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(-) Description

Title :  STRUCTURAL AND BIOCHEMICAL ANALYSIS OF A PROTOTYPICAL ATPASE FROM THE TYPE III SECRETION SYSTEM OF PATHOGENIC BACTERIA
 
Authors :  R. Zarivach, M. Vuckovic, W. Deng, B. B. Finlay, N. C. J. Strynadka
Date :  19 Dec 06  (Deposition) - 30 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Atpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zarivach, M. Vuckovic, W. Deng, B. B. Finlay, N. C. Strynadka
Structural Analysis Of A Prototypical Atpase From The Type Iii Secretion System.
Nat. Struct. Mol. Biol. V. 14 131 2007
PubMed-ID: 17237797  |  Reference-DOI: 10.1038/NSMB1196

(-) Compounds

Molecule 1 - ESCN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, RESIDUES 103-446
    Gene: ESCN
    Mutation: YES
    Organism Taxid: 574521
    Strain: E2348/69

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:328 , ASP A:333 , HOH A:1003BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWAREGLY A:180 , GLY A:182 , LYS A:183 , SER A:184 , THR A:185 , MET A:189 , LEU A:238 , PHE A:355 , GLN A:426 , SER A:427 , THR A:428 , HOH A:1037 , HOH A:1092 , HOH A:1107BINDING SITE FOR RESIDUE ADP A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:266 -Ser A:267
2Phe A:355 -Pro A:356
3Met A:404 -Gly A:405

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OBM)

(-) Exons   (0, 0)

(no "Exon" information available for 2OBM)

(-) 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:340
 aligned with B7UMA6_ECO27 | B7UMA6 from UniProtKB/TrEMBL  Length:446

    Alignment length:345
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     
         B7UMA6_ECO27   102 FKIRVGDALLGRLIDGIGRPMESNIVAPYLPFERSLYAEPPDPLLRQVIDQPFILGVRAIDGLLTCGIGQRIGIFAGSGVGKSTLLGMICNGASADIIVLALIGERGREVNEFLALLPQSTLSKCVLVVTTSDRPALERMKAAFTATTIAEYFRDQGKNVLLMMDSVTRYARAARDVGLASGEPDVRGGFPPSVFSSLPKLLERAGPAPKGSITAIYTVLLESDNVNDPIGDEVRSILDGHIVLTRELAEENHFPAIDIGLSASRVMHNVVTSEHLRAAAECKKLIATYKNVELLIRIGEYTMGQDPEADKAIKNRKLIQNFIQQSTKDISSYEKTIESLFKVVA 446
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------ATP-synt_ab-2obmA01 A:156-365                                                                                                                                                                                     --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhh..ee.................eeee......----......ee...hhhhhhhh.ee...eeeeee....hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhh..hhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh..ee....eeeeeeeee.......hhhhhhhhhhh.eeee.hhhhhhh...........ee.hhhhh.hhhhhhhhhhhhhhhhh...hhhhhh....-....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2obm A 102 HKIRVGDALLGRLIDGIGRPMESNIVAPYLPFERSLYAEPP----RQVIDQPFILGVRAIDGLLTCGIGQRIGIFAGSGVGKSTLLGMICNGASADIIVLALIGERGREVNEFLALLPQSTLSKCVLVVTTSDRPALERMKAAFTATTIAEYFRDQGKNVLLMMDSVTRYARAARDVGLASGEPDVRGGFPPSVFSSLPKLLERAGPAPKGSITAIYTVLLESDNVNDPIGDEVRSILDGHIVLTRELAEENHFPAIDIGLSASRVMHNVVTSEHLRAAAECKKLIATYKNPELLIRIGEY-MGQDPEADKAIKNRKLIQNFIQQSTKDISSYEKTIESLFKVVA 446
                                   111       121       131       141|    | 151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401| |    411       421       431       441     
                                                                  142  147                                                                                                                                                                                                                                                            402 |                                          
                                                                                                                                                                                                                                                                                                                                        404                                          


Chain A from PDB  Type:PROTEIN  Length:340
 aligned with O52140_ECOLX | O52140 from UniProtKB/TrEMBL  Length:446

    Alignment length:345
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     
         O52140_ECOLX   102 FKIRVGDALLGRLIDGIGRPMESNIVAPYLPFERSLYAEPPDPLLRQVIDQPFILGVRAIDGLLTCGIGQRIGIFAGSGVGKSTLLGMICNGASADIIVLALIGERGREVNEFLALLPQSTLSKCVLVVTTSDRPALERMKAAFTATTIAEYFRDQGKNVLLMMDSVTRYARAARDVGLASGEPDVRGGFPPSVFSSLPKLLERAGPAPKGSITAIYTVLLESDNVNDPIGDEVRSILDGHIVLTRELAEENHFPAIDIGLSASRVMHNVVTSEHLRAAAECKKLIATYKNVELLIRIGEYTMGQDPEADKAIKNRKLIQNFIQQSTKDISSYEKTIESLFKVVA 446
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------ATP-synt_ab-2obmA01 A:156-365                                                                                                                                                                                     --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhh..ee.................eeee......----......ee...hhhhhhhh.ee...eeeeee....hhhhhhhhhhhhh...eeeeeee..hhhhhhhhhh..hhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh..ee....eeeeeeeee.......hhhhhhhhhhh.eeee.hhhhhhh...........ee.hhhhh.hhhhhhhhhhhhhhhhh...hhhhhh....-....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2obm A 102 HKIRVGDALLGRLIDGIGRPMESNIVAPYLPFERSLYAEPP----RQVIDQPFILGVRAIDGLLTCGIGQRIGIFAGSGVGKSTLLGMICNGASADIIVLALIGERGREVNEFLALLPQSTLSKCVLVVTTSDRPALERMKAAFTATTIAEYFRDQGKNVLLMMDSVTRYARAARDVGLASGEPDVRGGFPPSVFSSLPKLLERAGPAPKGSITAIYTVLLESDNVNDPIGDEVRSILDGHIVLTRELAEENHFPAIDIGLSASRVMHNVVTSEHLRAAAECKKLIATYKNPELLIRIGEY-MGQDPEADKAIKNRKLIQNFIQQSTKDISSYEKTIESLFKVVA 446
                                   111       121       131       141|    | 151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401| |    411       421       431       441     
                                                                  142  147                                                                                                                                                                                                                                                            402 |                                          
                                                                                                                                                                                                                                                                                                                                        404
   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 2OBM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (13, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O52140_ECOLX | O52140)
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:0046961    proton-transporting ATPase activity, rotational mechanism    Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out), by a rotational mechanism.
biological process
    GO:0006754    ATP biosynthetic process    The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0044780    bacterial-type flagellum assembly    The assembly of a bacterial-type flagellum, a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope which functions in cell motility.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    GO:0030254    protein secretion by the type III secretion system    The process in which proteins are transferred into the extracellular milieu or directly into host cells by the bacterial type III secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030257    type III protein secretion system complex    A complex of approximately 20 proteins, most of which are located in the cytoplasmic membrane that carries out protein secretion in the bacterial type III secretion system; type III secretion also requires a cytoplasmic, probably membrane-associated ATPase.

Chain A   (B7UMA6_ECO27 | B7UMA6)
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: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:0046961    proton-transporting ATPase activity, rotational mechanism    Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out), by a rotational mechanism.
biological process
    GO:0006754    ATP biosynthetic process    The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0044780    bacterial-type flagellum assembly    The assembly of a bacterial-type flagellum, a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope which functions in cell motility.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    GO:0030254    protein secretion by the type III secretion system    The process in which proteins are transferred into the extracellular milieu or directly into host cells by the bacterial type III secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030257    type III protein secretion system complex    A complex of approximately 20 proteins, most of which are located in the cytoplasmic membrane that carries out protein secretion in the bacterial type III secretion system; type III secretion also requires a cytoplasmic, probably membrane-associated ATPase.

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(-) Related Entries Specified in the PDB File

2obl STRUCTURAL AND BIOCHEMICAL ANALYSIS OF A PROTOTYPICAL ATPASE FROM THE TYPE III SECRETION SYSTEM OF PATHOGENIC BACTERIA