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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI CLPX
 
Authors :  D. Y. Kim, K. K. Kim
Date :  25 Sep 03  (Deposition) - 23 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Clpp Binding Loop, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Y. Kim, K. K. Kim
Crystal Structure Of Clpx Molecular Chaperone From Helicobacter Pylori
J. Biol. Chem. V. 278 50664 2003
PubMed-ID: 14514695  |  Reference-DOI: 10.1074/JBC.M305882200

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21(DE3), B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 71-446
    Gene: CLPX
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695

 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
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:92 , VAL A:93 , ILE A:94 , THR A:151 , GLY A:152 , SER A:153 , GLY A:154 , LYS A:155 , THR A:156 , LEU A:157 , ILE A:351 , ALA A:395 , ARG A:396BINDING SITE FOR RESIDUE ADP A 487

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UM8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UM8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UM8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UM8)

(-) Exons   (0, 0)

(no "Exon" information available for 1UM8)

(-) 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:327
 aligned with CLPX_HELPY | O25926 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:364
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434    
           CLPX_HELPY    75 LLSYIPAPKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIEDFCLDIMFDLPKLKGSEVRITKDCVLKQAEPLIIA 438
               SCOP domains d1um8a_ A: ClpX                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1um8A01 A:75-341 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                      1um8A02 A:342-438  [code=1.10.8.60, no name defined]                                              CATH domains
               Pfam domains -----------------------------------------------------------------AAA_2-1um8A01 A:140-337                                                                                                                                                                               -----ClpB_D2-small-1um8A02 A:343-424                                                   -------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhh...eeeee.hhh.--------.hhhhhhhhhhh..hhhhhh..eeeee.hhhh--------------hhhhhhhhhhhhhh.ee.---------------.ee....eeeeee...hhhhhh.......................hhhhhhhhhhhhh..hhhhhh...eeee....hhhhhhhhhhh...hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeehhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1um8 A  75 LLSYIPAPKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPIAISDATSLT--------VENILTRLLQASDWNVQKAQKGIVFIDEIDKI--------------GEGVQQALLKIVEGSLVN---------------QIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIEDFCLDIMFDLPKLKGSEVRITKDCVLKQAEPLIIA 438
                                    84        94       104       114       124       134       144       154       164       174    |    -   |   194       204       214    |    -       234       244      |  -         -  |    274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434    
                                                                                                                                  179      188                            219            234              251             267
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: ClpB_D2-small] (9)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CLPX_HELPY | O25926)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    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: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.

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