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(-) Description

Title :  STRUCTURE OF THE CHARGE-TRANSFER INTERMEDIATE OF THE TRANSMEMBRANE REDOX CATALYST DSBB
 
Authors :  G. Malojcic, R. L. Owen, R. Glockshuber
Date :  22 Aug 08  (Deposition) - 25 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.70
Chains :  Asym. Unit :  B,C,E,F
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  E,F  (1x)
Keywords :  Membrane Protein Complex, Mechanism Of Disulfide Bond Formation, Oxidative Protein Folding In Escherichia Coli Periplasm, X-Ray Crystal Structure, Charge Transfer Reaction Intermediate, Four Helix Bundle, Periplasm, Redox- Active Center, Cell Inner Membrane, Cell Membrane, Chaperone, Electron Transport, Membrane, Oxidoreductase, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Malojcic, R. L. Owen, J. P. Grimshaw, R. Glockshuber
Preparation And Structure Of The Charge-Transfer Intermediate Of The Transmembrane Redox Catalyst Dsbb.
Febs Lett. V. 582 3301 2008
PubMed-ID: 18775700  |  Reference-DOI: 10.1016/J.FEBSLET.2008.07.063
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOL/DISULFIDE OXIDOREDUCTASE DSBA
    Chains: B, E
    EC Number: 1.8.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDSBA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DSBA, DSF, PPFA, B3860, JW3832
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: BL21(DE3)
 
Molecule 2 - THIOL/DISULFIDE OXIDOREDUCTASE DSBB
    Chains: C, F
    EC Number: 1.8.5.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDSBB
    Expression System Strain: HM125
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DSBB, ROXB, YCGA, B1185, JW5182
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: HM125
    Synonym: DISULFIDE BOND FORMATION PROTEIN B

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : BCEF
Biological Unit 1 (1x): BC  
Biological Unit 2 (1x):   EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1UQ12Ligand/IonUBIQUINONE-1
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1UQ11Ligand/IonUBIQUINONE-1
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1UQ11Ligand/IonUBIQUINONE-1

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS C:39 , CYS C:41 , CYS C:44 , GLU C:47 , ARG C:48 , HIS C:91 , MET C:142 , LEU C:146BINDING SITE FOR RESIDUE UQ1 C 501
2AC2SOFTWARELYS F:39 , PRO F:40 , CYS F:41 , CYS F:44 , GLU F:47 , ARG F:48 , HIS F:91 , MET F:142 , LEU F:146BINDING SITE FOR RESIDUE UQ1 F 501

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1B:30 -C:104
2E:30 -F:104

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val B:150 -Pro B:151
2Val E:150 -Pro E:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E9J)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.DSBA_ECOLI41-59
 		  2B:22-40
E:22-40
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.DSBA_ECOLI41-59
 		  1B:22-40
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.DSBA_ECOLI41-59
 		  1-
E:22-40

(-) Exons   (0, 0)

(no "Exon" information available for 3E9J)

(-) Sequences/Alignments

Asymmetric 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 B from PDB  Type:PROTEIN  Length:188
 aligned with DSBA_ECOLI | P0AEG4 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:188
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199        
           DSBA_ECOLI    20 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 207
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3e9jB00 B:1-188 Glutaredoxin                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................ee......hhhhhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..........ee...ee.........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e9j B   1 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHAYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain C from PDB  Type:PROTEIN  Length:134
 aligned with DSBB_ECOLI | P0A6M2 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:149
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153         
           DSBB_ECOLI    14 AWLLMAFTALALELTALWFQHVMLLKPCVLCIYERCALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.....................hhhhhh..hhhhhhhhhhhhhhhhhh................hhhhhh.......---------------hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e9j C  14 AWLLMAFTALALELTALWFQHVMLLKPCVLCIYERVALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVA---------------MPQWLLGIFIAYLIVAVLVVI 162
                                    23        33        43        53        63        73        83        93       103       113       123  |      -       143       153         
                                                                                                                                          126             142                    


Chain E from PDB  Type:PROTEIN  Length:188
 aligned with DSBA_ECOLI | P0AEG4 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:188
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199        
           DSBA_ECOLI    20 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 207
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3e9jE00 E:1-188 Glutaredoxin                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................ee......hhhhhhhhhh.hhhhhhhhhh...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..........ee...ee.........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e9j E   1 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHAYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        


Chain F from PDB  Type:PROTEIN  Length:134
 aligned with DSBB_ECOLI | P0A6M2 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:149
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153         
           DSBB_ECOLI    14 AWLLMAFTALALELTALWFQHVMLLKPCVLCIYERCALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh...................hhhhhh..hhhhhhhhhhhhhhhhhh................hhhhhh.......---------------hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e9j F  14 AWLLMAFTALALELTALWFQHVMLLKPCVLCIYERVALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVA---------------MPQWLLGIFIAYLIVAVLVVI 162
                                    23        33        43        53        63        73        83        93       103       113       123  |      -       143       153         
                                                                                                                                          126             142
   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  (0, 0)

(no "SCOP Domain" information available for 3E9J)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E9J)

(-) Gene Ontology  (15, 18)

Asymmetric Unit(hide GO term definitions)
Chain B,E   (DSBA_ECOLI | P0AEG4)
molecular function
    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:0003756    protein disulfide isomerase activity    Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0071236    cellular response to antibiotic    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain C,F   (DSBB_ECOLI | P0A6M2)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0022900    electron transport chain    A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
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.
    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

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

UniProtKB/Swiss-Prot
        DSBA_ECOLI | P0AEG4: 1a23 1a24 1a2j 1a2l 1a2m 1ac1 1acv 1bq7 1dsb 1fvj 1fvk 1ti1 1u3a 1un2 2b3s 2b6m 2hi7 2leg 2ndo 2zup 4tky 4zij
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(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3E9J)