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(-) Description

Title :  STRUCTURE OF THE COMPLEX BETWEEN BTUB AND COLICIN E3 RECEPTOR BINDING DOMAIN
 
Authors :  G. Kurisu, S. D. Zakharov, M. V. Zhalnina, S. Bano, V. Y. Eroukova, T. I. Rokitskaya, Y. N. Antonenko, M. C. Wiener, W. A. Cramer
Date :  12 Aug 03  (Deposition) - 25 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Barrel, Coiled-Coil, Transport Protein-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Kurisu, S. D. Zakharov, M. V. Zhalnina, S. Bano, V. Y. Eroukova, T. I. Rokitskaya, Y. N. Antonenko, M. C. Wiener, W. A. Cramer
The Structure Of Btub With Bound Colicin E3 R-Domain Implie A Translocon
Nat. Struct. Biol. V. 10 948 2003
PubMed-ID: 14528295  |  Reference-DOI: 10.1038/NSB997

(-) Compounds

Molecule 1 - VITAMIN B12 RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJC3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: COBALAMIN TRANSPORTER
 
Molecule 2 - COLICIN E3
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-216(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: R-DOMAIN(RESIDUES 314-448)
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: COLICIN E3 A CHAIN, RIBONUCLEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric/Biological Unit (5, 20)
No.NameCountTypeFull Name
1AAE1Ligand/IonACETOACETIC ACID
2GOL8Ligand/IonGLYCEROL
3GP12Ligand/IonGLUCOSAMINE 1-PHOSPHATE
4LDA7Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
5LIM2Ligand/Ion3-OXO-PENTADECANOIC ACID

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:317 , ARG A:336 , ASN A:337 , THR A:338 , ASP A:361 , AAE A:802 , LIM A:803BINDING SITE FOR RESIDUE GP1 A 801
02AC2SOFTWARESER A:146 , ASN A:147 , SER A:148 , LIM A:812BINDING SITE FOR RESIDUE GP1 A 811
03AC3SOFTWARETRP A:144 , GLY A:145 , VAL A:551 , GLY A:563 , LEU A:588 , GP1 A:811BINDING SITE FOR RESIDUE LIM A 812
04AC4SOFTWAREGLY A:204 , ALA A:205 , VAL A:218 , TRP A:250 , TYR A:269 , LDA A:605BINDING SITE FOR RESIDUE LDA A 601
05AC5SOFTWAREGLY A:204 , GLY A:220 , GLN A:248 , ASN A:302 , LDA A:603BINDING SITE FOR RESIDUE LDA A 602
06AC6SOFTWARETYR A:152 , VAL A:154 , LYS A:200 , THR A:201 , GLY A:222 , TYR A:223 , ASP A:224 , ILE A:261 , LDA A:602 , LDA A:607BINDING SITE FOR RESIDUE LDA A 603
07AC7SOFTWARETHR A:156 , GLN A:158 , ASN A:302 , ALA A:313 , VAL A:315 , ASP A:361 , LDA A:606BINDING SITE FOR RESIDUE LDA A 604
08AC8SOFTWARETRP A:250 , GLY A:344 , GLY A:355 , LDA A:601BINDING SITE FOR RESIDUE LDA A 605
09AC9SOFTWARETYR A:172 , TYR A:256 , SER A:263 , ASN A:302 , LDA A:604 , LDA A:607BINDING SITE FOR RESIDUE LDA A 606
10BC1SOFTWARETYR A:152 , TYR A:172 , SER A:263 , LDA A:603 , LDA A:606BINDING SITE FOR RESIDUE LDA A 607
11BC2SOFTWAREARG A:336 , GP1 A:801BINDING SITE FOR RESIDUE AAE A 802
12BC3SOFTWARETRP A:300 , THR A:338 , PHE A:594 , GP1 A:801BINDING SITE FOR RESIDUE LIM A 803
13BC4SOFTWAREASN A:72 , ALA A:73 , SER A:74BINDING SITE FOR RESIDUE GOL A 701
14BC5SOFTWARELEU A:103 , GLN A:105 , THR A:131 , SER A:155 , TYR A:203BINDING SITE FOR RESIDUE GOL A 702
15BC6SOFTWARETHR A:7 , ARG A:106BINDING SITE FOR RESIDUE GOL A 703
16BC7SOFTWARETYR A:256 , GLY A:258 , GLU A:259 , LEU A:260BINDING SITE FOR RESIDUE GOL A 704
17BC8SOFTWARELYS A:273 , TYR A:275BINDING SITE FOR RESIDUE GOL A 705
18BC9SOFTWAREARG A:367 , GLY A:369BINDING SITE FOR RESIDUE GOL A 706
19CC1SOFTWARESER A:545 , LYS A:571BINDING SITE FOR RESIDUE GOL A 707
20CC2SOFTWARETHR A:556 , HIS A:558 , TYR A:592BINDING SITE FOR RESIDUE GOL A 708

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UJW)

(-) 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 1UJW)

(-) 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 1UJW)

(-) 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:576
 aligned with BTUB_ECOLI | P06129 from UniProtKB/Swiss-Prot  Length:614

    Alignment length:591
                                    33        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       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613 
           BTUB_ECOLI    24 SPDTLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDVVAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLLDTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF 614
               SCOP domains d1ujwa_ A: Outer membrane cobalamin transporter BtuB                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ---1ujwA01 A:7-130 Ferric Hydroxamate Uptake Protein; Chain A, domain 1                                                        1ujwA02 A:131-594  [code=2.40.170.20, no name d               efined]                                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------Plug-1ujwA02 A:18-126                                                                                        ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TonB_dep_Rec-1ujwA01 A:370-593                                                                                                                                                                                                  - Pfam domains
         Sec.struct. author ....ee.......ee.......eeeeehhhhhhhh..hhhhhhh....eeeee.......eeeee...hhhhheeee..ee.hhhh..........hhhhh.eeeeee..hhhhhh.....eeeeee......eeeeeeeee...eeeeeeeeeee....eeeeeeeeeee...---------------.....eeeeeeeeeeee....eeeeeeeeeeeeeee.............eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeee...........eeeeeeeeeeeeeeeee...eeeeeeeeeeeeee...........eeeeeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeee..eeeeeeeeeeee..hhhhhhh.........eeeeeeeeeeeeee..eeeeeeeeeeeee...eee....eee....eeeeeeeeeeeeee..eee..eeeeeeeee............eeeeeeeeeee..eeeeeeeeee..ee............ee..eeeeeeeeeee....eeeeeeee..................eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TONB_DEPENDENT_REC PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ujw A   4 SPDTLVVTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHG---------------DNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLLDTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF 594
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173   |     -       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593 
                                                                                                                                                                                                       177             193                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with CEA3_ECOLX | P00646 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:116
                                   332       342       352       362       372       382       392       402       412       422       432      
           CEA3_ECOLX   323 YERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRKKKEDK 438
               SCOP domains d1ujwb_ B: Colicin E3 receptor domain                                                                                SCOP domains
               CATH domains 1ujwB00 B:323-438 Helix Hairpins                                                                                     CATH domains
               Pfam domains E2R135-1ujwB01 B:323-438                                                                                             Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1ujw B 323 YERARAELNQANEDVARNQERQAKAVQVYNSRKSELDAANKTLADAIAEIKQFNRFAHDPMAGGHRMWQMAGLKAQRAQTDVNNKQAAFDAAAKEKSDADAALSSAMESRKKKEDK 438
                                   332       342       352       362       372       382       392       402       412       422       432
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Coiled coil proteins (689)
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: MBB (97)
(-)
Clan: Ubiquitin (279)
(-)
Clan: no clan defined [family: E2R135] (3)

(-) Gene Ontology  (24, 24)

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.

Chain B   (CEA3_ECOLX | P00646)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a chromosome.

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    Tyr A:534 - Pro A:535   [ RasMol ]  
 

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  1ujw
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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 2gsk 2guf 2ysu 3m8b 3m8d 3rgm 3rgn
        CEA3_ECOLX | P00646: 1e44 1jch 2b5u 4udm 4v5k

(-) Related Entries Specified in the PDB File

1jch COLICIN E3
1nqe COBALAMIN TRANSPORTER