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(-) Description

Title :  CRYSTAL STRUCTURE OF TRIPEPTIDYL PEPTIDASE 2 (TPP II)
 
Authors :  C. K. Chuang
Date :  25 Feb 10  (Deposition) - 11 Aug 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.14
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (2x)
Keywords :  Spindle Complex, Aminopeptidase, Hydrolase, Phosphoprotein, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. K. Chuang, B. Rockel, G. Seyit, P. J. Walian, A. M. Schonegge, J. Peters, P. H. Zwart, W. Baumeister, B. K. Jap
Hybrid Molecular Structure Of The Giant Protease Tripeptidy Peptidase Ii.
Nat. Struct. Mol. Biol. V. 17 990 2010
PubMed-ID: 20676100  |  Reference-DOI: 10.1038/NSMB.1870

(-) Compounds

Molecule 1 - TRIPEPTIDYL-PEPTIDASE 2
    ChainsX
    EC Number3.4.14.10
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUS 463-770
    GeneCG3991, TPP II, TPPII
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymTRIPEPTIDYL-PEPTIDASE II, DTPP II, TPP-II, TRIPEPTIDYL AMINOPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit X
Biological Unit 1 (2x)X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 25)

Asymmetric Unit (1, 25)
No.NameCountTypeFull Name
1MSE25Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 50)
No.NameCountTypeFull Name
1MSE50Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3LXU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LXU)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Leu X:127 -Pro X:128
2Trp X:175 -Asp X:176
3Gly X:309 -Ser X:310
4Gly X:376 -Pro X:377
5Pro X:385 -Pro X:386
6Gln X:553 -Gly X:554
7Asp X:577 -Pro X:578
8Lys X:579 -Asp X:580
9Pro X:842 -Asp X:843
10Ala X:993 -Gln X:994

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LXU)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.TPP2_DROME359-369  1X:272-282
2SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.TPP2_DROME547-557  1X:460-470
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.TPP2_DROME359-369  2X:272-282
2SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.TPP2_DROME547-557  2X:460-470

(-) Exons   (0, 0)

(no "Exon" information available for 3LXU)

(-) 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 X from PDB  Type:PROTEIN  Length:1217
 aligned with TPP2_DROME | Q9V6K1 from UniProtKB/Swiss-Prot  Length:1441

    Alignment length:1337
                                   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       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384      1394      1404      1414      1424      1434       
          TPP2_DROME    105 KAETGVLNFLQKYPEYDGRDVTIAIFDSGVDPRATGLETLCDGKTVKVIERYDCSGCGDVDMKKKVTPDENGNIKGLSGNSLKLSPELMALNTDPEKAVRVGLKSFSDLLPSKVRNNIVAQAKLKHWDKPHKTATANASRKIVEFESQNPGEASKLPWDKKILKENLDFELEMLNSYEKVYGDIKTSYDCILFPTADGWLTIVDTTEQGDLDQALRIGEYSRTHETRNVDDFLSISVNVHDEGNVLEVVGMSSPHGTHVSSIASGNHSSRDVDGVAPNAKIVSMTIGDGRLGSMETGTALVRAMTKVMELCRDGRRIDVINMSYGEHANWSNSGRIGELMNEVVNKYGVVWVASAGNHGPALCTVGTPPDISQPSLIGVGAYVSPQMMEAEYAMREKLPGNVYTWTSRDPCIDGGQGVTVCAPGGAIASVPQFTMSKSQLMNGTSMAAPHVAGAVALLISGLKQQNIEYSPYSIKRAISVTATKLGYVDPFAQGHGLLNVEKAFEHLTEHRQSKDNMLRFSVRVGNNADKGIHLRQGVQRNSIDYNVYIEPIFYNDKEADPKDKFNFNVRLNLIASQPWVQCGAFLDLSYGTRSIAVRVDPTGLQPGVHSAVIRAYDTDCVQKGSLFEIPVTVVQPHVLESDQNTPVFEPASSKGDNSVEFQPNTIQRDFILVPERATWAELRMRITDPNRGEDIGKFFVHTNQLLPKQSCRKLETMKIVSVGSENESIMAFKVKSGRILELCIAKYWSNYGQSHLKYSLRFRGVEAHNPNAYVMHAGRGIHKLEIEALVAEDVQPQLQLKNAEVVLKPTEAKISPLSATRDVIPDGRQVYQNLLAFNLNVAKAADVSIYAPIFNDLLYEAEFESQMWMLFDANKALVATGDAHSHTSFTKLDKGEYTIRLQVRHEKRDLLEKISEANLVASFKLTSPLTLDFYENYNQCIVGGRKYVSSPLRLSTRVLYIAPITQERLTKANLPAQCAWLSGNLVFPQDEVGRRVAQHPFTYILNPAEKKSHTNGSSNGSSAAGSTATAAAVTTANGAKPKAPATPQAATSVTNPAAGDGISVQNDPPVDSSGSPASPKKGKANADDYAESFRDFQCSQIVKCELEMAEKIYNDVVAAHPKHLQANLLLIQNIESNQLKSQLPLTFVNAQKTSPPEAGESADKQKEDQKKVRSALERIVKLADKVIQETDSEALLSYYGLKNDTRADAAKIKTNMDKQKNTLIEALSKKGIAVAKLAVLDDCIKDSLAEINELYTEIIKFVDANDSKAIQFALWHAYAHGHYGRMYKYVVKLIEEKRTRDHFVELAAINGALGHEHIRTVINRMMITAFPSSFRLF 1441
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------Peptidase_S8-3lxuX01 X:39-522                                                                                                                                                                                                                                                                                                                                                                                                                                                                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPPII-3lxuX02 X:801-993                                                                                                                                                                          ---------------------------------                                                                        TPPII_N-3lxuX03 X:1099-1171                                              --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh........eeeeee......................eeee.....eee..ee.......-----------------------...................eeeeee........hhhhh..........................hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee......eeee...........eeee.........ee....eeeeeeehhh.eeeeee..hhhhhhhhhhhh...............eeeeee..........hhhhhhhhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhh...eeeee.....................eeeeeee........----------.................eeeeee.---------------...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..................hhhhhhhhhhh...hhhh.eeeeeee.......eee........eeeeeeeeeee................eeeeee....eee...ee.....eeeeeee.hhhh..eeeeeeeeeee.........eeeeeeeee...........ee..........eee.....eeeeee......eeeeeeee........eeeeeeeeee.....hhhh.eeeeeeeee....eeeeee.....eeeeeeee.......eeeeeeeeee.eee......eee.....eeeeeee...eeeeeeeeeeeeeeee....eeeee......ee...ee.eeeeeeeeeee...eeeeee.................eeee.....eeeee........eee..eeeeeeeeeee.hhhhhhhhh...eeeeeeeeeeeee....hhhhhhh.......eee...eeeeee...hhhhhhh......eeeeeeeeeee.hhhhhhhh.eeeeee.....------------------------------------------------------------------------...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_H---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lxu X   18 KAETGVLNFLQKYPEYDGRDVTIAIFDSGVDPRATGLETLCDGKTVKVIERYDCSGCGDVDmKKKVTPDENG-----------------------EKAVRVGLKSFSDLLPSKVRNNIVAQAKLKHWDKPHKTATANASRKIVEFESQNPGEASKLPWDKKILKENLDFELEmLNSYEKVYGDIKTSYDCILFPTADGWLTIVDTTEQGDLDQALRIGEYSRTHETRNVDDFLSISVNVHDEGNVLEVVGmSSPHGTHVSSIASGNHSSRDVDGVAPNAKIVSmTIGDGRLGSmETGTALVRAmTKVmELCRDGRRIDVINmSYGEHANWSNSGRIGELmNEVVNKYGVVWVASAGNHGPALCTVGTPPDISQPSLIGVGAYVSPQmmEA----------NVYTWTSRDPCIDGGQGVTVCAPG---------------LmNGTSmAAPHVAGAVALLISGLKQQNIEYSPYSIKRAISVTATKLGYVDPFAQGHGLLNVEKAFEHLTEHRQSKDNmLRFSVRVGNNADKGIHLRQGVQRNSIDYNVYIEPIFYNDKEADPKDKFNFNVRLNLIASQPWVQCGAFLDLSYGTRSIAVRVDPTGLQPGVHSAVIRAYDTDCVQKGSLFEIPVTVVQPHVLESDQNTPVFEPASSKGDNSVEFQPNTIQRDFILVPERATWAELRmRITDPNRGEDIGKFFVHTNQLLPKQSCRKLETmKIVSVGSENESImAFKVKSGRILELCIAKYWSNYGQSHLKYSLRFRGVEAHNPNAYVmHAGRGIHKLEIEALVAEDVQPQLQLKNAEVVLKPTEAKISPLSATRDVIPDGRQVYQNLLAFNLNVAKAADVSIYAPIFNDLLYEAEFESQmWmLFDANKALVATGDAHSHTSFTKLDKGEYTIRLQVRHEKRDLLEKISEANLVASFKLTSPLTLDFYENYNQCIVGGRKYVSSPLRLSTRVLYIAPITQERLTKANLPAQCAWLSGNLVFPQDEVGRRVAQHPFTYILNPAE------------------------------------------------------------------------GKANADDYAESFRDFQCSQIVKCELEmAEKIYNDVVAAHPKHLQANLLLIQNIESNQLKSQLPLTFVNAQKTSPPEAGESADKQKEDQKKVRSALERIVKLADKVIQETDSEALLSYYGLKNDTRADAAKIKTNmDKQKNTLIEALSKKGIAVAKLAVLDDCIKDSLAEINELYTEIIKFVDANDSKAIQFALWHAYAHGHYGRmYKYVVKLIEEKRTRDHFVELAAINGALGHEHIRTVINRmmITAFPSSFRLF 1354
                                    27        37        47        57        67        77 |      87 |       -         -     | 117       127       137       147       157       167       177       187  |    197       207       217       227       237       247       257       267|      277       287       297   |   307   |   317   |   327       337 |     347       357       367       377       387       397      |407         -|      427       437   |     -       457|    | 467       477       487       497       507       517       527      |537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697   |   707       717       727      |737       747       757       767       777       787    |  797       807       817       827       837       847       857       867       877      |887       897       907       917       927       937       947       957       967       977       987       997      1007      1017        |-         -         -         -         -         -         -         - |    1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227     |1237      1247      1257      1267      1277      1287      1297     |1307      1317      1327      1337    ||1347       
                                                                                        79-MSE    89                     113                                                                          190-MSE                                                                       268-MSE                          301-MSE   311-MSE   321-MSE           339-MSE           357-MSE                                        404-MSE       418                    441             457|    |                                                                    534-MSE                                                                                                                                                                701-MSE                          734-MSE      747-MSE                                      792-MSE                                                                                     884-MSE                                                                                                                                      1026                                                                     1099                      1125-MSE                                                                                                    1233-MSE                                                              1303-MSE                               1342-MSE        
                                                                                                                                                                                                                                                                                                                                             325-MSE                                                                         405-MSE                                              458-MSE|                                                                                                                                                                                                                                                                                                                                                                                                                                    886-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                 1343-MSE       
                                                                                                                                                                                                                                                                                                                                                                                                                               407                                                     463-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       

   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  (0, 0)

(no "SCOP Domain" information available for 3LXU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LXU)

(-) Pfam Domains  (3, 3)

Asymmetric Unit

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain X   (TPP2_DROME | Q9V6K1)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    GO:0008238    exopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain, in a reaction that requires a free N-terminal amino group, C-terminal carboxyl group or both.
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-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).
    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).
    GO:0008240    tripeptidyl-peptidase activity    Catalysis of the release of an N-terminal tripeptide from a polypeptide.
biological process
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    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.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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    Ala X:993 - Gln X:994   [ RasMol ]  
    Asp X:577 - Pro X:578   [ RasMol ]  
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