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(-) Description

Title :  PROLYL TRIPEPTIDYL AMINOPEPTIDASE MUTANT E636A COMPLEXD WITH AN INHIBITOR
 
Authors :  Y. Xu, Y. Nakajima, K. Ito, T. Yoshimoto
Date :  09 Jun 07  (Deposition) - 19 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Peptidase Family S9, Prolyl Oligopeptidase Family, 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: PG1316
    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
1AIO1Ligand/Ion[(2R)-1-(L-ALANYL-L-ISOLEUCYL)PYRROLIDIN-2-YL]BORONICACID
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1AIO2Ligand/Ion[(2R)-1-(L-ALANYL-L-ISOLEUCYL)PYRROLIDIN-2-YL]BORONICACID
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:1060BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWAREGLN A:203 , GLU A:205 , TYR A:518 , HIS A:522 , SER A:603 , TYR A:604 , TYR A:635 , TYR A:639 , VAL A:680 , HIS A:710 , HOH A:902 , HOH A:1179 , HOH A:1211 , HOH A:1223BINDING SITE FOR RESIDUE AIO A 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z3Z)

(-) 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 2Z3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z3Z)

(-) 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:651
 aligned with PTP_PORGI | Q7MUW6 from UniProtKB/Swiss-Prot  Length:732

    Alignment length:679
                                    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       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723         
            PTP_PORGI    54 VVGLQWMGDNYVFIEGDDLVFNKANGKSAQTTRFSAADLNALMPEGCKFQTTDAFPSFRTLDAGRGLVVLFTQGGLVGFDMLARKVTYLFDTNEETASLDFSPVGDRVAYVRNHNLYIARGGKLGEGMSRAIAVTIDGTETLVYGQAVHQREFGIEKGTFWSPKGSCLAFYRMDQSMVKPTPIVDYHPLEAESKPLYYPMAGTPSHHVTVGIYHLATGKTVYLQTGEPKEKFLTNLSWSPDENILYVAEVNRAQNECKVNAYDAETGRFVRTLFVETDKHYVEPLHPLTFLPGSNNQFIWQSRRDGWNHLYLYDTTGRLIRQVTKGEWEVTNFAGFDPKGTRLYFESTEASPLERHFYCIDIKGGKTKDLTPESGMHRTQLSPDGSAIIDIFQSPTVPRKVTVTNIGKGSHTLLEAKNPDTGYAMPEIRTGTIMAADGQTPLYYKLTMPLHFDPAKKYPVIVYVYGGPHAQLVTKTWRSSVGGWDIYMAQKGYAVFTVDSRGSANRGAAFEQVIHRRLGQTEMADQMCGVDFLKSQSWVDADRIGVHGWSYGGFMTTNLMLTHGDVFKVGVAGGPVIDWNRYEIMYGERYFDAPQENPEGYDAANLLKRAGDLKGRLMLIHGAIDPVVVWQHSLLFLDACVKARTYPDYYVYPSHEHNVMGPDRVHLYETITRYFTDHL 732
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------DPPIV_N-2z3zA02 A:124-452                                                                                                                                                                                                                                                                                                                ----------------------------------------------------------------------------------Peptidase_S9-2z3zA01 A:535-732                                                                                                                                                                         Pfam domains
         Sec.struct. author ....eee..eeeeee..eeeee.-------.eeeehhhhhh..-----------...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....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z3z A  54 VVGLQWMGDNYVFIEGDDLVFNK-------TTRFSAADLNALM-----------FPSFRTLDAGRGLVVLFTQGGLVGFDMLARKVTYLFDTNEETASLDFSPVGDRVAYVRNHNLYIARGGKLGEGMSRAIAVTIDGTETLVYGQAVHQREFGIEKGTFWSPKGSCLAFYRMDQSMVKPTPIVDYHPLEAESKPLYYPMAGTPSHHVTVGIYHLATGKTVYLQTGEPKEKFLTNLSWSPDENILYVAEVNRAQNECKVNAYDAETGRFVRTLFVETDKHYVEPLHPLTFLPGSNNQFIWQSRRDGWNHLYLYDTTGRLIRQVTKGEWEVTNFAGFDPKGTRLYFESTEASPLERHFYCIDIKGGKTKDLTPESGMHRTQLSPDGSAIIDIFQSPTVPRKVTVTNIGKGSHTLLEAK------AMPEIRTGTIMAADGQTPLYYKLTMPLHFDPAKKYPVIVYVYGGPHAQLVTKTW----GGWDIYMAQKGYAVFTVDSRGSANRGAAFEQVIHRRLGQTEMADQMCGVDFLKSQSWVDADRIGVHGWSYGGFMTTNLMLTHGDVFKVGVAGGPVIDWNRYAIMYGERYFDAPQENPEGYDAANLLKRAGDLKGRLMLIHGAIDPVVVWQHSLLFLDACVKARTYPDYYVYPSHEHNVMGPDRVHLYETITRYFTDHL 732
                                    63        73  |      -|       93  |      -    |  113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463      |  -   |   483       493       503       513       523      |  - |     543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723         
                                                 76      84          96         108                                                                                                                                                                                                                                                                                                                                                                       470    477                                                  530  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 2Z3Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z3Z)

(-) 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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  2z3z
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  3.4.14.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        PTP_PORGI | Q7MUW6: 2d5l 2dcm 2eep 2z3w

(-) Related Entries Specified in the PDB File

2d5l THE WILD-TYPE ENZYME
2dcm THE S603S MUTANT ENZYME COMPLEXED WITH A SUBSTRATE
2eep THE WILD-TYPE ENZYME COMPLEXED WITH AN INHIBITOR
2z3w THE SAME MUTANT ENZYME