Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF TLPA FROM BRADYRHIZOBIUM JAPONICUM
 
Authors :  G. Capitani, R. Rossmann, D. F. Sargent, M. G. Gruetter, T. J. Richmond, H. Hennecke
Date :  22 Jun 01  (Deposition) - 19 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Thioredoxin-Like, Double Disulfide Bridge, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Capitani, R. Rossmann, D. F. Sargent, M. G. Grutter, T. J. Richmond, H. Hennecke
Structure Of The Soluble Domain Of A Membrane-Anchored Thioredoxin-Like Protein From Bradyrhizobium Japonicum Reveals Unusual Properties.
J. Mol. Biol. V. 311 1037 2001
PubMed-ID: 11531338  |  Reference-DOI: 10.1006/JMBI.2001.4913
(for further references see the PDB file header)

(-) Compounds

Molecule 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMAL-P
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: SOLUBLE DOMAIN OF TLPA (RESIDUES 36-221)
    Gene: TLPA
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 375

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1JFU)

(-) Sites  (0, 0)

(no "Site" information available for 1JFU)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:10 -A:155
2A:72 -A:75
3B:10 -B:155
4B:72 -B:75

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Met A:144 -Pro A:145
2Met B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JFU)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TLPA_BRADU69-215
 		  2A:34-180
B:34-180
2THIOREDOXIN_1PS00194 Thioredoxin family active site.TLPA_BRADU99-117
 		  2A:64-82
B:64-82
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TLPA_BRADU69-215
 		  1A:34-180
-
2THIOREDOXIN_1PS00194 Thioredoxin family active site.TLPA_BRADU99-117
 		  1A:64-82
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TLPA_BRADU69-215
 		  1-
B:34-180
2THIOREDOXIN_1PS00194 Thioredoxin family active site.TLPA_BRADU99-117
 		  1-
B:64-82

(-) Exons   (0, 0)

(no "Exon" information available for 1JFU)

(-) 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 A from PDB  Type:PROTEIN  Length:176
 aligned with TLPA_BRADU | P43221 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:176
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209      
           TLPA_BRADU    40 TGDPACRAAVATAQKIAPLAHGEVAALTMASAPLKLPDLAFEDADGKPKKLSDFRGKTLLVNLWATWCVPCRKEMPALDELQGKLSGPNFEVVAINIDTRDPEKPKTFLKEANLTRLGYFNDQKAKVFQDLKAIGRALGMPTSVLVDPQGCEIATIAGPAEWASEDALKLIRAATG 215
               SCOP domains d1jfua_ A: Membrane-anchored thioredoxin-like protein TlpA, soluble domain                                                                                                       SCOP domains
               CATH domains 1jfuA00 A:5-180 Glutaredoxin                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..ee..........eee.....eee.hhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhh.......ee...hhhhhhhhh........eeeee.....eeeeee......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------THIOREDOXIN_2  PDB: A:34-180 UniProt: 69-215                                                                                                        PROSITE (1)
                PROSITE (2) -----------------------------------------------------------THIOREDOXIN_1      -------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jfu A   5 TGDPACRAAVATAQKIAPLAHGEVAALTMASAPLKLPDLAFEDADGKPKKLSDFRGKTLLVNLWATWCVPCRKEMPALDELQGKLSGPNFEVVAINIDTRDPEKPKTFLKEANLTRLGYFNDQKAKVFQDLKAIGRALGMPTSVLVDPQGCEIATIAGPAEWASEDALKLIRAATG 180
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174      


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with TLPA_BRADU | P43221 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:177
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       
           TLPA_BRADU    39 PTGDPACRAAVATAQKIAPLAHGEVAALTMASAPLKLPDLAFEDADGKPKKLSDFRGKTLLVNLWATWCVPCRKEMPALDELQGKLSGPNFEVVAINIDTRDPEKPKTFLKEANLTRLGYFNDQKAKVFQDLKAIGRALGMPTSVLVDPQGCEIATIAGPAEWASEDALKLIRAATG 215
               SCOP domains d1jfub_ B: Membrane-anchored thioredoxin-like protein TlpA, soluble domain                                                                                                        SCOP domains
               CATH domains 1jfuB00 B:4-180 Glutaredoxin                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh..ee..........eee.....eee.hhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhh.......ee...hhhhhhhhhh.......eeeee.....eeeeee......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------THIOREDOXIN_2  PDB: B:34-180 UniProt: 69-215                                                                                                        PROSITE (1)
                PROSITE (2) ------------------------------------------------------------THIOREDOXIN_1      -------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jfu B   4 PTGDPACRAAVATAQKIAPLAHGEVAALTMASAPLKLPDLAFEDADGKPKKLSDFRGKTLLVNLWATWCVPCRKEMPALDELQGKLSGPNFEVVAINIDTRDPEKPKTFLKEANLTRLGYFNDQKAKVFQDLKAIGRALGMPTSVLVDPQGCEIATIAGPAEWASEDALKLIRAATG 180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JFU)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TLPA_BRADU | P43221)
molecular function
    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:0016671    oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
    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:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0034599    cellular response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0017004    cytochrome complex assembly    The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
    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:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular 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: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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1jfu)
 
  Sites
(no "Sites" information available for 1jfu)
 
  Cis Peptide Bonds
    Met A:144 - Pro A:145   [ RasMol ]  
    Met B:144 - Pro B:145   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1jfu
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TLPA_BRADU | P43221
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TLPA_BRADU | P43221
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TLPA_BRADU | P43221: 4txo 4txv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1JFU)