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(-) Description

Title :  THE CRYSTAL STRUCTURE OF S603A MUTATED PROLYL TRIPEPTIDYL AMINOPEPTIDASE COMPLEXED WITH SUBSTRATE
 
Authors :  Y. Nakajima, K. Ito, Y. Xu, N. Yamada, Y. Onohara, T. Yoshimoto
Date :  09 Jan 06  (Deposition) - 19 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Peptidase Family S9, Serine Peptidase, Prolyl Oligopeptidase Family, Site-Directed Mutangenesis, 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
    Mutation: YES
    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
1GA01Ligand/IonGLYCYLALANYL-N-2-NAPHTHYL-L-PROLINEAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GA02Ligand/IonGLYCYLALANYL-N-2-NAPHTHYL-L-PROLINEAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:203 , GLU A:205 , TYR A:518 , ALA A:603 , TYR A:604 , TYR A:635 , GLU A:636 , TYR A:639 , HIS A:710BINDING SITE FOR RESIDUE GA0 A 801

(-) SS Bonds  (0, 0)

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

(-) 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 2DCM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DCM)

(-) 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:662
 aligned with PTP_PORGI | Q7MUW6 from UniProtKB/Swiss-Prot  Length:732

    Alignment length:680
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732
            PTP_PORGI    53 YVVGLQWMGDNYVFIEGDDLVFNKANGKSAQTTRFSAADLNALMPEGCKFQTTDAFPSFRTLDAGRGLVVLFTQGGLVGFDMLARKVTYLFDTNEETASLDFSPVGDRVAYVRNHNLYIARGGKLGEGMSRAIAVTIDGTETLVYGQAVHQREFGIEKGTFWSPKGSCLAFYRMDQSMVKPTPIVDYHPLEAESKPLYYPMAGTPSHHVTVGIYHLATGKTVYLQTGEPKEKFLTNLSWSPDENILYVAEVNRAQNECKVNAYDAETGRFVRTLFVETDKHYVEPLHPLTFLPGSNNQFIWQSRRDGWNHLYLYDTTGRLIRQVTKGEWEVTNFAGFDPKGTRLYFESTEASPLERHFYCIDIKGGKTKDLTPESGMHRTQLSPDGSAIIDIFQSPTVPRKVTVTNIGKGSHTLLEAKNPDTGYAMPEIRTGTIMAADGQTPLYYKLTMPLHFDPAKKYPVIVYVYGGPHAQLVTKTWRSSVGGWDIYMAQKGYAVFTVDSRGSANRGAAFEQVIHRRLGQTEMADQMCGVDFLKSQSWVDADRIGVHGWSYGGFMTTNLMLTHGDVFKVGVAGGPVIDWNRYEIMYGERYFDAPQENPEGYDAANLLKRAGDLKGRLMLIHGAIDPVVVWQHSLLFLDACVKARTYPDYYVYPSHEHNVMGPDRVHLYETITRYFTDHL 732
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eee.ee..ee.....------....hhhhhhhh...-------.....eeeee....eeeee....eeeee....eeeeee.........ee.....eeeeee..eeeeee...........ee........eee...hhhhh......eee.....eeeeeeee......eeeee......eeeee..........eeeeeeee.....eee.........eeeeeee.....eeeeeee.....eeeeeeee.....eeeeeeeee...........ee......eeeeee......eeeeee....eeee.......eeeeeee.....eeeeee........eeeeee..............eeeeee.....eeeeeee.....eeee.ee......eeeee..-----....eeeeeee......eeeeeee..........eeeeee...................hhhhhhhhh..eeeee........hhhhhhh.....hhhhhhhhhhhhhhhhh...eeeeeeeeeeehhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dcm A  53 YVVGLQWMGDNYVFIEGDDLVFNKA------TTRFSAADLNALMPE-------DAFPSFRTLDAGRGLVVLFTQGGLVGFDMLARKVTYLFDTNEETASLDFSPVGDRVAYVRNHNLYIARGGKLGEGMSRAIAVTIDGTETLVYGQAVHQREFGIEKGTFWSPKGSCLAFYRMDQSMVKPTPIVDYHPLEAESKPLYYPMAGTPSHHVTVGIYHLATGKTVYLQTGEPKEKFLTNLSWSPDENILYVAEVNRAQNECKVNAYDAETGRFVRTLFVETDKHYVEPLHPLTFLPGSNNQFIWQSRRDGWNHLYLYDTTGRLIRQVTKGEWEVTNFAGFDPKGTRLYFESTEASPLERHFYCIDIKGGKTKDLTPESGMHRTQLSPDGSAIIDIFQSPTVPRKVTVTNIGKGSHTLLEAKN-----AMPEIRTGTIMAADGQTPLYYKLTMPLHFDPAKKYPVIVYVYGGPHAQLVTKTWRSSVGGWDIYMAQKGYAVFTVDSRGSANRGAAFEQVIHRRLGQTEMADQMCGVDFLKSQSWVDADRIGVHGWAYGGFMTTNLMLTHGDVFKVGVAGGPVIDWNRYEIMYGERYFDAPQENPEGYDAANLLKRAGDLKGRLMLIHGAIDPVVVWQHSLLFLDACVKARTYPDYYVYPSHEHNVMGPDRVHLYETITRYFTDHL 732
                                    62        72    |    - |      92     |   -   |   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462        |-    |  482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732
                                                   77     84            98     106                                                                                                                                                                                                                                                                                                                                                                          471   477
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 2DCM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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: 2d5l 2eep 2z3w 2z3z

(-) Related Entries Specified in the PDB File

2d5l