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(-) Description

Title :  UNBOUND FORM OF TOMATO INHIBITOR-II
 
Authors :  I. H. Barrette-Ng, K. K. -S. Ng, M. M. Cherney, G. Pearce, U. Ghani, C. A. R M. N. G. James
Date :  03 Jun 03  (Deposition) - 16 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  B,D  (2x)
Biol. Unit 6:  A,B,C,D  (1x)
Keywords :  Proteinase Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. H. Barrette-Ng, K. K. -S. Ng, M. M. Cherney, G. Pearce, U. Ghani, C. A. Ryan, M. N. G. James
Unbound Form Of Tomato Inhibitor-Ii Reveals Interdomain Flexibility And Conformational Variability In The Reactive Site Loops
J. Biol. Chem. V. 278 31391 2003
PubMed-ID: 12788916  |  Reference-DOI: 10.1074/JBC.M304562200

(-) Compounds

Molecule 1 - WOUND-INDUCED PROTEINASE INHIBITOR II
    Chains: A, B, C, D
    Organism Scientific: SOLANUM LYCOPERSICUM
    Organism Taxid: 4081
    Strain: BONNY BEST

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (2x):  B D
Biological Unit 6 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 5 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 6 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:29 , CYS B:30 , CYS B:31 , ASP B:65BINDING SITE FOR RESIDUE SO4 B 501
2AC2SOFTWAREASN A:29 , CYS A:30 , CYS A:31 , ASP A:65BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWAREASN C:29 , CYS C:30 , CYS C:31 , ASP C:65BINDING SITE FOR RESIDUE SO4 C 503
4AC4SOFTWAREARG C:75 , SER C:76 , GLN C:77BINDING SITE FOR RESIDUE SO4 C 504
5AC5SOFTWAREARG B:56 , ASN D:29 , CYS D:30 , CYS D:31 , ASP D:65BINDING SITE FOR RESIDUE SO4 D 505
6AC6SOFTWAREARG A:75 , GLN A:77BINDING SITE FOR RESIDUE SO4 A 506
7AC7SOFTWAREARG A:75 , LYS A:95 , GLU A:109 , ARG D:75 , HOH D:531BINDING SITE FOR RESIDUE SO4 D 507
8AC8SOFTWAREARG B:75 , TYR B:98 , GLU B:109 , PRO C:74BINDING SITE FOR RESIDUE SO4 B 508

(-) SS Bonds  (32, 32)

Asymmetric Unit
No.Residues
1A:3 -A:91
2A:7 -A:87
3A:15 -A:97
4A:27 -A:64
5A:30 -A:48
6A:31 -A:60
7A:37 -A:73
8A:90 -A:108
9B:3 -B:91
10B:7 -B:87
11B:15 -B:97
12B:27 -B:64
13B:30 -B:48
14B:31 -B:60
15B:37 -B:73
16B:90 -B:108
17C:3 -C:91
18C:7 -C:87
19C:15 -C:97
20C:27 -C:64
21C:30 -C:48
22C:31 -C:60
23C:37 -C:73
24C:90 -C:108
25D:3 -D:91
26D:7 -D:87
27D:15 -D:97
28D:27 -D:64
29D:30 -D:48
30D:31 -D:60
31D:37 -D:73
32D:90 -D:108

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:83 -Pro A:84
2Tyr B:83 -Pro B:84
3Tyr C:83 -Pro C:84
4Tyr D:83 -Pro D:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PJU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PJU)

(-) Exons   (0, 0)

(no "Exon" information available for 1PJU)

(-) 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:115
 aligned with IP21_SOLLC | P05119 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:115
                                    36        46        56        66        76        86        96       106       116       126       136     
           IP21_SOLLC    27 ACTRECGNLGFGICPRSEGSPLNPICINCCSGYKGCNYYNSFGKFICEGESDPKRPNACTFNCDPNIAYSRCPRSQGKSLIYPTGCTTCCTGYKGCYYFGKDGKFVCEGESDEPK 141
               SCOP domains d1pjua2       d1pjua1 A:16-74 Wound-induced proteinase inhibitor-II      d1pjua2 A:2-15,A:75-116                    SCOP domains
               CATH domains 1pjuA02               1pjuA01 A:24-86  [code=3.30.60.30, no name defined]            1pjuA02 A:2-23,A:87-115      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.......................eee.....eeee.........ee.........eee........ee...............eee.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1pju A   2 ACTRECGNLGFGICPRSEGSPLNPICINCCSGYKGCNYYNSFGKFICEGESDPKRPNACTFNCDPNIAYSRCPRSQGKSLIYPTGCTTCCTGYKGCYYFGKDGKFVCEGESDEPK 116
                                    11        21        31        41        51        61        71        81        91       101       111     


Chain B from PDB  Type:PROTEIN  Length:113
 aligned with IP21_SOLLC | P05119 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:113
                                    37        47        57        67        77        87        97       107       117       127       137   
           IP21_SOLLC    28 CTRECGNLGFGICPRSEGSPLNPICINCCSGYKGCNYYNSFGKFICEGESDPKRPNACTFNCDPNIAYSRCPRSQGKSLIYPTGCTTCCTGYKGCYYFGKDGKFVCEGESDEP 140
               SCOP domains d1pjub2      d1pjub1 B:16-74 Wound-induced proteinase inhibitor-II      d1pjub2 B:3-15,B:75-115                   SCOP domains
               CATH domains 1pjuB02              1pjuB01 B:24-86  [code=3.30.60.30, no name defined]            1pjuB02 B:3-23,B:87-115       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.......................eee.....eeee.........ee.........eee........ee...............eee.....eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1pju B   3 CTRECGNLGFGICPRSEGSPLNPICINCCSGYKGCNYYNSFGKFICEGESDPKRPNACTFNCDPNIAYSRCPRSQGKSLIYPTGCTTCCTGYKGCYYFGKDGKFVCEGESDEP 115
                                    12        22        32        42        52        62        72        82        92       102       112   


Chain C from PDB  Type:PROTEIN  Length:114
 aligned with IP21_SOLLC | P05119 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:114
                                    36        46        56        66        76        86        96       106       116       126       136    
           IP21_SOLLC    27 ACTRECGNLGFGICPRSEGSPLNPICINCCSGYKGCNYYNSFGKFICEGESDPKRPNACTFNCDPNIAYSRCPRSQGKSLIYPTGCTTCCTGYKGCYYFGKDGKFVCEGESDEP 140
               SCOP domains d1pjuc2       d1pjuc1 C:16-74 Wound-induced proteinase inhibitor-II      d1pjuc2 C:2-15,C:75-115                   SCOP domains
               CATH domains 1pjuC02               1pjuC01 C:24-86  [code=3.30.60.30, no name defined]            1pjuC02 C:2-23,C:87-115       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eee.......................eee.....eeee..........ee........eee........ee...............eee.....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1pju C   2 ACTRECGNLGFGICPRSEGSPLNPICINCCSGYKGCNYYNSFGKFICEGESDPKRPNACTFNCDPNIAYSRCPRSQGKSLIYPTGCTTCCTGYKGCYYFGKDGKFVCEGESDEP 115
                                    11        21        31        41        51        61        71        81        91       101       111    


Chain D from PDB  Type:PROTEIN  Length:114
 aligned with IP21_SOLLC | P05119 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:114
                                    36        46        56        66        76        86        96       106       116       126       136    
           IP21_SOLLC    27 ACTRECGNLGFGICPRSEGSPLNPICINCCSGYKGCNYYNSFGKFICEGESDPKRPNACTFNCDPNIAYSRCPRSQGKSLIYPTGCTTCCTGYKGCYYFGKDGKFVCEGESDEP 140
               SCOP domains d1pjud2       d1pjud1 D:16-74 Wound-induced proteinase inhibitor-II      d1pjud2 D:2-15,D:75-115                   SCOP domains
               CATH domains 1pjuD02               1pjuD01 D:24-86  [code=3.30.60.30, no name defined]            1pjuD02 D:2-23,D:87-115       CATH domains
           Pfam domains (1) -------------------------------------------------------Prot_inhib_II-1pjuD01 D:57-110                        ----- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------Prot_inhib_II-1pjuD02 D:57-110                        ----- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------Prot_inhib_II-1pjuD03 D:57-110                        ----- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------Prot_inhib_II-1pjuD04 D:57-110                        ----- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------Prot_inhib_II-1pjuD05 D:57-110                        ----- Pfam domains (5)
           Pfam domains (6) -------------------------------------------------------Prot_inhib_II-1pjuD06 D:57-110                        ----- Pfam domains (6)
           Pfam domains (7) -------------------------------------------------------Prot_inhib_II-1pjuD07 D:57-110                        ----- Pfam domains (7)
           Pfam domains (8) -------------------------------------------------------Prot_inhib_II-1pjuD08 D:57-110                        ----- Pfam domains (8)
         Sec.struct. author ........eeeee.......................eee.....eeee..........ee........eee........ee...............eeee....eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1pju D   2 ACTRECGNLGFGICPRSEGSPLNPICINCCSGYKGCNYYNSFGKFICEGESDPKRPNACTFNCDPNIAYSRCPRSQGKSLIYPTGCTTCCTGYKGCYYFGKDGKFVCEGESDEP 115
                                    11        21        31        41        51        61        71        81        91       101       111
   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  (1, 8)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 8)

Asymmetric Unit
(-)
Clan: no clan defined [family: Prot_inhib_II] (6)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (IP21_SOLLC | P05119)
molecular function
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    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.
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.

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  1pju
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 Related Entries

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

UniProtKB/Swiss-Prot
        IP21_SOLLC | P05119: 1oyv

(-) Related Entries Specified in the PDB File

1oyv TOMATO INHIBITOR-II IN COMPLEX WITH SUBTILISIN CARLSBERG