Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  ATTACHMENT OF AN NMR-INVISIBLE SOLUBILITY ENHANCEMENT TAG (INSET) USING A SORTASE-MEDIATED PROTEIN LIGATION METHOD
 
Authors :  H. Kumeta, Y. Kobashigawa, K. Ogura, F. Inagaki
Date :  07 Dec 08  (Deposition) - 03 Feb 09  (Release) - 07 Apr 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sortase, Protein Ligation, Gb1, Intein, Inset, Solubility Enhancement, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kobashigawa, H. Kumeta, K. Ogura, F. Inagaki
Attachment Of An Nmr-Invisible Solubility Enhancement Tag Using A Sortase-Mediated Protein Ligation Method
J. Biomol. Nmr V. 43 145 2009
PubMed-ID: 19140010  |  Reference-DOI: 10.1007/S10858-008-9296-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHIMERA OF PROTO-ONCOGENE VAV, LINKER, IMMUNOGLOBULIN G-BINDING PROTEIN G
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET
    Expression System Vector TypeVECTOR
    FragmentSH3 2 DOMAIN OF PROTO-ONCOGENE VAV, UNP RESIDUES 228-282 OF IMMUNOGLOBULIN G-BINDING PROTEIN G
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS, SYNTHETIC, STREPTOCOCCUS SP. 'GROUP G'
    Organism Taxid10090, 32630, 1320
    Other DetailsA SOLUBILITY-ENHANCEMENT TAG (SET) GB1, DOMAIN OF IMMUNOGLOBULIN G-BINDING PROTEIN G (INVISIBLE GB1 TAG), IS NON-LABELED AND ATTACHED TO THE C-TERMINAL OF 13C/15N-LABELED VAV SH3 DOMAIN WITH PROTEIN LIGATION
    SynonymP95VAV, IGG-BINDING PROTEIN G

 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 2KBT)

(-) Sites  (0, 0)

(no "Site" information available for 2KBT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GRAM_POS_ANCHORINGPS50847 Gram-positive cocci surface proteins LPxTG motif profile.SPG1_STRSG414-448  1A:845-848
2SH3PS50002 Src homology 3 (SH3) domain profile.VAV_MOUSE617-660
782-842
  1-
A:784-842

(-) Exons   (0, 0)

(no "Exon" information available for 2KBT)

(-) 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 A from PDB  Type:PROTEIN  Length:69
 aligned with SPG1_STRSG | P06654 from UniProtKB/Swiss-Prot  Length:448

    Alignment length:151
                                   276       286       296       306       316       326       336       346       356       366       376       386       396       406       416 
           SPG1_STRSG   267 GEWTYDDATKTFTVTEKPEVIDASELTPAVTTYKLVINGKTLKGETTTKAVDAETAEKAFKQYANDNGVDGVWTYDDATKTFTVTEMVTEVPGDAPTEPEKPEASIPLVPLTPATPIAKDDAKKDDTKKEDAKKPEAKKDDAKKAETLPTT 417
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------SH3_1-2kb----tA01 A--------:788-834-------------------            --------------      --------------      ------------------------------------- Pfam domains
         Sec.struct. author ......eeee.......----......--------.....eee-------------------eee......eee--------------eee..e--------------eeeee...eee...-----------------------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------GRAM PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kbt A 780 GPGTFGTAKARYDFCAR----DRSELS--------LKEGDIIK-------------------ILNKKGQQGWWR--------------GEIYGR--------------IGWFPSNYVEEDYS-----------------------EYLPET 848
                                   789      |  - |    |  -     | 807  |      -         -  |    818   |     -       824   |     -       830       840 |       -         -     | 847 
                                          796  797  802      803    810                 811        822            823  828            829          842                     843     

Chain A from PDB  Type:PROTEIN  Length:69
 aligned with VAV_MOUSE | P27870 from UniProtKB/Swiss-Prot  Length:845

    Alignment length:74
                                                                                                845   
                                   784       794       804       814       824       834       844|   
            VAV_MOUSE   775 KPPAGSTKYFGTAKARYDFCARDRSELSLKEGDIIKILNKKGQQGWWRGEIYGRIGWFPSNYVEEDYSEYC---   -
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------SH3_1-2kbtA01 A:788-834                        -------------- Pfam domains
         Sec.struct. author ..--..---..eeee..................eeeeee......eeeeee..eeeeee...eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------SH3  PDB: A:784-842 UniProt: 782-842                         ------ PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2kbt A 780 GP--GT---FGTAKARYDFCARDRSELSLKEGDIIKILNKKGQQGWWRGEIYGRIGWFPSNYVEEDYSEYLPET 848
                             |  || 784       794       804       814       824       834       844    
                           781  || 784                                                                
                              782|                                                                    
                               783                                                                    

   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  (0, 0)

(no "SCOP Domain" information available for 2KBT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KBT)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: SH3 (175)

(-) Gene Ontology  (30, 30)

NMR Structure(hide GO term definitions)
Chain A   (SPG1_STRSG | P06654)
molecular function
    GO:0019864    IgG binding    Interacting selectively and non-covalently with an immunoglobulin of an IgG isotype.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A   (VAV_MOUSE | P27870)
molecular function
    GO:0030676    Rac guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rac family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    GO:0042110    T cell activation    The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0006909    phagocytosis    An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
    GO:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0045785    positive regulation of cell adhesion    Any process that activates or increases the frequency, rate or extent of cell adhesion.
    GO:0045954    positive regulation of natural killer cell mediated cytotoxicity    Any process that activates or increases the frequency, rate or extent of natural killer cell mediated cytotoxicity.
    GO:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0008361    regulation of cell size    Any process that modulates the size of a cell.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
    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:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2kbt)
 
  Sites
(no "Sites" information available for 2kbt)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2kbt)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2kbt
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SPG1_STRSG | P06654
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  VAV_MOUSE | P27870
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SPG1_STRSG | P06654
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  VAV_MOUSE | P27870
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPG1_STRSG | P066541em7 1gb1 1igc 1igd 1le3 1mpe 1mvk 1pga 1pgb 1pgx 1pn5 1q10 2cwb 2den 2gb1 2igd 2igh 2j52 2j53 2ju6 2k0p 2klk 2lgi 2mbb 2n7j 2nmq 2plp 2rmm 2rpv 3gb1 3mp9 4kgr 4kgs 4kgt
        VAV_MOUSE | P278701f5x 1gcp 1gcq 1k1z 2vrw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2KBT)