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(-) Description

Title :  CRYSTAL STRUCTURE OF CASPASE-1 FROM SPODOPTERA FRUGIPERDA
 
Authors :  C. M. Forsyth, D. Lemongello, P. D. Friesen, A. J. Fisher
Date :  18 Jul 02  (Deposition) - 20 Jan 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,D,E  (1x)
Biol. Unit 2:  C,F  (2x)
Keywords :  Caspase, Cysteine Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. M. Forsyth, D. Lemongello, D. J. Lacount, P. D. Friesen, A. J. Fisher
Crystal Structure Of An Invertebrate Caspase.
J. Biol. Chem. V. 279 7001 2004
PubMed-ID: 14645217  |  Reference-DOI: 10.1074/JBC.M312472200

(-) Compounds

Molecule 1 - CASPASE-1
    ChainsA, B, C
    EC Number3.4.22.36
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET22B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism CommonFALL ARMYWORM
    Organism ScientificSPODOPTERA FRUGIPERDA
    Organism Taxid7108
 
Molecule 2 - ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE
    ChainsD, E, F
    EngineeredYES
    Other DetailsTHE PEPTIDE IS A SYNTHETIC TETRAPEPTIDE INHIBITOR.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB DE 
Biological Unit 2 (2x)  C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
10QE3Mod. Amino AcidCHLOROMETHANE
2ACE3Mod. Amino AcidACETYL GROUP
3EDO8Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
10QE2Mod. Amino AcidCHLOROMETHANE
2ACE2Mod. Amino AcidACETYL GROUP
3EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
10QE2Mod. Amino AcidCHLOROMETHANE
2ACE2Mod. Amino AcidACETYL GROUP
3EDO8Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:184 , THR A:216 , VAL A:217 , TYR A:220 , GLN A:279 , VAL A:280 , HIS B:207BINDING SITE FOR RESIDUE EDO A 506
02AC2SOFTWAREPRO B:45 , VAL B:46 , TYR B:53 , ASN B:54 , HIS B:57 , ASP B:127 , GLY B:168 , LYS B:169 , PRO B:170BINDING SITE FOR RESIDUE EDO B 503
03AC3SOFTWAREHIS A:207 , ASP B:184 , THR B:216 , VAL B:217 , GLN B:279 , VAL B:280BINDING SITE FOR RESIDUE EDO B 507
04AC4SOFTWAREGLU C:138 , GLY C:140 , MET C:141 , LEU C:142 , PRO C:151 , CYS C:178 , GLN C:179 , PHE C:214BINDING SITE FOR RESIDUE EDO C 501
05AC5SOFTWAREASP C:248 , ILE C:249 , LEU C:250 , THR C:254 , LEU C:287 , ARG C:289 , LEU C:290 , LEU C:291BINDING SITE FOR RESIDUE EDO C 502
06AC6SOFTWAREASP C:184 , HIS C:207 , THR C:216 , VAL C:217 , GLN C:279 , VAL C:280BINDING SITE FOR RESIDUE EDO C 504
07AC7SOFTWARELEU C:183 , ASP C:184 , GLY C:185 , GLY C:186BINDING SITE FOR RESIDUE EDO C 508
08AC8SOFTWARELYS A:77 , ARG A:79 , THR A:135 , HIS A:136 , GLY A:137 , GLN A:176 , CYS A:178 , PHE A:221 , SER A:222 , TRP A:223 , ARG A:224 , ASN A:225 , THR A:226 , SER A:266 , ASN A:267 , MET A:274 , HIS B:74 , HOH D:1050BINDING SITE FOR CHAIN D OF ACE-ASP-GLU-VAL-ASP- CHLOROMETHYLKETONE
09AC9SOFTWAREHIS A:74 , ARG B:79 , THR B:135 , HIS B:136 , GLY B:137 , GLN B:176 , CYS B:178 , PHE B:221 , SER B:222 , TRP B:223 , ARG B:224 , ASN B:225 , THR B:226 , SER B:266 , ASN B:267 , MET B:274 , HOH E:1013 , HOH E:1173BINDING SITE FOR CHAIN E OF ACE-ASP-GLU-VAL-ASP- CHLOROMETHYLKETONE
10BC1SOFTWAREHIS C:74 , ARG C:79 , THR C:135 , HIS C:136 , GLY C:137 , GLN C:176 , CYS C:178 , PHE C:221 , SER C:222 , TRP C:223 , ARG C:224 , ASN C:225 , THR C:226 , SER C:266 , ASN C:267 , HOH F:1088 , HOH F:1091BINDING SITE FOR CHAIN F OF ACE-ASP-GLU-VAL-ASP- CHLOROMETHYLKETONE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M72)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M72)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M72)

(-) PROSITE Motifs  (4, 12)

Asymmetric Unit (4, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.CASP1_SPOFR59-182
 
 
  3A:59-182
B:59-182
C:59-182
2CASPASE_HISPS01121 Caspase family histidine active site.CASP1_SPOFR123-137
 
 
  3A:123-137
B:123-137
C:123-137
3CASPASE_CYSPS01122 Caspase family cysteine active site.CASP1_SPOFR169-180
 
 
  3A:169-180
B:169-180
C:169-180
4CASPASE_P10PS50207 Caspase family p10 domain profile.CASP1_SPOFR200-295
 
 
  3A:201-295
B:200-295
C:201-295
Biological Unit 1 (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.CASP1_SPOFR59-182
 
 
  2A:59-182
B:59-182
-
2CASPASE_HISPS01121 Caspase family histidine active site.CASP1_SPOFR123-137
 
 
  2A:123-137
B:123-137
-
3CASPASE_CYSPS01122 Caspase family cysteine active site.CASP1_SPOFR169-180
 
 
  2A:169-180
B:169-180
-
4CASPASE_P10PS50207 Caspase family p10 domain profile.CASP1_SPOFR200-295
 
 
  2A:201-295
B:200-295
-
Biological Unit 2 (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.CASP1_SPOFR59-182
 
 
  2-
-
C:59-182
2CASPASE_HISPS01121 Caspase family histidine active site.CASP1_SPOFR123-137
 
 
  2-
-
C:123-137
3CASPASE_CYSPS01122 Caspase family cysteine active site.CASP1_SPOFR169-180
 
 
  2-
-
C:169-180
4CASPASE_P10PS50207 Caspase family p10 domain profile.CASP1_SPOFR200-295
 
 
  2-
-
C:201-295

(-) Exons   (0, 0)

(no "Exon" information available for 1M72)

(-) 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:247
 aligned with CASP1_SPOFR | P89116 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:256
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289      
          CASP1_SPOFR    40 RVARMPVDRNAPYYNMNHKHRGMAIIFNHEHFDIHSLKSRTGTNVDSDNLSKVLKTLGFKVTVFPNLKSEEINKFIQQTAEMDHSDADCLLVAVLTHGELGMLYAKDTHYKPDNLWYYFTADKCPTLAGKPKLFFIQACQGDRLDGGITLSRTETDGSPSTSYRIPVHADFLIAFSTVPGYFSWRNTTRGSWFMQALCEELRYAGTERDILTLLTFVCQKVALDFESNAPDSAMMHQQKQVPCITSMLTRLLVFGK 295
               SCOP domains d1m72a_ A: Caspase-1                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1m72A00 A:40-295  [code=3.40.50.1460, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeeeeeee.............hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhh.....eeeeeeeee..ee..eee....ee..hhhhhh.....hhhhh...eeeeee..........eeee.---------.eee.....eeeee........eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhh......eeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------CASPASE_P20  PDB: A:59-182 UniProt: 59-182                                                                                  -----------------CASPASE_P10  PDB: A:201-295 UniProt: 200-295                                                     PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS ------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m72 A  40 RVARMPVDRNAPYYNMNHKHRGMAIIFNHEHFDIHSLKSRTGTNVDSDNLSKVLKTLGFKVTVFPNLKSEEINKFIQQTAEMDHSDADCLLVAVLTHGELGMLYAKDTHYKPDNLWYYFTADKCPTLAGKPKLFFIQACQGDRLDGGITLSR---------SYRIPVHADFLIAFSTVPGYFSWRNTTRGSWFMQALCEELRYAGTERDILTLLTFVCQKVALDFESNAPDSAMMHQQKQVPCITSMLTRLLVFGK 295
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189 |       - |     209       219       229       239       249       259       269       279       289      
                                                                                                                                                                                 191       201                                                                                              

Chain B from PDB  Type:PROTEIN  Length:248
 aligned with CASP1_SPOFR | P89116 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:256
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      
          CASP1_SPOFR    41 VARMPVDRNAPYYNMNHKHRGMAIIFNHEHFDIHSLKSRTGTNVDSDNLSKVLKTLGFKVTVFPNLKSEEINKFIQQTAEMDHSDADCLLVAVLTHGELGMLYAKDTHYKPDNLWYYFTADKCPTLAGKPKLFFIQACQGDRLDGGITLSRTETDGSPSTSYRIPVHADFLIAFSTVPGYFSWRNTTRGSWFMQALCEELRYAGTERDILTLLTFVCQKVALDFESNAPDSAMMHQQKQVPCITSMLTRLLVFGKK 296
               SCOP domains d1m72b_ B: Caspase-1                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1m72B00 B:41-296  [code=3.40.50.1460, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...............eeeeeeeee.............hhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhh....eeeeeeeee..ee..eee....ee..hhhhhh.....hhhhh...eeeeee..........eeee.--------.eeee.....eeeee........eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhh......eeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------CASPASE_P20  PDB: B:59-182 UniProt: 59-182                                                                                  -----------------CASPASE_P10  PDB: B:200-295 UniProt: 200-295                                                    - PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS -------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m72 B  41 VARMPVDRNAPYYNMNHKHRGMAIIFNHEHFDIHSLKSRTGTNVDSDNLSKVLKTLGFKVTVFPNLKSEEINKFIQQTAEMDHSDADCLLVAVLTHGELGMLYAKDTHYKPDNLWYYFTADKCPTLAGKPKLFFIQACQGDRLDGGITLSR--------TSYRIPVHADFLIAFSTVPGYFSWRNTTRGSWFMQALCEELRYAGTERDILTLLTFVCQKVALDFESNAPDSAMMHQQKQVPCITSMLTRLLVFGKK 296
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190|      200       210       220       230       240       250       260       270       280       290      
                                                                                                                                                                                191      200                                                                                                

Chain C from PDB  Type:PROTEIN  Length:252
 aligned with CASP1_SPOFR | P89116 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:261
                                                                                                                                                                                                                                                                                             299 
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299 
          CASP1_SPOFR    40 RVARMPVDRNAPYYNMNHKHRGMAIIFNHEHFDIHSLKSRTGTNVDSDNLSKVLKTLGFKVTVFPNLKSEEINKFIQQTAEMDHSDADCLLVAVLTHGELGMLYAKDTHYKPDNLWYYFTADKCPTLAGKPKLFFIQACQGDRLDGGITLSRTETDGSPSTSYRIPVHADFLIAFSTVPGYFSWRNTTRGSWFMQALCEELRYAGTERDILTLLTFVCQKVALDFESNAPDSAMMHQQKQVPCITSMLTRLLVFGKKQSH-   -
               SCOP domains d1m72c_ C: Caspase-1                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1m72C00 C:40-300  [code=3.40.50.1460, no name defined]                                                                                                                                                                                                                CATH domains
           Pfam domains (1) ---------------------Peptidase_C14-1m72C01 C:61-293                                                                                                                                                                                                           ------- Pfam domains (1)
           Pfam domains (2) ---------------------Peptidase_C14-1m72C02 C:61-293                                                                                                                                                                                                           ------- Pfam domains (2)
           Pfam domains (3) ---------------------Peptidase_C14-1m72C03 C:61-293                                                                                                                                                                                                           ------- Pfam domains (3)
         Sec.struct. author ......................eeeeee.............hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh.......eeeeee..ee..eee....ee.hhhhhhh.....hhhhh...eeeeee...............---------.........eeeee........eee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhh......eeee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------CASPASE_P20  PDB: C:59-182 UniProt: 59-182                                                                                  -----------------CASPASE_P10  PDB: C:201-295 UniProt: 200-295                                                    ----- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS ------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m72 C  40 RVARMPVDRNAPYYNMNHKHRGMAIIFNHEHFDIHSLKSRTGTNVDSDNLSKVLKTLGFKVTVFPNLKSEEINKFIQQTAEMDHSDADCLLVAVLTHGELGMLYAKDTHYKPDNLWYYFTADKCPTLAGKPKLFFIQACQGDRLDGGITLSR---------SYRIPVHADFLIAFSTVPGYFSWRNTTRGSWFMQALCEELRYAGTERDILTLLTFVCQKVALDFESNAPDSAMMHQQKQVPCITSMLTRLLVFGKKQSHL 300
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189 |       - |     209       219       229       239       249       259       269       279       289       299 
                                                                                                                                                                                 191       201                                                                                                   

Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..ee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1m72 D 500 xDEVDx 505
                            |    |
                          500-ACE|
                               505-0QE

Chain E from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..ee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1m72 E 500 xDEVDx 505
                            |    |
                            |    |
                          500-ACE|
                               505-0QE

Chain F from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..ee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1m72 F 500 xDEVDx 505
                            |    |
                            |    |
                          500-ACE|
                               505-0QE

   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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CASP1_SPOFR | P89116)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CASP1_SPOFR | P891162nn3

(-) Related Entries Specified in the PDB File

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