee.....eeeeeee.....eeeeeee....eeeeeee.---.......eeeeeee......eeeeeee..........eeeeee...................hhhhhhhh...eeeee........hhhhhhh.....hhhhhhhhhhhhhhhhh...eeeeeeeeeeehhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5l A  45 EFYNFYPE--VGLQWMGDNYVFIEGDDLVFNK-------TTRFSAADLNALMP-----------PSFRTLDAGRGLVVLFTQGGLVGFDMLARKVTYLFDTNEETASLDFSPVGDRVAYVRNHNLYIARGGKLGEGMSRAIAVTIDGTETLVYGQAVHQREFGIEKGTFWSPKGSCLAFYRMDQSMVKPTPIVDYHPLEAESKPLYYPMAGTPSHHVTVGIYHLATGKTVYLQTGEPKEKFLTNLSWSPDENILYVAEVNRAQNECKVNAYDAETGRFVRTLFVETDKHYVEPLHPLTFLPGSNNQFIWQSRRDGWNHLYLYDTTGRLIRQVTKGEWEVTNFAGFDPKGTRLYFESTEASPLERHFYCIDIKGGKTKDLTPESGMHRTQLSPDGSAIIDIFQSPTVPRKVTVTNIGKGSHTLLEAK---TGYAMPEIRTGTIMAADGQTPLYYKLTMPLHFDPAKKYPVIVYVYGGPHAQLVTKTWRSSVGGWDIYMAQKGYAVFTVDSRGSANRGAAFEQVIHRRLGQTEMADQMCGVDFLKSQSWVDADRIGVHGWSYGGFMTTNLMLTHGDVFKVGVAGGPVIDWNRYEIMYGERYFDAPQENPEGYDAANLLKRAGDLKGRLMLIHGAIDPVVVWQHSLLFLDACVKARTYPDYYVYPSHEHNVMGPDRVHLYETITRYFTDHL 732
                                   | -|       64        74 |      84        94  |      -    |  114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464     | 474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724        
                                  52 55                   76      84           97         109                                                                                                                                                                                                                                                                                                                                                                      470 474
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2D5L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D5L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D5L)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (PTP_PORGI | Q7MUW6)
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.
    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/Swiss-Prot
        PTP_PORGI | Q7MUW6: 2dcm 2eep 2z3w 2z3z

(-) Related Entries Specified in the PDB File

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