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(-) Description

Title :  HUMAN P47 PX DOMAIN COMPLEX WITH SULPHATES
 
Authors :  D. Karathanassis, J. Bravo, O. Perisic, C. M. Pacold, R. L. Williams
Date :  07 Nov 02  (Deposition) - 20 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  P47, Nadph Oxidase, Px Domain, Phospholipid-Binding, Phosphoinositide-Binding, Sh3 Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Karathanassis, R. V. Stahelin, J. Bravo, O. Perisic, C. M. Pacold, W. Cho, R. L. Williams
Binding Of The Px Domain Of P47Phox To Phosphatidylinositol 3. 4-Bisphosphate And Phosphatidic Acid Is Masked By An Intramolecular Interaction
Embo J. V. 21 5057 2002
PubMed-ID: 12356722  |  Reference-DOI: 10.1093/EMBOJ/CDF519

(-) Compounds

Molecule 1 - NEUTROPHIL CYTOSOL FACTOR 1
    CellNEUTROPHIL
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICIA COLI
    Expression System PlasmidPJL
    Expression System StrainC41
    Expression System Taxid562
    Expression System VariantDE3
    FragmentPX DOMAIN, RESIDUES 1-123
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNCF-1, NEUTROPHIL NADPH OXIDASE FACTOR 1, P47-PHOX, 47 KDA NEUTROPHIL OXIDASE FACTOR, NCF-47K, 47 KDA AUTOSOMAL CHRONIC GRANULOMATOUS DISEASE PROTEIN
    TissueBLOOD

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric/Biological Unit (2, 17)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2SO47Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:43 , PHE A:44 , THR A:45 , ARG A:90 , HOH A:2019 , HOH A:2067 , HOH A:2068BINDING SITE FOR RESIDUE SO4 A1124
2AC2SOFTWAREHIS A:51 , LYS A:55 , ARG A:70 , HIS A:74 , LEU A:75 , HOH A:2033 , LYS C:31BINDING SITE FOR RESIDUE SO4 A1125
3AC3SOFTWAREARG B:43 , PHE B:44 , THR B:45 , ARG B:90 , HOH B:2010 , HOH B:2082BINDING SITE FOR RESIDUE SO4 B1124
4AC4SOFTWARELYS A:31 , HIS B:51 , LYS B:55 , ARG B:70 , HIS B:74 , LEU B:75 , HOH B:2043 , HOH B:2083BINDING SITE FOR RESIDUE SO4 B1125
5AC5SOFTWAREARG C:43 , PHE C:44 , THR C:45 , HOH C:2010 , HOH C:2041BINDING SITE FOR RESIDUE SO4 C1124
6AC6SOFTWARELYS B:31 , HIS C:51 , LYS C:55 , ARG C:70 , HIS C:74 , LEU C:75 , HOH C:2042BINDING SITE FOR RESIDUE SO4 C1125
7AC7SOFTWAREASP A:34 , LYS B:16 , GLN C:84 , ARG C:85 , HOH C:2043BINDING SITE FOR RESIDUE SO4 C1126

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O7K)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val A:19 -Pro A:20
2Val B:19 -Pro B:20
3Val C:19 -Pro C:20

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 9)

Asymmetric/Biological Unit (3, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_012476R42QNCF1_HUMANDisease (CGD1)  ---A/B/CR42Q
2UniProtVAR_014735R90HNCF1_HUMANPolymorphism13447A/B/CR90H
3UniProtVAR_018479G99SNCF1_HUMANPolymorphism17856077A/B/CS99S

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PXPS50195 PX domain profile.NCF1_HUMAN4-125
 
 
  3A:4-123
B:4-123
C:4-123

(-) Exons   (0, 0)

(no "Exon" information available for 1O7K)

(-) 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:124
 aligned with NCF1_HUMAN | P14598 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:124
                             1                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119    
           NCF1_HUMAN     - -MGDTFIRHIALLGFEKRFVPSQHYVYMFLVKWQDLSEKVVYRRFTEIYEFHKTLKEMFPIEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCGTLMSLPTKISRCPHLLDFFKVRPD 123
               SCOP domains d1o7ka_ A: p47phox NADPH oxidase                                                                                             SCOP domains
               CATH domains 1o7kA00 A:0-123 PX Domain                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeee.....eeeeeeeeee....eeeeeehhhhhhhhhhhhhh.........hhhhh......hhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------Q-----------------------------------------------H--------S------------------------ SAPs(SNPs)
                    PROSITE ----PX  PDB: A:4-123 UniProt: 4-125                                                                                          PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o7k A   0 HmGDTFIRHIALLGFEKRFVPSQHYVYmFLVKWQDLSEKVVYRRFTEIYEFHKTLKEmFPIEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCSTLmSLPTKISRCPHLLDFFKVRPD 123
                             |       9        19       |29        39        49       |59        69        79        89        99  |    109       119    
                             |                        27-MSE                        57-MSE                                      102-MSE                 
                             1-MSE                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with NCF1_HUMAN | P14598 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:120
                                    13        23        33        43        53        63        73        83        93       103       113       123
           NCF1_HUMAN     4 TFIRHIALLGFEKRFVPSQHYVYMFLVKWQDLSEKVVYRRFTEIYEFHKTLKEMFPIEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCGTLMSLPTKISRCPHLLDFFKVRPD 123
               SCOP domains d1o7kb_ B: p47phox NADPH oxidase                                                                                         SCOP domains
               CATH domains 1o7kB00 B:4-123 PX Domain                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------Q-----------------------------------------------H--------S------------------------ SAPs(SNPs)
                    PROSITE PX  PDB: B:4-123 UniProt: 4-125                                                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o7k B   4 TFIRHIALLGFEKRFVPSQHYVYmFLVKWQDLSEKVVYRRFTEIYEFHKTLKEmFPIEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCSTLmSLPTKISRCPHLLDFFKVRPD 123
                                    13        23   |    33        43        53   |    63        73        83        93       103       113       123
                                                  27-MSE                        57-MSE                                      102-MSE                 

Chain C from PDB  Type:PROTEIN  Length:120
 aligned with NCF1_HUMAN | P14598 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:120
                                    13        23        33        43        53        63        73        83        93       103       113       123
           NCF1_HUMAN     4 TFIRHIALLGFEKRFVPSQHYVYMFLVKWQDLSEKVVYRRFTEIYEFHKTLKEMFPIEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCGTLMSLPTKISRCPHLLDFFKVRPD 123
               SCOP domains d1o7kc_ C: p47phox NADPH oxidase                                                                                         SCOP domains
               CATH domains 1o7kC00 C:4-123 PX Domain                                                                                                CATH domains
           Pfam domains (1) PX-1o7kC01 C:4-121                                                                                                    -- Pfam domains (1)
           Pfam domains (2) PX-1o7kC02 C:4-121                                                                                                    -- Pfam domains (2)
           Pfam domains (3) PX-1o7kC03 C:4-121                                                                                                    -- Pfam domains (3)
         Sec.struct. author ..eeeeeeeeeeee.....eeeeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------Q-----------------------------------------------H--------S------------------------ SAPs(SNPs)
                    PROSITE PX  PDB: C:4-123 UniProt: 4-125                                                                                          PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o7k C   4 TFIRHIALLGFEKRFVPSQHYVYmFLVKWQDLSEKVVYRRFTEIYEFHKTLKEmFPIEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCSTLmSLPTKISRCPHLLDFFKVRPD 123
                                    13        23   |    33        43        53   |    63        73        83        93       103       113       123
                                                  27-MSE                        57-MSE                                      102-MSE                 

   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/Biological Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Family: PX (17)
1aPX-1o7kC01C:4-121
1bPX-1o7kC02C:4-121
1cPX-1o7kC03C:4-121

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (NCF1_HUMAN | P14598)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0035091    phosphatidylinositol binding    Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0043325    phosphatidylinositol-3,4-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
    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:0016175    superoxide-generating NADPH oxidase activity    Catalysis of the reaction: NAD(P)H + O2 = NAD(P)H + O2-.
biological process
    GO:0002479    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0006968    cellular defense response    A defense response that is mediated by cells.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0045730    respiratory burst    A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
    GO:0042554    superoxide anion generation    The enzymatic generation of superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species, by a cell in response to environmental stress, thereby mediating the activation of various stress-inducible signaling pathways.
    GO:0006801    superoxide metabolic process    The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0043020    NADPH oxidase complex    A enzyme complex of which the core is a heterodimer composed of a light (alpha) and heavy (beta) chain, and requires several other water-soluble proteins of cytosolic origin for activity. Functions in superoxide generation by the NADPH-dependent reduction of O2.
    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:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0032010    phagolysosome    A membrane-bounded intracellular vesicle formed by maturation of an early phagosome following the ingestion of particulate material by phagocytosis; during maturation, phagosomes acquire markers of late endosomes and lysosomes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCF1_HUMAN | P145981gd5 1k4u 1kq6 1ng2 1ov3 1uec 1w70 1wlp

(-) Related Entries Specified in the PDB File

1gd5 SOLUTION STRUCTURE OF THE PX DOMAIN FROM HUMAN P47PHOXNADPH OXIDASE
1k4u SOLUTION STRUCTURE OF THE C-TERMINAL SH3 DOMAIN OF P67PHOXCOMPLEXED WITH THE C- TERMINAL TAIL REGION OF P47PHOX