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(-) Description

Title :  PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB WITH UREA BOUND
 
Authors :  J. N. Henderson, E. G. Sweeney, J. Goers, C. Wreden, K. G. Hicks, R. Parth K. J. Guillemin, S. J. Remington
Date :  23 Oct 11  (Deposition) - 27 Jun 12  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homodimer, Four-Helix Bundle, Pas Domain, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Goers Sweeney, J. N. Henderson, J. Goers, C. Wreden, K. G. Hicks, J. K. Foster, R. Parthasarathy, S. J. Remington, K. Guillemin
Structure And Proposed Mechanism For The Ph-Sensing Helicobacter Pylori Chemoreceptor Tlpb.
Structure V. 20 1177 2012
PubMed-ID: 22705207  |  Reference-DOI: 10.1016/J.STR.2012.04.021

(-) Compounds

Molecule 1 - CHEMORECEPTOR TLPB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBH4
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PERIPLASMIC PORTION
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 102617
    Strain: SS1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO43Ligand/IonSULFATE ION
4URE2Ligand/IonUREA

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:103 , ASP A:114 , TYR A:136 , TYR A:140 , TYR A:153 , LYS A:166 , HOH A:407BINDING SITE FOR RESIDUE URE A 301
02AC2SOFTWARELYS A:54 , ARG A:55 , THR A:58 , MET A:99 , HOH A:450 , LYS B:54 , SO4 B:302 , HOH B:641 , HOH B:669BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREGLN A:68 , HIS A:71 , HOH A:667 , HOH A:679 , ARG B:92BINDING SITE FOR RESIDUE PEG A 303
04AC4SOFTWAREGLN A:68 , HIS A:71 , HOH A:417 , HOH A:667 , ARG B:92BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREGLY A:98 , MET A:99 , GLU A:192 , HOH A:511 , HOH A:593 , HOH A:613BINDING SITE FOR RESIDUE GOL A 305
06AC6SOFTWARETYR A:52 , TYR A:186 , HOH A:493BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWARELYS A:119 , GLN A:123 , ASN B:108BINDING SITE FOR RESIDUE GOL A 307
08AC8SOFTWAREVAL A:134 , TYR A:135 , HOH A:488 , HOH A:616 , HOH A:638 , HOH A:652BINDING SITE FOR RESIDUE GOL A 308
09AC9SOFTWAREVAL B:103 , ASP B:114 , TYR B:136 , TYR B:140 , TYR B:153 , LYS B:166 , HOH B:403BINDING SITE FOR RESIDUE URE B 301
10BC1SOFTWARELYS A:54 , SO4 A:302 , LYS B:54 , ARG B:55 , THR B:58 , HOH B:439 , HOH B:641 , HOH B:669BINDING SITE FOR RESIDUE SO4 B 302
11BC2SOFTWAREASN B:94 , ASP B:95 , LYS B:157 , GOL B:307 , HOH B:411 , HOH B:430 , HOH B:438 , HOH B:486 , HOH B:498 , HOH B:523 , HOH B:539 , HOH B:602BINDING SITE FOR RESIDUE GOL B 303
12BC3SOFTWARELYS B:97 , GLY B:98 , MET B:99 , GLU B:192 , HOH B:409 , HOH B:517 , HOH B:651 , HOH B:658BINDING SITE FOR RESIDUE GOL B 304
13BC4SOFTWARETYR B:52 , LYS B:165 , HOH B:613BINDING SITE FOR RESIDUE GOL B 305
14BC5SOFTWARETYR B:158 , HOH B:429 , HOH B:676BINDING SITE FOR RESIDUE GOL B 306
15BC6SOFTWARETYR B:158 , GOL B:303 , HOH B:438 , HOH B:523 , HOH B:602BINDING SITE FOR RESIDUE GOL B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UB6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UB6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UB6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UB6)

(-) Exons   (0, 0)

(no "Exon" information available for 3UB6)

(-) 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:164
 aligned with B6JPK4_HELP2 | B6JPK4 from UniProtKB/TrEMBL  Length:561

    Alignment length:164
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196    
         B6JPK4_HELP2    37 LAQLMEHLETGQYKKREKTLAYMTKILEQGIHEYYKNFDNATARKMALDYFKRINDDKGMIYMVVVDKNGVVLFDPVNPKTVGQSGLDAQSVDGVYYVRGYLEAAKKGGGYTYYKMPKYDGGVPEKKFAYSHYDEVSQMVIAATSYYTDINTENQAIKEGVNKV 200
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eee...hhhhh.............hhhhhhhhhhhh..eeeeeee........eeeeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ub6 A  40 LAQLMEHLETGQYKKREKTLAYMTKILEQGIHEYYKSFDNDTARKMALDYFKRINDDKGMIYMVVVDKNGVVLFDPVNPKTVGQSGLDAQSVDGVYYVRGYLEAAKKGGGYTYYKMPKYDGGVPEKKFAYSHYDEVSQMVIAATSYYTDINTENKAIKEGVNKV 203
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199    


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with B6JPK4_HELP2 | B6JPK4 from UniProtKB/TrEMBL  Length:561

    Alignment length:164
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196    
         B6JPK4_HELP2    37 LAQLMEHLETGQYKKREKTLAYMTKILEQGIHEYYKNFDNATARKMALDYFKRINDDKGMIYMVVVDKNGVVLFDPVNPKTVGQSGLDAQSVDGVYYVRGYLEAAKKGGGYTYYKMPKYDGGVPEKKFAYSHYDEVSQMVIAATSYYTDINTENQAIKEGVNKV 200
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...eeeeee....eee...hhhhh.............hhhhhhhhhhhh..eeeeeee........eeeeeeeeee....eeeeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ub6 B  40 LAQLMEHLETGQYKKREKTLAYMTKILEQGIHEYYKSFDNDTARKMALDYFKRINDDKGMIYMVVVDKNGVVLFDPVNPKTVGQSGLDAQSVDGVYYVRGYLEAAKKGGGYTYYKMPKYDGGVPEKKFAYSHYDEVSQMVIAATSYYTDINTENKAIKEGVNKV 203
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
   Legend:   → Mismatch (orange background)
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  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 3UB6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UB6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UB6)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B6JPK4_HELP2 | B6JPK4)
molecular function
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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.

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 Related Entries

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

UniProtKB/TrEMBL
        B6JPK4_HELP2 | B6JPK4: 3ub7 3ub8 3ub9

(-) Related Entries Specified in the PDB File

3ub7 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB WITH ACETAMIDE BOUND
3ub8 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB WITH FORMAMIDE BOUND
3ub9 PERIPLASMIC PORTION OF THE HELICOBACTER PYLORI CHEMORECEPTOR TLPB WITH HYDROXYUREA BOUND