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(-) Description

Title :  SOLUTION STRUCTURE OF ASC2
 
Authors :  A. Natarajan, R. Ghose, J. M. Hill
Date :  11 Jul 06  (Deposition) - 25 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  Q  (20x)
Keywords :  Pyrin Domain, Six Helix Bundle, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Natarajan, R. Ghose, J. M. Hill
Structure And Dynamics Of Asc2, A Pyrin Domain-Only Protein That Regulates Inflammatory Signaling
J. Biol. Chem. V. 281 31863 2006
PubMed-ID: 16905547  |  Reference-DOI: 10.1074/JBC.M605458200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRIN-ONLY PROTEIN 1
    Chains: Q
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PQE-30
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: PYRIN DOMAIN
    Gene: POP1, PYDC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ASC2

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2HM2)

(-) Sites  (0, 0)

(no "Site" information available for 2HM2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HM2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HM2)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DAPINPS50824 DAPIN domain profile.PYDC1_HUMAN1-89  1Q:1-89

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003029641ENSE00001172467chr16:31228414-31228064351PYDC1_HUMAN1-1111111Q:1-8989
1.2ENST000003029642ENSE00001172458chr16:31227478-31227283196PYDC1_HUMAN-00--

(-) Sequences/Alignments

NMR Structure
   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 Q from PDB  Type:PROTEIN  Length:89
 aligned with PYDC1_HUMAN | Q8WXC3 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:89
                                    10        20        30        40        50        60        70        80         
           PYDC1_HUMAN    1 MGTKREAILKVLENLTPEELKKFKMKLGTVPLREGFERIPRGALGQLDIVDLTDKLVASYYEDYAAELVVAVLRDMRMLEEAARLQRAA 89
               SCOP domains d2hm2q_ Q: automated matches                                                              SCOP domains
               CATH domains 2hm2Q00 Q:1-89 Death Domain, Fas                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..hhhhhhhhhhhh............hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE DAPIN  PDB: Q:1-89 UniProt: 1-89                                                          PROSITE
               Transcript 1 Exon 1.1  PDB: Q:1-89 UniProt: 1-111 [INCOMPLETE]                                         Transcript 1
                  2hm2 Q  1 MGTKREAILKVLENLTPEELKKFKMKLGTVPLREGFERIPRGALGQLDIVDLTDKLVASYYEDYAAELVVAVLRDMRMLEEAARLQRAA 89
                                    10        20        30        40        50        60        70        80
   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, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HM2)

(-) Gene Ontology  (40, 40)

NMR Structure(hide GO term definitions)
Chain Q   (PYDC1_HUMAN | Q8WXC3)
molecular function
    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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0097202    activation of cysteine-type endopeptidase activity    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0002218    activation of innate immune response    Any process that initiates an innate immune response. Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. Examples of this process include activation of the hypersensitive response of Arabidopsis thaliana and activation of any NOD or TLR signaling pathway in vertebrate species.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0032611    interleukin-1 beta production    The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0044351    macropinocytosis    An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size.
    GO:0002277    myeloid dendritic cell activation involved in immune response    The change in morphology and behavior of a myeloid dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
    GO:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    GO:1900226    negative regulation of NLRP3 inflammasome complex assembly    Any process that stops, prevents or reduces the frequency, rate or extent of NLRP3 inflammasome complex assembly.
    GO:0050713    negative regulation of interleukin-1 beta secretion    Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0009968    negative regulation of signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
    GO:0010804    negative regulation of tumor necrosis factor-mediated signaling pathway    Any process that decreases the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:2000406    positive regulation of T cell migration    Any process that activates or increases the frequency, rate or extent of T cell migration.
    GO:0030838    positive regulation of actin filament polymerization    Any process that activates or increases the frequency, rate or extent of actin polymerization.
    GO:0042104    positive regulation of activated T cell proliferation    Any process that activates or increases the rate or extent of activated T cell proliferation.
    GO:0002588    positive regulation of antigen processing and presentation of peptide antigen via MHC class II    Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class II.
    GO:0090197    positive regulation of chemokine secretion    Any process that increases the rate, frequency or extent of chemokine secretion, the regulated release of chemokines from a cell.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0032729    positive regulation of interferon-gamma production    Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0050718    positive regulation of interleukin-1 beta secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of interleukin-1 beta from a cell.
    GO:0032755    positive regulation of interleukin-6 production    Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0043281    regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that modulates the activity of a cysteine-type endopeptidase involved in apoptosis.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0031647    regulation of protein stability    Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
    GO:0009617    response to bacterium    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 bacterium.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0008385    IkappaB kinase complex    A trimeric protein complex that phosphorylates inhibitory-kappaB (I-kappaB) proteins. The complex is composed of two kinase subunits (alpha and beta) and a regulatory gamma subunit (also called NEMO). In a resting state, NF-kappaB dimers are bound to inhibitory IKB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
    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: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: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.

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        PYDC1_HUMAN | Q8WXC3: 4qob

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