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(-) Description

Title :  NMR STRUCTURE OF THE PASTA DOMAIN 2 AND 3 OF MYCOBACTERIUM TUBERCULOSIS OF PKNB
 
Authors :  P. Barthe, G. Mukamolova, C. Roumestand, M. Cohen-Gonsaud
Date :  17 Feb 10  (Deposition) - 14 Apr 10  (Release) - 26 May 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (30x)
Keywords :  Kinase, External Domain, Signaling, Stpk, Resuscitation, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Barthe, G. V. Mukamolova, C. Roumestand, M. Cohen-Gonsaud
The Structure Of Pknb Extracellular Pasta Domain From Mycobacterium Tuberculosis Suggests A Ligand-Dependent Kinase Activation
Structure V. 18 606 2010
PubMed-ID: 20462494  |  Reference-DOI: 10.1016/J.STR.2010.02.013

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PKNB
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET21-TEV
    Expression System Vector TypeVECTOR
    FragmentPASTA DOMAINS 2 AND 3, RESIDUES 423-557
    GeneRV0014C
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid83332
    StrainH37RV
    SynonymPKNB

 Structural Features

(-) Chains, Units

  
NMR Structure (30x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2KUE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASTAPS51178 PASTA domain profile.PKNB_MYCTO356-422
423-490
491-557
558-626
  2-
A:423-490
A:491-557
-
PKNB_MYCTU356-422
423-490
491-557
558-626
  2-
A:423-490
A:491-557
-

(-) Exons   (0, 0)

(no "Exon" information available for 2KUE)

(-) 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:135
 aligned with PKNB_MYCTO | P9WI80 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:135
                                   432       442       452       462       472       482       492       502       512       522       532       542       552     
           PKNB_MYCTO   423 GPEQREIPDVSTLTYAEAVKKLTAAGFGRFKQANSPSTPELVGKVIGTNPPANQTSAITNVVIIIVGSGPATKDIPDVAGQTVDVAQKNLNVYGFTKFSQASVDSPRPAGEVTGTNPPAGTTVPVDSVIELQVSK 557
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------PASTA-2kueA01 A:495-557                                         Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------PASTA-2kueA02 A:495-557                                         Pfam domains (2)
         Sec.struct. author ...eee.......hhhhhhhhhhhh....eeeeeee.hhhhh..eeee......eee....eeeeeee...eee.......hhhhhhhhhhhhh...eeeeee........eeee......eee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) PASTA  PDB: A:423-490 UniProt: 423-490                              PASTA  PDB: A:491-557 UniProt: 491-557                              PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kue A 423 GPEQREIPDVSTLTYAEAVKKLTAAGFGRFKQANSPSTPELVGKVIGTNPPANQTSAITNVVIIIVGSGPATKDIPDVAGQTVDVAQKNLNVYGFTKFSQASVDSPRPAGEVTGTNPPAGTTVPVDSVIELQVSK 557
                                   432       442       452       462       472       482       492       502       512       522       532       542       552     

Chain A from PDB  Type:PROTEIN  Length:135
 aligned with PKNB_MYCTU | P9WI81 from UniProtKB/Swiss-Prot  Length:626

    Alignment length:135
                                   432       442       452       462       472       482       492       502       512       522       532       542       552     
           PKNB_MYCTU   423 GPEQREIPDVSTLTYAEAVKKLTAAGFGRFKQANSPSTPELVGKVIGTNPPANQTSAITNVVIIIVGSGPATKDIPDVAGQTVDVAQKNLNVYGFTKFSQASVDSPRPAGEVTGTNPPAGTTVPVDSVIELQVSK 557
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------PASTA-2kueA01 A:495-557                                         Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------PASTA-2kueA02 A:495-557                                         Pfam domains (2)
         Sec.struct. author ...eee.......hhhhhhhhhhhh....eeeeeee.hhhhh..eeee......eee....eeeeeee...eee.......hhhhhhhhhhhhh...eeeeee........eeee......eee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PASTA  PDB: A:423-490 UniProt: 423-490                              PASTA  PDB: A:491-557 UniProt: 491-557                              PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kue A 423 GPEQREIPDVSTLTYAEAVKKLTAAGFGRFKQANSPSTPELVGKVIGTNPPANQTSAITNVVIIIVGSGPATKDIPDVAGQTVDVAQKNLNVYGFTKFSQASVDSPRPAGEVTGTNPPAGTTVPVDSVIELQVSK 557
                                   432       442       452       462       472       482       492       502       512       522       532       542       552     

   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 2KUE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

NMR Structure

(-) Gene Ontology  (27, 39)

NMR Structure(hide GO term definitions)
Chain A   (PKNB_MYCTU | P9WI81)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0045717    negative regulation of fatty acid biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    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.
    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:0043388    positive regulation of DNA binding    Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051338    regulation of transferase activity    Any process that modulates the frequency, rate or extent of transferase activity, the 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.
    GO:0052572    response to host immune response    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 detecting the immune response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

Chain A   (PKNB_MYCTO | P9WI80)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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: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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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
        PKNB_MYCTO | P9WI801mru 1o6y 2fum 2kud 2kuf 2kui 3f61 3f69
        PKNB_MYCTU | P9WI811mru 1o6y 2fum 2kud 2kuf 2kui 3f61 3f69 5e0y 5e0z 5e10 5e12

(-) Related Entries Specified in the PDB File

2kud SOLUTION STRUCTURE OF THE PASTA DOMAIN 1 AND 2
2kuf SOLUTION STRUCTURE OF THE PASTA DOMAIN 3 AND 4
2kui SOLUTION STRUCTURE OF THE PASTA DOMAIN RELATED ID: 16733 RELATED DB: BMRB