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(-) Description

Title :  PROLYL TRIPEPTIDYL AMINOPEPTIDASE MUTANT E636A
 
Authors :  Y. Xu, Y. Nakajima, K. Ito, T. Yoshimoto
Date :  07 Jun 07  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Prolyl Oligopeptidase Family, Peptidase Family S9, Serine Protease, Proline-Specific Peptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Xu, Y. Nakajima, K. Ito, H. Zheng, H. Oyama, U. Heiser, T. Hoffmann, U. T. Gartner, H. U. Demuth, T. Yoshimoto
Novel Inhibitor For Prolyl Tripeptidyl Aminopeptidase From Porphyromonas Gingivalis And Details Of Substrate-Recognition Mechanism
J. Mol. Biol. V. 375 708 2008
PubMed-ID: 18042490  |  Reference-DOI: 10.1016/J.JMB.2007.09.077

(-) Compounds

Molecule 1 - DIPEPTIDYL AMINOPEPTIDASE IV
    Chains: A
    EC Number: 3.4.14.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:321 , SER A:347 , ASN A:349 , GLN A:350 , HOH A:1048BINDING SITE FOR RESIDUE SO4 A 902
2AC2SOFTWARETYR A:518 , SER A:603 , TYR A:604 , TYR A:635 , TYR A:639 , VAL A:681 , HOH A:1030BINDING SITE FOR RESIDUE GOL A 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z3W)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:280 -Pro A:281
2Gly A:460 -Lys A:461

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z3W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z3W)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z3W)

(-) 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:655
 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 -----------------------------------------------------------------------DPPIV_N-2z3wA02 A:124-452                                                                                                                                                                                                                                                                                                                ----------------------------------------------------------------------------------Peptidase_S9-2z3wA01 A:535-732                                                                                                                                                                         Pfam domains
         Sec.struct. author .....eee..eeeeee..eeeee.-------.eeeehhhhhhhh..---------...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......ee......eeeeee.....eeeeeee......eeeeee....eeeeee..------....eeeeeee......eeeeeee..........eeeeee...............---.hhhhhhhhh..eeeee........hhhhhhh.....hhhhhhhhhhhhhhhhh...eeeeeeeeeeehhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3w A  53 YVVGLQWMGDNYVFIEGDDLVFNK-------TTRFSAADLNALMPE---------FPSFRTLDAGRGLVVLFTQGGLVGFDMLARKVTYLFDTNEETASLDFSPVGDRVAYVRNHNLYIARGGKLGEGMSRAIAVTIDGTETLVYGQAVHQREFGIEKGTFWSPKGSCLAFYRMDQSMVKPTPIVDYHPLEAESKPLYYPMAGTPSHHVTVGIYHLATGKTVYLQTGEPKEKFLTNLSWSPDENILYVAEVNRAQNECKVNAYDAETGRFVRTLFVETDKHYVEPLHPLTFLPGSNNQFIWQSRRDGWNHLYLYDTTGRLIRQVTKGEWEVTNFAGFDPKGTRLYFESTEASPLERHFYCIDIKGGKTKDLTPESGMHRTQLSPDGSAIIDIFQSPTVPRKVTVTNIGKGSHTLLEAK------AMPEIRTGTIMAADGQTPLYYKLTMPLHFDPAKKYPVIVYVYGGPHAQLVTKTWR---GGWDIYMAQKGYAVFTVDSRGSANRGAAFEQVIHRRLGQTEMADQMCGVDFLKSQSWVDADRIGVHGWSYGGFMTTNLMLTHGDVFKVGVAGGPVIDWNRYAIMYGERYFDAPQENPEGYDAANLLKRAGDLKGRLMLIHGAIDPVVVWQHSLLFLDACVKARTYPDYYVYPSHEHNVMGPDRVHLYETITRYFTDHL 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        |-  |    542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732
                                                  76      84            98       108                                                                                                                                                                                                                                                                                                                                                                       470    477                                                   531 535
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2Z3W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z3W)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: AB_hydrolase (347)
(-)
Clan: Beta_propeller (192)

(-) 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 2dcm 2eep 2z3z

(-) Related Entries Specified in the PDB File

2d5l THE WILD-TYPE PROTEIN
2dcm THE S603A MUTANT PROTEIN COMPLEXED WITH SUBSTRATE
2eep THE WILD-TYPE PROTEIN COMPLEXD WITH INHIBITOR
2z3z THE SAME MUTANT ENZYME COMPLEXD WITH AN INHIBITOR