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(-) Description

Title :  NMR STRUCTURE OF THE SUBSTRATE BINDING DOMAIN OF DNAK IN THE APO FORM
 
Authors :  M. Pellecchia, D. L. Montgomery, S. Y. Stevens, C. W. Van Der Kooi, H. Feng, L. M. Gierasch, E. R. P. Zuiderweg
Date :  23 Nov 99  (Deposition) - 08 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Dnak, Chaperone, Substrate Binding Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Pellecchia, D. L. Montgomery, S. Y. Stevens, C. W. Vander Kooi, H. P. Feng, L. M. Gierasch, E. R. Zuiderweg
Structural Insights Into Substrate Binding By The Molecular Chaperone Dnak.
Nat. Struct. Biol. V. 7 298 2000
PubMed-ID: 10742174  |  Reference-DOI: 10.1038/74062
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNAK
    Chains: A
    Fragment: SUBSTRATE BINDING DOMAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: MOLECULAR CHAPERONE

 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 1DG4)

(-) Sites  (0, 0)

(no "Site" information available for 1DG4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DG4)

(-) Cis Peptide Bonds  (1, 15)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 8, 9, 11, 13, 15, 17, 18, 19, 20Ile A:418 -Pro A:419

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DG4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DG4)

(-) Exons   (0, 0)

(no "Exon" information available for 1DG4)

(-) 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:111
 aligned with DNAK_ECOLI | P0A6Y8 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:111
                                   406       416       426       436       446       456       466       476       486       496       506 
           DNAK_ECOLI   397 LSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGL 507
               SCOP domains d1dg4a_ A: DnaK                                                                                                 SCOP domains
               CATH domains 1dg4A00 A:397-507 Substrate Binding Domain Of DNAk; Chain A, domain 1                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eee..........eee............eeeeeeee.........eeeeeeeee...........eeeeeee.....eeeeeee.....eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1dg4 A 397 LSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGL 507
                                   406       416       426       436       446       456       466       476       486       496       506
   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 beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DG4)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (DNAK_ECOLI | P0A6Y8)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0044183    protein binding involved in protein folding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules) that contributes to the process of protein folding.
    GO:0016989    sigma factor antagonist activity    The function of binding to a sigma factor and stopping, preventing or reducing the rate of its transcriptional activity.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0034620    cellular response to unfolded protein    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an unfolded protein stimulus.
    GO:0070389    chaperone cofactor-dependent protein refolding    The process of assisting in the restoration of the biological activity of an unfolded or misfolded protein, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release.
    GO:0051085    chaperone mediated protein folding requiring cofactor    The process of assisting in the correct posttranslational noncovalent assembly of proteins, which is dependent on additional protein cofactors. This process occurs over one or several cycles of nucleotide hydrolysis-dependent binding and release.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0043241    protein complex disassembly    The disaggregation of a protein complex into its constituent components. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:1903506    regulation of nucleic acid-templated transcription    Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0009408    response to heat    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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
cellular component
    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: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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    Ile A:418 - Pro A:419   [ RasMol ]  
 

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  1dg4
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  DNAK_ECOLI | P0A6Y8
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNAK_ECOLI | P0A6Y8: 1bpr 1dkg 1dkx 1dky 1dkz 1q5l 2bpr 2kho 3dpo 3dpp 3dpq 3qnj 4b9q 4e81 4ezn 4ezo 4ezp 4ezq 4ezr 4ezs 4ezt 4ezu 4ezv 4ezw 4ezx 4ezy 4ezz 4f00 4f01 4hy9 4hyb 4jn4 4jne 4jnf 4jwc 4jwd 4jwe 4jwi 4r5g 4r5i 4r5j 4r5k 4r5l

(-) Related Entries Specified in the PDB File

1dkz 1DKZ CONTAINS THE SAME PROTEIN COMPLEXED WITH THE PEPTIDE NRLLLTG
2bpr 2BPR CONTAINS THE SAME PROTEIN INTRAMOLECULARLY BOUND WITH ITS N-TERMINAL TAIL