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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UNCOMPLEXED PELLE DEATH DOMAIN
 
Authors :  T. Xiao, K. H. Gardner, S. R. Sprang
Date :  02 May 01  (Deposition) - 31 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Single Helix, Mpd Crystallization, Structural Transition, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Xiao, K. H. Gardner, S. R. Sprang
Cosolvent-Induced Transformation Of A Death Domain Tertiary Structure
Proc. Natl. Acad. Sci. Usa V. 99 11151 2002
PubMed-ID: 12177432  |  Reference-DOI: 10.1073/PNAS.172188399
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE SERINE/THREONINE-PROTEIN KINASE PELLE
    ChainsA, B
    EC Number2.7.1.37
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Cellular LocationCYTOPLASM
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDEATH DOMAIN
    GenePELLE
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymPELLE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:86 , LYS A:127 , HOH B:11 , LYS B:107 , HIS B:111BINDING SITE FOR RESIDUE TRS B 201
2AC2SOFTWARELYS A:127 , GLU B:123 , ASP B:124BINDING SITE FOR RESIDUE TRS B 202
3AC3SOFTWAREHOH A:6 , HOH A:13 , HIS A:111 , PHE B:86 , LYS B:127BINDING SITE FOR RESIDUE TRS A 203
4AC4SOFTWAREGLU A:123 , ASP A:124 , LYS B:127BINDING SITE FOR RESIDUE TRS A 204
5AC5SOFTWAREILE A:129BINDING SITE FOR RESIDUE MPD A 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IK7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IK7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IK7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IK7)

(-) Exons   (0, 0)

(no "Exon" information available for 1IK7)

(-) 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:52
 aligned with KPEL_DROME | Q05652 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:52
                                    87        97       107       117       127  
           KPEL_DROME    78 RGRSASNEFLNIWGGQYNHTVQTLFALFKKLKLHNAMRLIKDYVSEDLHKYI 129
               SCOP domains d1ik7a_ A: Pelle death domain                        SCOP domains
               CATH domains 1ik7A00 A:78-129 Single helix bin                    CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 1ik7 A  78 RGRSASNEFLNIWGGQYNHTVQTLFALFKKLKLHNAMRLIKDYVSEDLHKYI 129
                                    87        97       107       117       127  

Chain B from PDB  Type:PROTEIN  Length:49
 aligned with KPEL_DROME | Q05652 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:49
                                    90       100       110       120         
           KPEL_DROME    81 SASNEFLNIWGGQYNHTVQTLFALFKKLKLHNAMRLIKDYVSEDLHKYI 129
               SCOP domains d1ik7b_ B: Pelle death domain                     SCOP domains
               CATH domains 1ik7B00 B:81-129 Single helix bin                 CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 1ik7 B  81 SASNEFLNIWGGQYNHTVQTLFALFKKLKLHNAMRLIKDYVSEDLHKYI 129
                                    90       100       110       120         

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IK7)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KPEL_DROME | Q05652)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0008063    Toll signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Toll on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0019732    antifungal humoral response    An immune response against a fungus mediated through a body fluid. An example of this process is the antifungal humoral response in Drosophila melanogaster.
    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:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0048262    determination of dorsal/ventral asymmetry    Determination of asymmetry from the dorsal to the ventral side; as, the dorsoventral axis.
    GO:0009950    dorsal/ventral axis specification    The establishment, maintenance and elaboration of the dorsal/ventral axis. The dorsal/ventral axis is defined by a line that runs orthogonal to both the anterior/posterior and left/right axes. The dorsal end is defined by the upper or back side of an organism. The ventral end is defined by the lower or front side of an organism.
    GO:0035172    hemocyte proliferation    The multiplication or reproduction of hemocytes, resulting in the expansion of the cell population. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0030162    regulation of proteolysis    Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    GO:0009620    response to fungus    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 a stimulus from a fungus.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007352    zygotic specification of dorsal/ventral axis    The specification of the dorsal/ventral axis of the embryo, through the products of genes expressed in the zygote.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KPEL_DROME | Q056521d2z 1ygo

(-) Related Entries Specified in the PDB File

1d2z 1D2Z IS THE CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE DEATH DOMAINS OF PELLE AND TUBE