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(-) Description

Title :  CRYSTAL STRUCTURE OF AN INSECT INHIBITOR WITH A FUNGAL TRYPSIN
 
Authors :  P. Leone, A. Roussel, C. Kellenberger
Date :  21 May 08  (Deposition) - 23 Dec 08  (Release) - 23 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Hydrolase/Inhibitor, Canonical Inhibitor, Inhibitor, Serine Protease, Species Selectivity, Insect, Zymogen, Protease, Secreted, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Leone, A. Roussel, C. Kellenberger
Structure Of Locusta Migratoria Protease Inhibitor 3 (Lmpi-3) In Complex With Fusarium Oxysporum Trypsin.
Acta Crystallogr. , Sect. D V. 64 1165 2008
PubMed-ID: 19020355  |  Reference-DOI: 10.1107/S0907444908030400

(-) Compounds

Molecule 1 - TRYPSIN
    Chains: E
    EC Number: 3.4.21.4
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Taxid: 4932
    Fragment: PEPTIDASE S1, RESIDUES 25-248
    Organism Common: MOLD
    Organism Scientific: FUSARIUM OXYSPORUM
    Organism Taxid: 5507
 
Molecule 2 - PACIFASTIN-RELATED SERINE PROTEASE INHIBITOR
    Chains: I
    Fragment: RESIDUES 25-57
    Organism Common: LOCUST
    Organism Scientific: LOCUSTA MIGRATORIA
    Organism Taxid: 7004
    Synonym: LMPI-3
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2VU8)

(-) Sites  (0, 0)

(no "Site" information available for 2VU8)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1E:42 -E:58
2E:168 -E:182
3E:191 -E:220
4I:4 -I:19
5I:14 -I:32
6I:17 -I:27

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VU8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VU8)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TRYP_FUSOX25-248  1E:16-242
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TRYP_FUSOX61-66  1E:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TRYP_FUSOX198-209  1E:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 2VU8)

(-) Sequences/Alignments

Asymmetric/Biological 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 E from PDB  Type:PROTEIN  Length:224
 aligned with TRYP_FUSOX | P35049 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:224
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244    
          TRYP_FUSOX     25 IVGGTSASAGDFPFIVSISRNGGPWCGGSLLNANTVLTAAHCVSGYAQSGFQIRAGSLSRTSGGITSSLSSVRVHPSYSGNNNDLAILKLSTSIPSGGNIGYARLAASGSDPVAGSSATVAGWGATSEGGSSTPVNLLKVTVPIVSRATCRAQYGTSAITNQMFCAGVSSGGKDSCQGDSGGPIVDSSNTLIGAVSWGNGCARPNYSGVYASVGALRSFIDTYA  248
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vu8E01     2vu8E02 E:28-120,E:233-242 Trypsin-like serine proteases                                  2vu8E01 E:16-27,E:121-232 Trypsin-like serine proteases                                                         2vu8E02    CATH domains
               Pfam domains Trypsin-2vu8E01 E:16-238                                                                                                                                                                                                    ---- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhhh..hhh.eeeee.........eeeeeeeeee...........eeeee..........................eeeeee...............eeeeeeeehhhhhhhhhhhhhh...eeee................eee.....eeeeeeee.........eeeee...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: E:16-242 UniProt: 25-248                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vu8 E   16 IVGGTSASAGDFPFIVSISRNGGPWCGGSLLNANTVLTAAHCVSGYAQSGFQIRAGSLSRTSGGITSSLSSVRVHPSYSGNNNDLAILKLSTSIPSGGNIGYARLAASGSDPVAGSSATVAGWGATSEGGSSTPVNLLKVTVPIVSRATCRAQYGTSAITNQMFCAGVSSGGKDSCQGDSGGPIVDSSNTLIGAVSWGNGCARPNYSGVYASVGALRSFIDTYA  242
                                    25        35|       46        56   |||| 62   |||  73  ||    86        96|      108       118       128       138       148       158       168     | 177       186  |    195      |204|      219  |    228       238    
                                              35|                    59A|||    65A||     76|              96|                                                                       173A        184A 188A          201A  ||     217|  |                     
                                               37                     59B||      66|      80               99                                                                                                          204|      219  |                     
                                                                       59C|       69                                                                                                                                    209        221A                     
                                                                        59D                                                                                                                                                                                 


Chain I from PDB  Type:PROTEIN  Length:33
 aligned with Q8WQ22_LOCMI | Q8WQ22 from UniProtKB/TrEMBL  Length:145

    Alignment length:33
                                    34        44        54   
        Q8WQ22_LOCMI     25 ECTPGQTKKQDCNTCTCTPTGIWGCTRKACRTT   57
               SCOP domains --------------------------------- SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains Pacifastin_I-2vu8I01 I:3-35       Pfam domains
         Sec.struct. author ................................. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
                 Transcript --------------------------------- Transcript
                2vu8 I    3 ECTPGQTKKQDCNTCTCTPTGIWGCTRKACRTT   35
                                    12        22        32
   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 2VU8)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_PA (797)
(-)
Clan: no clan defined [family: Pacifastin_I] (6)

(-) Gene Ontology  (8, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (TRYP_FUSOX | P35049)
molecular function
    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).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain I   (Q8WQ22_LOCMI | Q8WQ22)
molecular function
    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:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  TRYP_FUSOX | P35049
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRYP_FUSOX | P35049: 1fn8 1fy4 1fy5 1gdn 1gdq 1gdu 1ppz 1pq5 1pq7 1pq8 1pqa 1try 1xvm 1xvo 2g51 2g52
UniProtKB/TrEMBL
        Q8WQ22_LOCMI | Q8WQ22: 1wo9

(-) Related Entries Specified in the PDB File

1fn8 FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
1fy4 FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
1fy5 FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
1gdn FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
1gdq FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
1gdu FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION
1ppz TRYPSIN COMPLEXES AT ATOMIC AND ULTRA-HIGH RESOLUTION
1pq5 TRYPSIN AT PH 5, 0.85 A
1pq7 TRYPSIN AT 0.8 A, PH5 / BORAX
1pq8 TRYPSIN AT PH 4 AT ATOMIC RESOLUTION
1pqa TRYPSIN WITH PMSF AT ATOMIC RESOLUTION
1try MOL_ID: 1; MOLECULE: TRYPSIN; CHAIN: NULL; EC: 3.4.21.4
1wo9 SELECTIVE INHIBITION OF TRYPSINS BY INSECT PEPTIDES: ROLEOF P6-P10 LOOP
1xvm TRYPSIN FROM FUSARIUM OXYSPORUM- ROOM TEMPERATURE TO ATOMICRESOLUTION
1xvo TRYPSIN FROM FUSARIUM OXYSPORUM AT PH 6