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(-) Description

Title :  CRYSTAL STRUCTURE OF CASPASE-6 INACTIVATION MUTATION
 
Authors :  Q. Cao, X. J. Wang, D. F. Liu, L. F. Li, X. D. Su
Date :  20 Dec 11  (Deposition) - 28 Mar 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apoptotic Protease, Caspase Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Cao, X. J. Wang, C. W. Liu, D. F. Liu, L. F. Li, Y. Q. Gao, X. D. Su
Inhibitory Mechanism Of Caspase-6 Phosphorylation Revealed By Crystal Structures, Molecular Dynamics Simulations, And Biochemical Assays
J. Biol. Chem. V. 287 15371 2012
PubMed-ID: 22433863  |  Reference-DOI: 10.1074/JBC.M112.351213

(-) Compounds

Molecule 1 - CASPASE-6
    ChainsA, B
    EC Number3.4.22.59
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 21-293
    GeneCASP6
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCASP-6, APOPTOTIC PROTEASE MCH-2, CASPASE-6 SUBUNIT P18, CASPASE-6 SUBUNIT P11

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3V6L)

(-) Sites  (0, 0)

(no "Site" information available for 3V6L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V6L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly B:165 -Asn B:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_029242E35KCASP6_HUMANPolymorphism11574697A/BE35K
2UniProtVAR_016130A109TCASP6_HUMANPolymorphism5030674A/BA109T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 8)

Asymmetric/Biological Unit (4, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CASPASE_P20PS50208 Caspase family p20 domain profile.CASP6_HUMAN43-167
 
  2A:43-166
B:43-166
2CASPASE_HISPS01121 Caspase family histidine active site.CASP6_HUMAN108-122
 
  2A:108-122
B:108-122
3CASPASE_CYSPS01122 Caspase family cysteine active site.CASP6_HUMAN154-165
 
  2A:154-165
B:154-165
4CASPASE_P10PS50207 Caspase family p10 domain profile.CASP6_HUMAN196-290
 
  2A:196-290
B:196-290

(-) Exons   (5, 10)

Asymmetric/Biological Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002651641bENSE00001018825chr4:110624629-110624512118CASP6_HUMAN1-14140--
1.3ENST000002651643ENSE00000935048chr4:110619498-11061945643CASP6_HUMAN14-28150--
1.4bENST000002651644bENSE00000935047chr4:110618924-110618778147CASP6_HUMAN28-77502A:31-77
B:30-77
47
48
1.5bENST000002651645bENSE00000935046chr4:110617642-11061756677CASP6_HUMAN77-103272A:77-103
B:77-103
27
27
1.6cENST000002651646cENSE00000935045chr4:110615856-110615681176CASP6_HUMAN103-161592A:103-161
B:103-161
59
59
1.7cENST000002651647cENSE00000935044chr4:110612165-110612006160CASP6_HUMAN162-215542A:162-215 (gaps)
B:162-215 (gaps)
54
54
1.8dENST000002651648dENSE00001820381chr4:110610724-110609898827CASP6_HUMAN215-293792A:215-292 (gaps)
B:215-292 (gaps)
78
78

(-) 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:239
 aligned with CASP6_HUMAN | P55212 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:262
                                    40        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  
          CASP6_HUMAN    31 FDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPLDVVDNQTEKLDTNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPKS 292
               SCOP domains d3v6la_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeee....hhhhh.....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh.......eeeeeeeeee..eee....eeehhhhhhhhhhhhhhhhh...eeeeeeee...--------------------...eeeee...........eeeee......eeeee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....---..........eeee............ Sec.struct. author
                 SAPs(SNPs) ----K-------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------CASPASE_P20  PDB: A:43-166 UniProt: 43-167                                                                                   ----------------------------CASPASE_P10  PDB: A:196-290 UniProt: 196-290                                                   -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS ------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4b  PDB: A:31-77 UniProt: 28-77         -------------------------Exon 1.6c  PDB: A:103-161 UniProt: 103-161                 Exon 1.7c  PDB: A:162-215 (gaps) UniProt: 162-215     ----------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.5b  PDB: A:77-103   ---------------------------------------------------------------------------------------------------------------Exon 1.8d  PDB: A:215-292 (gaps) UniProt: 215-293 [INCOMPLETE]                 Transcript 1 (2)
                 3v6l A  31 FDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGN--------------------TNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVEQRRVDF---PSAIGKKQVPCFASMLTKKLHFFPKS 292
                                    40        50        60        70        80        90       100       110       120       130       140       150       160     |   -         -      |190       200       210       220       230       240       250       260  |   |270       280       290  
                                                                                                                                                                 166                  187                                                                         263 267                         

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with CASP6_HUMAN | P55212 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:263
                                    39        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   
          CASP6_HUMAN    30 MFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGNQHDVPVIPLDVVDNQTEKLDTNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPSAIGKKQVPCFASMLTKKLHFFPKS 292
               SCOP domains d3v6lb_ B: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeee....hhhhh.....hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh.......eeeeeeeeee..eee....eeehhhhhhhhhhhhhhhhh...eeeeeeee...--------------------...eeeee...........eeeee......eeeee...eehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...--.hhhhh......eeee............ Sec.struct. author
                 SAPs(SNPs) -----K-------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------CASPASE_P20  PDB: B:43-166 UniProt: 43-167                                                                                   ----------------------------CASPASE_P10  PDB: B:196-290 UniProt: 196-290                                                   -- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------CASPASE_HIS    -------------------------------CASPASE_CYS ------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4b  PDB: B:30-77 UniProt: 28-77          -------------------------Exon 1.6c  PDB: B:103-161 UniProt: 103-161                 Exon 1.7c  PDB: B:162-215 (gaps) UniProt: 162-215     ----------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.5b  PDB: B:77-103   ---------------------------------------------------------------------------------------------------------------Exon 1.8d  PDB: B:215-292 (gaps) UniProt: 215-293 [INCOMPLETE]                 Transcript 1 (2)
                 3v6l B  30 MFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIFIIQACRGN--------------------TNITEVDAASVYTLPAGADFLMCYSVAEGYYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVEQRRVD--KDPSAIGKKQVPCFASMLTKKLHFFPKS 292
                                    39        49        59        69        79        89        99       109       119       129       139       149       159      |  -         -       189       199       209       219       229       239       249       259  |  | 269       279       289   
                                                                                                                                                                  166                  187                                                                        262  |                           
                                                                                                                                                                                                                                                                     265                           

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V6L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V6L)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CASP6_HUMAN | P55212)
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: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: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:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0006921    cellular component disassembly involved in execution phase of apoptosis    The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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    Gly B:165 - Asn B:166   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        CASP6_HUMAN | P552121mi9 2wdp 3k7e 3nkf 3nr2 3od5 3p45 3p4u 3qnw 3s70 3s8e 3v6m 4ejf 4fxo 4hva 4iyr 4n5d 4n6g 4n7j 4n7m 4nbk 4nbl 4nbn

(-) Related Entries Specified in the PDB File

3nr2 3od5 3v6m