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(-) Description

Title :  IN MESO CRYSTAL STRUCTURE OF THE COBALAMIN TRANSPORTER, BTUB
 
Authors :  M. Caffrey, V. Cherezov, E. Yamashita, W. A. Cramer
Date :  29 Apr 06  (Deposition) - 05 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Cubic Mesophase, Cobalamin, Btub, Colicin, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Cherezov, E. Yamashita, W. Liu, M. Zhalnina, W. A. Cramer, M. Caffre
In Meso Structure Of The Cobalamin Transporter, Btub, At 1. 95 A Resolution.
J. Mol. Biol. V. 364 716 2006
PubMed-ID: 17028020  |  Reference-DOI: 10.1016/J.JMB.2006.09.022

(-) Compounds

Molecule 1 - VITAMIN B12 TRANSPORTER BTUB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: COBALAMIN RECEPTOR, OUTER MEMBRANE COBALAMIN TRANSLOCATOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MPG11Ligand/Ion1-MONOOLEOYL-RAC-GLYCEROL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:214 , TYR A:256 , ASN A:302 , LEU A:342 , ALA A:466 , VAL A:479 , TYR A:481 , MPG A:704 , MPG A:705BINDING SITE FOR RESIDUE MPG A 701
02AC2SOFTWAREILE A:140 , SER A:141 , ALA A:142 , VAL A:154 , ASP A:171 , LYS A:200 , THR A:201 , LEU A:202 , GLY A:222 , ASP A:224 , LEU A:559 , GLY A:590 , TYR A:592BINDING SITE FOR RESIDUE MPG A 702
03AC3SOFTWARELEU A:254 , SER A:263 , VAL A:298 , TRP A:300 , VAL A:315 , THR A:338 , TYR A:383 , HOH A:1143 , HOH A:1153BINDING SITE FOR RESIDUE MPG A 703
04AC4SOFTWAREASN A:302 , ALA A:313 , GLY A:314 , ALA A:357 , ARG A:358 , GLY A:369 , THR A:370 , TRP A:371 , THR A:391 , TRP A:431 , ALA A:468 , PHE A:470 , THR A:472 , MPG A:701 , MPG A:705 , MPD A:904BINDING SITE FOR RESIDUE MPG A 704
05AC5SOFTWAREILE A:311 , GLY A:344 , ALA A:357 , TRP A:371 , THR A:472 , HIS A:477 , VAL A:479 , VAL A:503 , TYR A:505 , MPG A:701 , MPG A:704BINDING SITE FOR RESIDUE MPG A 705
06AC6SOFTWARETYR A:296 , TRP A:317 , LYS A:319BINDING SITE FOR RESIDUE MPG A 706
07AC7SOFTWAREGLY A:307 , GLN A:346 , TYR A:520 , TYR A:522 , SER A:545 , MPG A:711 , HOH A:1133 , HOH A:1156BINDING SITE FOR RESIDUE MPG A 707
08AC8SOFTWARETHR A:138 , VAL A:154 , TYR A:221 , GLN A:248 , PHE A:594 , HOH A:1103BINDING SITE FOR RESIDUE MPG A 708
09AC9SOFTWARELEU A:160 , GLY A:161 , ASP A:162 , LYS A:163 , THR A:164 , HIS A:208 , GLY A:216 , PHE A:217 , TYR A:586BINDING SITE FOR RESIDUE MPG A 709
10BC1SOFTWARETHR A:373 , SER A:374 , ALA A:375 , ALA A:387 , SER A:388 , GLU A:419 , GLY A:420 , ALA A:421 , MPG A:711BINDING SITE FOR RESIDUE MPG A 710
11BC2SOFTWAREGLN A:346 , THR A:373 , TYR A:389 , LYS A:416 , TRP A:418 , MPG A:707 , MPG A:710BINDING SITE FOR RESIDUE MPG A 711
12BC3SOFTWARETHR A:30 , ARG A:31 , GLN A:105 , ARG A:106 , HOH A:1162BINDING SITE FOR RESIDUE FMT A 801
13BC4SOFTWAREASN A:86 , ASP A:95 , TYR A:223 , SER A:272 , MET A:293 , HOH A:999 , HOH A:1051BINDING SITE FOR RESIDUE MPD A 901
14BC5SOFTWAREGLN A:318 , GLN A:320 , GLN A:335 , ASN A:337 , ALA A:395 , ASN A:397 , HOH A:1167BINDING SITE FOR RESIDUE MPD A 902
15BC6SOFTWARESER A:91 , ALA A:94 , TYR A:405 , TYR A:446 , TYR A:453 , HOH A:1026BINDING SITE FOR RESIDUE MPD A 903
16BC7SOFTWARESER A:286 , SER A:359 , HIS A:368 , GLY A:369 , ALA A:427 , ASP A:471 , MPG A:704BINDING SITE FOR RESIDUE MPD A 904

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:534 -Pro A:535

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:582-594

(-) Exons   (0, 0)

(no "Exon" information available for 2GUF)

(-) 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:551
 aligned with BTUB_ECOLI | P06129 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:594
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610    
           BTUB_ECOLI    21 QDTSPDTLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDVVAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLLDTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF 614
               SCOP domains d2gufa_ A: Outer membrane cobalamin transporter BtuB                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------2gufA01 A:7-130 Ferric Hydroxamate Uptake Protein;       Chain A, domain 1                                                  2gufA02 A:131-594  [code=2.40.170.20, no name                   defined]                                                                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee.......ee.hhh...eeeeehhhhhhhh...hhhhhh....eeee.------..eeee..ee.hhheeee..ee......hhhhhhhhhhhhhh.eeeeee..hhhhhh.....eeeeee......eeeeeeeee...eeeeeeeeeee....eeeeeeeeeeee.------------------..eeeeeeeeeeeee....eeeeeeeeeeeeee..-----------.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeee...........eeeeeeeeeeeeeeeee...eeeeeeeeeeeeeee....hhhhheeeeeeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeee..eeeeeeeeeeee..hhhhhhh.........eeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeee............eeeeeeeeeee..eeeeeeeeee..eeeee......eeeee..eeeeeeeeeee....eeeeeeee.......--------...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TONB_DEPENDENT_REC PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2guf A   1 QDTSPDTLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQ------LSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTH------------------DGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNY-----------DTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDY--------AGREYTLSGSYTF 594
                                    10        20        30        40        50     |   -  |     70        80        90       100       110       120       130       140       150       160       170     |   -         -    |  200       210       220        |-         -|      250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570  |      - |     590    
                                                                                  56     63                                                                                                              176                195                               229         241                                                                                                                                                                                                                                                                                                                                         573      582
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GUF)

(-) 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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  2guf
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  BTUB_ECOLI | P06129
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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 2ysu 3m8b 3m8d 3rgm 3rgn

(-) Related Entries Specified in the PDB File

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