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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FIRST NUCELOTIDE BINDING DOMAIN OF CLPB
 
Authors :  L. Jingzhi, S. Bingdong
Date :  05 Jun 01  (Deposition) - 05 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Li, B. Sha
Crystal Structure Of E. Coli Hsp100 Clpb Nucleotide-Binding Domain 1 (Nbd1) And Mechanistic Studies On Clpb Atpase Activity.
J. Mol. Biol. V. 318 1127 2002
PubMed-ID: 12054807  |  Reference-DOI: 10.1016/S0022-2836(02)00188-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLPB PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FIRST NUCLEOTIDE BINDING DOMAIN (RESIDUES 159- 351)
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: HEAT SHOCK PROTEIN F84.1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:209 , GLY A:211 , LYS A:212BINDING SITE FOR RESIDUE MG A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JBK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLPAB_1PS00870 Chaperonins clpA/B signature 1.CLPB_ECOLI294-306  1A:294-306

(-) Exons   (0, 0)

(no "Exon" information available for 1JBK)

(-) 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:189
 aligned with CLPB_ECOLI | P63284 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:195
                                   166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346     
           CLPB_ECOLI   157 QRQALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILR 351
               SCOP domains d1jbka_ A: ClpB, AAA+ modules                                                                                                                                                                       SCOP domains
               CATH domains 1jbkA00 A:157-351 P-loop containing nucleotide triphosphate hydrolases                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------AAA-1jbkA01 A:202-341                                                                                                                       ---------- Pfam domains
         Sec.struct. author .hhhhhhheeehhhhhhh........hhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhh..hhhhh..eeeeehhhhhhh...hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh..------..hhhhhhhhhhh....eeeeehhhhhhhhh..hhhhhh.eeeee....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------CLPAB_1      --------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jbk A 157 HMQALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGA------MDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILR 351
                                   166       176       186       196       206       216       226       236       246       256       266       276       286      |296       306       316       326       336       346     
                                                                                                                                                           286    293
   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)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CLPB_ECOLI | P63284)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042623    ATPase activity, coupled    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
biological process
    GO:0019538    protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    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.
    GO:0006986    response to unfolded protein    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 an unfolded protein stimulus.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CLPB_ECOLI | P63284: 1khy 4ciu 4d2q 4d2u 4d2x

(-) Related Entries Specified in the PDB File

1nbd 1NBD BELONGS TO THE AAA ATPASE FAMILY