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(-) Description

Title :  CRYSTAL STRUCTURE OF A PAPAYA LATEX SERINE PROTEASE INHIBITOR (PPI) AT 1.7A RESOLUTION
 
Authors :  A. Garcia-Pino
Date :  29 May 11  (Deposition) - 02 Nov 11  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kunitz-Sti Fold, Protease Inhibitor, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Azarkan, S. Martinez-Rodriguez, L. Buts, D. Baeyens-Volant, A. Garcia-Pino
The Plasticity Of The Beta-Trefoil Fold Constitutes An Evolutionary Platform For Protease Inhibition
J. Biol. Chem. V. 286 43726 2011
PubMed-ID: 22027836  |  Reference-DOI: 10.1074/JBC.M111.291310

(-) Compounds

Molecule 1 - LATEX SERINE PROTEINASE INHIBITOR
    Chains: A, B
    Organism Common: MAMON
    Organism Scientific: CARICA PAPAYA
    Organism Taxid: 3649

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 22)

Asymmetric/Biological Unit (6, 22)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION
2FUC2Ligand/IonALPHA-L-FUCOSE
3GOL4Ligand/IonGLYCEROL
4NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
5NH43Ligand/IonAMMONIUM ION
6SO47Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:117 , HOH A:215 , HOH A:216 , GLU B:113 , HIS B:117BINDING SITE FOR RESIDUE CO A 185
02AC2SOFTWAREASP A:52 , ASP A:55 , HOH A:352 , ASP B:52 , ASP B:55BINDING SITE FOR RESIDUE CO A 186
03AC3SOFTWARETYR B:37 , GLY B:38 , HOH B:343 , HOH B:344BINDING SITE FOR RESIDUE NH4 B 185
04AC4SOFTWAREGLY A:118 , PHE A:119 , GLU A:120 , HOH A:267 , HOH A:281BINDING SITE FOR RESIDUE NH4 A 187
05AC5SOFTWAREGLY A:38 , HOH A:212 , HOH A:325 , HOH A:377BINDING SITE FOR RESIDUE NH4 A 188
06AC6SOFTWAREGLU A:75 , SER A:76 , LYS A:129 , LYS A:130BINDING SITE FOR RESIDUE GOL A 189
07AC7SOFTWARELYS A:138 , ASN A:155 , ASN A:172BINDING SITE FOR RESIDUE GOL A 190
08AC8SOFTWARELYS B:66 , SER B:144 , TYR B:145 , HOH B:261 , HOH B:323BINDING SITE FOR RESIDUE GOL B 186
09AC9SOFTWARETYR A:163 , HOH A:355 , HOH A:385 , PHE B:160 , ARG B:164 , ARG B:166 , HOH B:262BINDING SITE FOR RESIDUE GOL B 187
10BC1SOFTWAREGLY B:17 , ASP B:19 , ASN B:84 , NAG B:189 , FUC B:190 , HOH B:233BINDING SITE FOR RESIDUE NAG B 188
11BC2SOFTWARENAG B:188 , HOH B:257BINDING SITE FOR RESIDUE NAG B 189
12BC3SOFTWARENAG B:188BINDING SITE FOR RESIDUE FUC B 190
13BC4SOFTWAREGLY A:17 , ASP A:19 , ASN A:84 , NAG A:202 , FUC A:203 , HOH A:219BINDING SITE FOR RESIDUE NAG A 201
14BC5SOFTWARENAG A:201 , FUC A:203BINDING SITE FOR RESIDUE NAG A 202
15BC6SOFTWAREASN A:183 , NAG A:201 , NAG A:202BINDING SITE FOR RESIDUE FUC A 203
16BC7SOFTWARELYS A:66 , ASN A:67 , ARG B:147 , ARG B:149BINDING SITE FOR RESIDUE SO4 A 191
17BC8SOFTWAREARG A:99 , ILE A:104 , GLY A:105 , HOH A:227 , ALA B:2 , ARG B:74BINDING SITE FOR RESIDUE SO4 A 192
18BC9SOFTWARELYS B:44 , CYS B:45 , HOH B:305 , HOH B:365BINDING SITE FOR RESIDUE SO4 B 191
19CC1SOFTWARELYS A:43 , LYS A:44 , CYS A:45BINDING SITE FOR RESIDUE SO4 A 193
20CC2SOFTWAREARG B:99 , TRP B:106 , PRO B:152BINDING SITE FOR RESIDUE SO4 B 192
21CC3SOFTWARESER A:76 , LYS A:127 , LYS A:129 , HIS A:140 , CYS A:142 , HOH A:248 , HOH A:318 , HOH A:361BINDING SITE FOR RESIDUE SO4 A 194
22CC4SOFTWARETHR A:148 , ARG A:149BINDING SITE FOR RESIDUE SO4 A 195

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:45 -A:89
2A:142 -A:153
3B:45 -B:89
4B:142 -B:153

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys A:45 -Pro A:46
2Cys B:45 -Pro B:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S8K)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOYBEAN_KUNITZPS00283 Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.LSPI_CARPA6-22
 		  2A:6-22
B:6-22

(-) Exons   (0, 0)

(no "Exon" information available for 3S8K)

(-) 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 A from PDB  Type:PROTEIN  Length:183
 aligned with LSPI_CARPA | P80691 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   
           LSPI_CARPA     2 APKPIVDIDGKPVLYGVDYFVVSAIWGAGGGGLTVYGPGNKKKCPLSVVQDPFDNGEPIIFSAIKNVKDNIVFESVDLNVKFNITINCNETTAWKVDRFPGVIGWTVTLGGEKGYHGFESTHSMFKIKKAGLPFSYKFHFCPSYPRTRLIPCNNVDIFFDKYRIRRLILTNDAKEFVFIKTNR 184
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee..hhhhh.eeeee..........eeeee.......eeeee..............eeeee............eeeee..eeeeeee........hhhhhhhh.eeee......eeeee............eeeeeee.....eeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SOYBEAN_KUNITZ   ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s8k A   2 APKPIVDIDGKPVLYGVDYFVVSAIWGAGGGGLTVYGPGNKKKCPLSVVQDPFDNGEPIIFSAIKNVKDNIVRESVDLNVKFNITINCNETTAWKVDRFPGVIGWTVTLGGEKGYHGFESTHSMFKIKKAGLPFSYKFHFCPSYPRTRLIPCNNVDIFFDKYRIRRLILTNDAKEFVFIKTNR 184
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   


Chain B from PDB  Type:PROTEIN  Length:182
 aligned with LSPI_CARPA | P80691 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
           LSPI_CARPA     2 APKPIVDIDGKPVLYGVDYFVVSAIWGAGGGGLTVYGPGNKKKCPLSVVQDPFDNGEPIIFSAIKNVKDNIVFESVDLNVKFNITINCNETTAWKVDRFPGVIGWTVTLGGEKGYHGFESTHSMFKIKKAGLPFSYKFHFCPSYPRTRLIPCNNVDIFFDKYRIRRLILTNDAKEFVFIKTN 183
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee..hhhhh.eeeee..........eeeee.......eeeee..............eeeee............eeeee..eeeeeee........hhhhhhhh.eeee......eeeee............eeeeeee.....eeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SOYBEAN_KUNITZ   ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s8k B   2 APKPIVDIDGKPVLYGVDYFVVSAIWGAGGGGLTVYGPGNKKKCPLSVVQDPFDNGEPIIFSAIKNVKDNIVRESVDLNVKFNITINCNETTAWKVDRFPGVIGWTVTLGGEKGYHGFESTHSMFKIKKAGLPFSYKFHFCPSYPRTRLIPCNNVDIFFDKYRIRRLILTNDAKEFVFIKTN 183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   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 3S8K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S8K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S8K)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LSPI_CARPA | P80691)
molecular function
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LSPI_CARPA | P80691: 3s8j

(-) Related Entries Specified in the PDB File

3s8j