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(-) Description

Title :  CRYSTAL STRUCTURE OF DRICE
 
Authors :  X. Li, J. Wang, Y. Shi
Date :  20 Jun 11  (Deposition) - 10 Aug 11  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Caspase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Li, J. Wang, Y. Shi
Structural Mechanisms Of Diap1 Auto-Inhibition And Diap1-Mediated Inhibition Of Drice.
Nat Commun V. 2 408 2011
PubMed-ID: 21811237  |  Reference-DOI: 10.1038/NCOMMS1418

(-) Compounds

Molecule 1 - CASPASE
    ChainsA, B, C, D
    EC Number3.4.22.-
    FragmentUNP RESIDUES 78-332
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymDRICE, CASPASE SUBUNIT P21, CASPASE SUBUNIT P12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3SIR)

(-) Sites  (0, 0)

(no "Site" information available for 3SIR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SIR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (4, 16)

Asymmetric Unit (4, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.DRICE_DROME92-215
 
 
 
  4A:19-142
B:19-138
C:19-139
D:19-137
2CASPASE_HISPS01121 Caspase family histidine active site.DRICE_DROME156-170
 
 
 
  4A:83-97
B:83-96
C:83-95
D:83-95
3CASPASE_CYSPS01122 Caspase family cysteine active site.DRICE_DROME202-213
 
 
 
  4A:129-140
B:129-138
C:129-139
D:129-137
4CASPASE_P10PS50207 Caspase family p10 domain profile.DRICE_DROME235-330
 
 
 
  4A:163-256
B:163-256
C:168-256
D:170-257
Biological Unit 1 (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.DRICE_DROME92-215
 
 
 
  2A:19-142
B:19-138
-
-
2CASPASE_HISPS01121 Caspase family histidine active site.DRICE_DROME156-170
 
 
 
  2A:83-97
B:83-96
-
-
3CASPASE_CYSPS01122 Caspase family cysteine active site.DRICE_DROME202-213
 
 
 
  2A:129-140
B:129-138
-
-
4CASPASE_P10PS50207 Caspase family p10 domain profile.DRICE_DROME235-330
 
 
 
  2A:163-256
B:163-256
-
-
Biological Unit 2 (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.DRICE_DROME92-215
 
 
 
  2-
-
C:19-139
D:19-137
2CASPASE_HISPS01121 Caspase family histidine active site.DRICE_DROME156-170
 
 
 
  2-
-
C:83-95
D:83-95
3CASPASE_CYSPS01122 Caspase family cysteine active site.DRICE_DROME202-213
 
 
 
  2-
-
C:129-139
D:129-137
4CASPASE_P10PS50207 Caspase family p10 domain profile.DRICE_DROME235-330
 
 
 
  2-
-
C:168-256
D:170-257

(-) Exons   (0, 0)

(no "Exon" information available for 3SIR)

(-) 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:214
 aligned with DRICE_DROME | O01382 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:301
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328 
          DRICE_DROME    29 ALGSVGSGGAGSSGLVAGSSHPYGSGAIGQLANGYSSPSSSYRKNVAKMVTDRHAAEYNMRHKNRGMALIFNHEHFEVPTLKSRAGTNVDCENLTRVLKQLDFEVTVYKDCRYKDILRTIEYAASQNHSDSDCILVAILSHGEMGYIYAKDTQYKLDNIWSFFTANHCPSLAGKPKLFFIQACQGDRLDGGVTMQRSQTETDGDSSMSYKIPVHADFLIAYSTVPGFYSWRNTTRGSWFMQSLCAELAANGKRLDILTLLTFVCQRVAVDFESCTPDTPEMHQQKQIPCITTMLTRILRFS 329
               SCOP domains d3sir                                             a_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....---------------------------------------------.............eeeeeeeeee...-----------.hhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhh.....eeeeeeeeee..........hhhhhhhhhhhhhh...hhhhh...eeeeeeee....ee.-----------------.ee......eeeeeeee............hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..--------------...eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------CASPASE_P20  PDB: A:19-142 UniProt: 92-215                                                                                  -------------------CASPASE_P10  PDB: A:163-256 UniProt: 235-330                                                    PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS -------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sir A   1 ALGSV---------------------------------------------TDRHAAEYNMRHKNRGMALIFNHEHF-----------NVDCENLTRVLKQLDFEVTVYKDCRYKDILRTIEYSASQNHSDSDCILVAILSHGEMGYIYAKDTQYKLDNIWSFFTANHCPSLAGKPKLFFIQACQGDRLDG-----------------SYKIPVHADFLIAYSTVPGFYSWRNTTRGSWFMQSLCAELAANGKRLDILTLLTFVCQRVAVDF--------------QIPCITTMLTRILRFS 256
                                |    -         -         -         -         -|       15        25     |   -       |45        55        65        75        85        95       105       115       125       135       145         -       165       175       185       195       205       215       225|        -     | 245       255 
                                5                                             6                       31          43                                                                                                   145               163                                                            226            241               

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with DRICE_DROME | O01382 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:247
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       
          DRICE_DROME    83 AAEYNMRHKNRGMALIFNHEHFEVPTLKSRAGTNVDCENLTRVLKQLDFEVTVYKDCRYKDILRTIEYAASQNHSDSDCILVAILSHGEMGYIYAKDTQYKLDNIWSFFTANHCPSLAGKPKLFFIQACQGDRLDGGVTMQRSQTETDGDSSMSYKIPVHADFLIAYSTVPGFYSWRNTTRGSWFMQSLCAELAANGKRLDILTLLTFVCQRVAVDFESCTPDTPEMHQQKQIPCITTMLTRILRFS 329
               SCOP domains d3sirb_ B: automat               ed matches                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee.---------------hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh.....eeeeeeeee..-----------------.................eeeeeee.------------------------.........eeeeeee..--------...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....-----------...eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CASPASE_P20  PDB: B:19-138 UniProt: 92-215                                                                                  -------------------CASPASE_P10  PDB: B:163-256 UniProt: 235-330                                                    PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS -------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sir B  10 AAEYNMRHKNRGMALIFN---------------NVDCENLTRVLKQLDFEVTVYKDCRYKDILRTIEYSASQNHSDSDCILVAILSH-----------------IWSFFTANHCPSLAGKPKLFFIQAC------------------------SYKIPVHADFLIAYSTVP--------TRGSWFMQSLCAELAANGKRLDILTLLTFVCQRVAVDFESC-----------QIPCITTMLTRILRFS 256
                                    19       | -         -   |    49        59        69        79        89      |  -         -    |  119       129        |-         -         -   |   169       179|      189       199       209       219       229         - |     249       
                                            27              43                                                   96               114                     138                      163              180      189                                     229         241               

Chain C from PDB  Type:PROTEIN  Length:162
 aligned with DRICE_DROME | O01382 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:247
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       
          DRICE_DROME    83 AAEYNMRHKNRGMALIFNHEHFEVPTLKSRAGTNVDCENLTRVLKQLDFEVTVYKDCRYKDILRTIEYAASQNHSDSDCILVAILSHGEMGYIYAKDTQYKLDNIWSFFTANHCPSLAGKPKLFFIQACQGDRLDGGVTMQRSQTETDGDSSMSYKIPVHADFLIAYSTVPGFYSWRNTTRGSWFMQSLCAELAANGKRLDILTLLTFVCQRVAVDFESCTPDTPEMHQQKQIPCITTMLTRILRFS 329
               SCOP domains d3sirc_ C: automate              d matches                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.--------------hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh.........eeeeee.-----------------..........hhhhh...eeeeeeee.----------------------------....eeeeeeee.-----------hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.---------------...eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CASPASE_P20  PDB: C:19-139 UniProt: 92-215                                                                                  -------------------CASPASE_P10  PDB: C:168-256 UniProt: 235-330                                                    PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS -------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sir C  10 AAEYNMRHKNRGMALIFNH--------------NVDCENLTRVLKQLDFEVTVYKDCRYKDILRTIEYSASQNHSDSDCILVAILS-----------------NIWSFFTANHCPSLAGKPKLFFIQACQ----------------------------VHADFLIAYSTVP-----------SWFMQSLCAELAANGKRLDILTLLTFVCQRVAVD---------------QIPCITTMLTRILRFS 256
                                    19        |-         -   |    49        59        69        79        89     |   -         -   |   119       129       139         -         -       169       179|        -  |    199       209       219     |   -         - |     249       
                                             28             43                                                  95               113                       139                          168         180         192                              225             241               

Chain D from PDB  Type:PROTEIN  Length:169
 aligned with DRICE_DROME | O01382 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:250
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
          DRICE_DROME    83 AAEYNMRHKNRGMALIFNHEHFEVPTLKSRAGTNVDCENLTRVLKQLDFEVTVYKDCRYKDILRTIEYAASQNHSDSDCILVAILSHGEMGYIYAKDTQYKLDNIWSFFTANHCPSLAGKPKLFFIQACQGDRLDGGVTMQRSQTETDGDSSMSYKIPVHADFLIAYSTVPGFYSWRNTTRGSWFMQSLCAELAANGKRLDILTLLTFVCQRVAVDFESCTPDTPEMHQQKQIPCITTMLTRILRFSDKQ 332
               SCOP domains d3sird_ D: automate              d matches                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.--------------.hhhhhhhhhhhhh..eeeeee.---hhhhhhhhhhhh........eeeeee.------------------.........hhhhh...eeeeeee--------------------------------..eeeeeee.............hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..--------------....eee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CASPASE_P20  PDB: D:19-137 UniProt: 92-215                                                                                  -------------------CASPASE_P10  PDB: D:170-257 UniProt: 235-330                                                    -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS ----------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sir D  10 AAEYNMRHKNRGMALIFNH--------------NVDCENLTRVLKQLDFEVTVYKD---KDILRTIEYSASQNHSDSDCILVAILS------------------IWSFFTANHCPSLAGKPKLFFIQA--------------------------------ADFLIAYSTVPGFYSWRNTTRGSWFMQSLCAELAANGKRLDILTLLTFVCQRVAVDF--------------QIPCITTMLTRILRFSDKQ 259
                                    19        |-         -   |    49        59     |  69        79        89     |   -         -    |  119       129       | -         -         -         -|      179       189       199       209       219      |  -         - |     249       259
                                             28             43                    65  69                        95                114                    137                              170                                                     226            241                  

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DRICE_DROME | O01382)
molecular function
    GO:1990525    BIR domain binding    Interacting selectively and non-covalently with a Baculovirus Inhibitor of apoptosis protein Repeat (BIR) domain.
    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:0097153    cysteine-type endopeptidase activity involved in apoptotic process    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, and contributing to the apoptotic process.
    GO:0097200    cysteine-type endopeptidase activity involved in execution phase of apoptosis    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, and contributing to the execution phase of apoptosis.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0097194    execution phase of apoptosis    A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are 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:0016322    neuron remodeling    The developmentally regulated remodeling of neuronal projections such as pruning to eliminate the extra dendrites and axons projections set up in early stages of nervous system development.
    GO:0045476    nurse cell apoptotic process    Any apoptotic process in a nurse cell. During late oogenesis, following the transfer of substances from the nurse cells to the oocyte, nurse cell remnants are cleared from the egg chamber by apoptotic process.
    GO:0046672    positive regulation of compound eye retinal cell programmed cell death    Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the compound eye retina.
    GO:2001269    positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of cysteine-type endopeptidase activity involved in apoptotic signaling pathway.
    GO:0012501    programmed cell death    A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
    GO:0010623    programmed cell death involved in cell development    The activation of endogenous cellular processes that result in the death of a cell as part of its development.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0046668    regulation of retinal cell programmed cell death    Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the retina.
    GO:0010165    response to X-ray    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of X-ray radiation. An X-ray is a form of electromagnetic radiation with a wavelength in the range of 10 nanometers to 100 picometers (corresponding to frequencies in the range 30 PHz to 3 EHz).
    GO:0035070    salivary gland histolysis    The stage-specific break down of the larval salivary glands during Drosophila metamorphosis, to allow replacement of larval structures by tissues and structures that form the adult fly.
    GO:0048515    spermatid differentiation    The process whose specific outcome is the progression of a spermatid over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    GO:0035103    sterol regulatory element binding protein cleavage    The proteolytic release of a transcriptionally active sterol regulatory element binding protein (SREBP) from intracellular membranes, freeing it to move to the nucleus to upregulate transcription of target genes, in response to altered levels of one or more lipids.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DRICE_DROME | O013823sip

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