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(-) Description

Title :  CRYSTAL STRUCTURE OF HELICOBACTER PYLORI ATP DEPENDENT PROTEASE, FTSH
 
Authors :  S. H. Kim, G. B. Kang, H. -E. Song, S. J. Park, M. -H. Bae, S. H. Eom
Date :  05 Sep 07  (Deposition) - 09 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ftsh, Atpase Domain, Helicobacter Pylori, Atp-Binding, Cell Cycle, Cell Division, Hydrolase, Membrane, Metal-Binding, Metalloprotease, Nucleotide-Binding, Protease, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. H. Kim, G. B. Kang, H. -E. Song, S. J. Park, M. -H. Bea, S. H. Eom
Structural Studies On Helicobacter Pyloriatp-Dependent Protease, Ftsh
J. Synchrotron Radiat. V. 15 208 2008
PubMed-ID: 18421140  |  Reference-DOI: 10.1107/S090904950706846X

(-) Compounds

Molecule 1 - CELL DIVISION PROTEASE FTSH HOMOLOG
    ChainsA, B
    EC Number3.4.24.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentATPASE DOMAIN, UNP RESIDUES 160-419
    GeneFTSH
    MutationYES
    Organism CommonCAMPYLOBACTER PYLORI
    Organism ScientificHELICOBACTER PYLORI
    Organism Taxid210

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2R62)

(-) Sites  (0, 0)

(no "Site" information available for 2R62)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R62)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:262 -Pro A:263
2Ala B:262 -Pro B:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R62)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AAAPS00674 AAA-protein family signature.FTSH_HELPY311-329
 
  2A:311-329
B:311-329
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AAAPS00674 AAA-protein family signature.FTSH_HELPY311-329
 
  1A:311-329
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AAAPS00674 AAA-protein family signature.FTSH_HELPY311-329
 
  1-
B:311-329

(-) Exons   (0, 0)

(no "Exon" information available for 2R62)

(-) Sequences/Alignments

Asymmetric 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:249
 aligned with FTSH_HELPY | P71408 from UniProtKB/Swiss-Prot  Length:632

    Alignment length:259
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409         
           FTSH_HELPY   160 INAEKPNVRFNDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKEVRQQHLKEAVERGIAGLEK 418
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhh............................hhhhhhhh...eeee.hhhhh..----------.........................eeee........hhhhhh................hhhhhhhhhh.....................hhhhhhhhhhhhhhh.........hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------AAA  PDB: A:311-329----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r62 A 160 INAEKPNVRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGK----------NDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKEVRQQHLKEAVERGIAGLEK 418
                                   169       179       189       199       209       219       229       239       249       259       269      |  -       289       299       309       319       329       339       349       359       369       379       389       399       409         
                                                                                                                                              276        287                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with FTSH_HELPY | P71408 from UniProtKB/Swiss-Prot  Length:632

    Alignment length:259
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409         
           FTSH_HELPY   160 INAEKPNVRFNDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKEVRQQHLKEAVERGIAGLEK 418
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------AAA-2r62B01 B:206-341                                                                                                                   -----------------------------------------------------------Peptidase_M41-2r62 Pfam domains (1)
           Pfam domains (2) ----------------------------------------------AAA-2r62B02 B:206-341                                                                                                                   -----------------------------------------------------------Peptidase_M41-2r62 Pfam domains (2)
         Sec.struct. author ................hhhhhhhhhhhhhhhh...hhhhh.....eeeee.....hhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh...eee.hhhhhh.----------.........hhhhhh...........eeeee.hhhhh......................hhhhh.hhhhh...........hhhhhh.....hhhhhhhhhhhhhh............hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------AAA  PDB: B:311-329----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r62 B 160 INAEKPNVRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGK----------NDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKEVRQQHLKEAVERGIAGLEK 418
                                   169       179       189       199       209       219       229       239       249       259       269      |  -       289       299       309       319       329       339       349       359       369       379       389       399       409         
                                                                                                                                              276        287                                                                                                                                   

   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 2R62)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R62)

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FTSH_HELPY | P71408)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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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  Cis Peptide Bonds
    Ala A:262 - Pro A:263   [ RasMol ]  
    Ala B:262 - Pro B:263   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        FTSH_HELPY | P714082r65

(-) Related Entries Specified in the PDB File

2r65 THE SAME PROTEIN IN COMPLEX WITH ADP