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(-) Description

Title :  CRYSTAL STRUCTURE OF SPIN-LABELED BTUB V10R1 WITH BOUND CALCIUM AND CYANOCOBALAMIN
 
Authors :  D. M. Freed, P. S. Horanyi, M. C. Wiener, D. S. Cafiso
Date :  17 Mar 10  (Deposition) - 15 Sep 10  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, R1, Spin Label, Cell Membrane, Cell Outer Membrane, Ion Transport, Membrane, Metal-Binding, Phage Recognition, Porin, Receptor, Tonb Box, Transmembrane, Transport, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Freed, P. S. Horanyi, M. C. Wiener, D. S. Cafiso
Conformational Exchange In A Membrane Transport Protein Is Altered In Protein Crystals.
Biophys. J. V. 99 1604 2010
PubMed-ID: 20816073  |  Reference-DOI: 10.1016/J.BPJ.2010.06.026

(-) Compounds

Molecule 1 - VITAMIN B12 TRANSPORTER BTUB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BTUB, BFE, CER, DCRC, B3966, JW3938
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1C8E6Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2CA3Ligand/IonCALCIUM ION
3CNC1Ligand/IonCO-CYANOCOBALAMIN
4MTN1Ligand/IonS-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:57 , GLN A:62 , LEU A:63 , SER A:65 , PHE A:67 , GLY A:89 , SER A:91 , SER A:93 , ASN A:185 , TYR A:229 , ASP A:230 , ASN A:276 , THR A:289 , ARG A:497 , TYR A:531 , TYR A:579 , HOH A:842NULL
02AC2SOFTWAREARG A:358 , ARG A:367 , THR A:370 , PHE A:470 , ASP A:471 , THR A:472 , GLY A:473 , C8E A:704NULL
03AC3SOFTWARETRP A:317 , THR A:338 , ASP A:361 , SER A:363 , TYR A:383 , PHE A:422 , TRP A:431NULL
04AC4SOFTWAREILE A:261 , ASN A:302 , ALA A:313 , ILE A:433 , ALA A:466 , THR A:467 , C8E A:702NULL
05AC5SOFTWAREGLY A:344 , LEU A:345 , PHE A:353 , GLY A:355 , THR A:373NULL
06AC6SOFTWARETYR A:256 , GLY A:435 , TYR A:436 , GLY A:463NULL
07AC7SOFTWAREALA A:357NULL
08AC8SOFTWAREASP A:179 , GLN A:191 , ASP A:193 , ASP A:195 , ASP A:230NULL
09AC9SOFTWAREASP A:193 , ASP A:195 , TYR A:229 , ASP A:230NULL
10BC1SOFTWAREHIS A:174 , HIS A:176NULL

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M8D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M8D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M8D)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TONB_DEPENDENT_REC_2PS01156 TonB-dependent receptor proteins signature 2.BTUB_ECOLI597-614  1A:577-594

(-) Exons   (0, 0)

(no "Exon" information available for 3M8D)

(-) 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:583
 aligned with BTUB_ECOLI | P06129 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:588
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606        
           BTUB_ECOLI    27 TLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDVVAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLLDTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF 614
               SCOP domains d3m8da_ A: Outer membrane cobalamin transporter BtuB                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------Plug-3m8dA02 A:18-126                                                                                        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TonB_dep_Rec-3m8dA01 A:370-593                                                                                                                                                                                                  - Pfam domains
         Sec.struct. author .ee.......ee.hhh...eeeeehhhhhhhh..hhhhhhh....eeeee.......eeeee...hhh.eeeee..ee..........hhhhhhhhhh.eeeeee..hhhhhh.....eeeeee......eeeeeeeee...eeeeeeeeeee....eeeeeeeeeeee.....................eeeeeeeeeeeee....eeeeeeeeeeeeeee.............eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeee...........eeeeeeeeeeeeeeeee...eeeeeeeeeeeeee..-----....eeeeeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeee..eeeeeeeeeeee..hhhhhhh.........eeeeeeeeeeeeee..eeeeeeeeeeeeeeeeee.hhhh.eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeee............eeeeeeeeeee..eeeeeeeeee..eeeee......eeeee..eeeeeeeeeee....eeeeeeee..................eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TONB_DEPENDENT_REC PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m8d A   7 TLVCTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDVVAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLLDTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTP-----EDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF 594
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       | -   |   336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586        
                                                                                                                                                                                                                                                                                                                                                       324   330
   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: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M8D)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: MBB (97)
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BTUB_ECOLI | P06129)
molecular function
    GO:0015235    cobalamin transporter activity    Enables the directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0015288    porin activity    Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
biological process
    GO:0015889    cobalamin transport    The directed movement of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    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:0046930    pore complex    Any small opening in a membrane that allows the passage of gases and/or liquids.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BTUB_ECOLI | P06129: 1nqe 1nqf 1nqg 1nqh 1ujw 2gsk 2guf 2ysu 3m8b 3rgm 3rgn

(-) Related Entries Specified in the PDB File

3m8b CRYSTAL STRUCTURE OF SPIN-LABELED BTUB V10R1 IN THE APO STATE