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(-) Description

Title :  CRYSTAL STRUCTURE OF CHOLINE BINDING PROTEIN OPUBC FROM BACILLUS SUBTILIS
 
Authors :  M. Pittelkow, B. Tschapek, S. H. J. Smits, L. Schmitt, E. Bremer
Date :  22 Mar 11  (Deposition) - 15 Jun 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym./Biol. Unit :  A
Keywords :  Substrate Binding Protein, Choline Binding, Abc-Transporter, Choline, Extracellular, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Pittelkow, B. Tschapek, S. H. Smits, L. Schmitt, E. Bremer
The Crystal Structure Of The Substrate-Binding Protein Opub From Bacillus Subtilis In Complex With Choline.
J. Mol. Biol. V. 411 53 2011
PubMed-ID: 21658392  |  Reference-DOI: 10.1016/J.JMB.2011.05.037

(-) Compounds

Molecule 1 - CHOLINE-BINDING PROTEIN
    Chains: A
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 535025
    Strain: JH642

 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
1CHT1Ligand/IonCHOLINE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:19 , TYR A:71 , ASP A:74 , ASN A:115 , TYR A:117 , TYR A:197 , TYR A:221BINDING SITE FOR RESIDUE CHT A 285

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R6U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:12 -Thr A:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_OPUBC_BACSU_004 *G84ROPUBC_BACSU  ---  ---AG62R
2UniProtVAR_OPUBC_BACSU_005 *D111EOPUBC_BACSU  ---  ---AD89E
3UniProtVAR_OPUBC_BACSU_006 *E146KOPUBC_BACSU  ---  ---AE124K
4UniProtVAR_OPUBC_BACSU_007 *T155NOPUBC_BACSU  ---  ---AT133N
5UniProtVAR_OPUBC_BACSU_008 *G194SOPUBC_BACSU  ---  ---AG172S
6UniProtVAR_OPUBC_BACSU_009 *K252QOPUBC_BACSU  ---  ---AK230Q
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R6U)

(-) Exons   (0, 0)

(no "Exon" information available for 3R6U)

(-) 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:272
 aligned with OPUBC_BACSU | Q45462 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:272
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303  
          OPUBC_BACSU    34 QTIKIGAQSMSESEIIASMLGQLIEHHTDLKTTTIKNLGSNAVQQQALMNGEIDIAATRYTGDALTGTLRMEPEKDPDKALALTQREFKKRYDLKWYDSYGFDNTYAFTVSKELADQYHLETVSDVKKWAPQLKLGVDNYWMKLKGNGYQDFTKTYGMTFGGTYPMQIGLVYDAVKSGKMDIVLAYSTDGRIKSYGLKMLKDDKQFFPPYDCSPVVPEKVLKEHPELEGIIKKMLGKIDTATMQELNYEVDGNLKEPSVVAKEYLEKHRYFE 305
               SCOP domains d3r6ua_ A: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains OpuAC-3r6uA01 A:12-278                                                                                                                                                                                                                                                     ----- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhh....eeeeeehhhhhhhh.......hhhhhhhhhhhhhhhhhheee.........eeeeeehhhhhhhh...hhhhhhhhhh.eeee..hhhhh...hhhhhhhhhh....eeee.hhhhhhhhhhh....eeeee...hhhhhh.eee............eeeeeehhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------R--------------------------E----------------------------------K--------N--------------------------------------S---------------------------------------------------------Q----------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r6u A  12 QTIKIGAQSMSESEIIASMLGQLIEHHTDLKTTTIKNLGSNAVQQQALMNGEIDIAATRYTGDALTGTLRMEPEKDPDKALALTQREFKKRYDLKWYDSYGFDNTYAFTVSKELADQYHLETVSDVKKWAPQLKLGVDNYWMKLKGNGYQDFTKTYGMTFGGTYPMQIGLVYDAVKSGKMDIVLAYSTDGRIKSYGLKMLKDDKQFFPPYDCSPVVPEKVLKEHPELEGIIKKMLGKIDTATMQELNYEVDGNLKEPSVVAKEYLEKHRYFE 283
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 3R6U)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (OPUBC_BACSU | Q45462)
molecular function
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006865    amino acid transport    The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0071705    nitrogen compound transport    The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    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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 Related Entries

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(-) Related Entries Specified in the PDB File

1sw2 CRYSTAL STRUCTURE OF PROX FROM ARCHEOGLOBUS FULGIDUS IN COMPLEX WITH GLYCINE BETAINE
2b4l CRYSTAL STRUCTURE OF THE BINDING PROTEIN OPUAC IN COMPLEX WITH GLYCINE BETAINE