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(-) Description

Title :  STRUCTURE OF NADPH DEPENDENT THIOREDOXIN REDUCTASE
 
Authors :  S. Dai, H. Eklund
Date :  22 Sep 96  (Deposition) - 12 Mar 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hypothetical Protein, Redox-Active Center, Oxidoreductase, Disulfide Oxidoreductase, Thioredoxin Reductase, Flavin Adenine Dinuleotide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Dai, M. Saarinen, S. Ramaswamy, Y. Meyer, J. P. Jacquot, H. Eklund
Crystal Structure Of Arabidopsis Thaliana Nadph Dependent Thioredoxin Reductase At 2. 5 A Resolution.
J. Mol. Biol. V. 264 1044 1996
PubMed-ID: 9000629  |  Reference-DOI: 10.1006/JMBI.1996.0695
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NADPH DEPENDENT THIOREDOXIN REDUCTASE
    Chains: A
    EC Number: 1.6.4.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: ATTHIREDB
    Expression System Plasmid: PET-3D
    Expression System Taxid: 562
    Gene: ATTHIREDB
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: PET
    Synonym: NTR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:56 , GLU A:57 , LYS A:67 , LYS A:70 , HOH A:701BINDING SITE FOR RESIDUE SO4 A 440
2AC2SOFTWAREVAL A:11 , GLY A:12 , SER A:13 , GLY A:14 , PRO A:15 , ALA A:16 , PHE A:34 , GLU A:35 , GLY A:36 , ILE A:37 , ALA A:38 , GLY A:41 , GLN A:42 , LEU A:43 , VAL A:49 , ASN A:51 , VAL A:84 , ALA A:111 , ILE A:112 , GLY A:113 , CYS A:138 , GLY A:285 , ASP A:286 , ARG A:293 , GLN A:294 , ALA A:295 , ALA A:298 , HOH A:506 , HOH A:507 , HOH A:516 , HOH A:519 , HOH A:522 , HOH A:524 , HOH A:526 , HOH A:545 , HOH A:585 , HOH A:630BINDING SITE FOR RESIDUE FAD A 400
3ACTUNKNOWNCYS A:135 , CYS A:138 , ALA A:136 , ASP A:139 , GLY A:140 , GLU A:159ACTIVE SITE.
4FADUNKNOWNGLY A:12 , SER A:13 , GLY A:14 , PRO A:15 , ALA A:16 , GLY A:36 , GLY A:41 , THR A:46 , GLU A:50 , ASN A:51 , GLY A:61 , GLY A:113 , SER A:133 , ASP A:139 , GLY A:285 , ASP A:286FAD BINDING SITE.

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:135 -A:138

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:92 -Pro A:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRIDINE_REDOX_2PS00573 Pyridine nucleotide-disulphide oxidoreductases class-II active site.TRXB1_ARATH189-211  1A:135-155
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRIDINE_REDOX_2PS00573 Pyridine nucleotide-disulphide oxidoreductases class-II active site.TRXB1_ARATH189-211  2A:135-155

(-) Exons   (0, 0)

(no "Exon" information available for 1VDC)

(-) 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:322
 aligned with TRXB1_ARATH | Q39243 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:322
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365  
         TRXB1_ARATH     46 LETHNTRLCIVGSGPAAHTAAIYAARAELKPLLFEGWMANDIAPGGQLTTTTDVENFPGFPEGILGVELTDKFRKQSERFGTTIFTETVTKVDFSSKPFKLFTDSKAILADAVILATGAVAKRLSFVGSGEASGGFWNRGISACAVCDGAAPIFRNKPLAVIGGGDSAMEEANFLTKYGSKVYIIHRRDAFRASKIMQQRALSNPKIDVIWNSSVVEAYGDGERDVLGGLKVKNVVTGDVSDLKVSGLFFAIGHEPATKFLDGGVELDSDGYVVTKPGTTQTSVPGVFAAGDVQDKKYRQAITAAGTGCMAALDAEHYLQEI  367
               SCOP domains d1vdca1 A:1-117,A:244-316 Thioredoxin reductase                                                                           d1vdca2 A:118-243 Thioredoxin reductase                                                                                           d1vdca1 A:1-117,A:244-316 Thioredoxin reductase                        SCOP domains
               CATH domains 1vdcA01 A:1-116,A:245-315  [code=3.50.50.60, no name defined]                                                            1vdcA02 A:117-244  [code=3.50.50.60, no name defined]                                                                               1vdcA01 A:1-116,A:245-315  [code=3.50.50.60, no name defined]       - CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-1vdcA01 A:147-225                                                  ---------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------Pyr_redox_2-1vdcA02 A:7-292                                                                                                                                                                                                                                                                         ------------------------ Pfam domains (2)
         Sec.struct. author .eeeee.eeee...hhhhhhhhhhhh.....eee....hhh.....hhhh...............hhhhhhhhhhhhhh...eee.....eee.....eeee...eeeee.eeee...eee.......................hhhh...hhh...eeeee...hhhhhhhhhhhh...eeeee.........hhhhhhhh....eeee..eeeeeee.........eeeeee.....eeeee..eeee...eee..hhh.........................eee.hhhh......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------PYRIDINE_REDOX_2       ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1vdc A    1 LETHNTRLCIVGSGPAAHTAAIYAARAELKPLLFEGWMANDIAPGGQLTTTTDVENFPGFPEGILGVELTDKFRKQSERFGTTIFTETVTKVDFSSKPFKLFTDSKAILADAVILAIGAVAKRLSFVGSGEVLGGFWNRGISACAVCDGAAPIFRNKPLAVIGGGDSAMEEANFLTKYGSKVYIIHRRDAFRASKIMQQRALSNPKIDVIWNSSVVEAYGDGERDVLGGLKVKNVVTGDVSDLKVSGLFFAIGHEPATKFLDGGVELDSDGYVVTKPGTTQTSVPGVFAAGDVQDKKYRQAITAAGTGCMAALDAEHYLQEI  316
                                    10        20        30      |36D|       45        55        65        75        85        95       105       115       125   | ||131       141||     149       159       169       179       189       199       211       221       231       241       251       261|      274       284       294       304       314  
                                                              36A||||                                                                                         128B |||         141A|                                                               207|                                                261A    268|                                           
                                                               36B|||                                                                                           129B||          141B                                                                210                                                         273                                           
                                                                36C||                                                                                            129C|                                                                                                                                                                                        
                                                                 36D|                                                                                             129D                                                                                                                                                                                        
                                                                  36E
   Legend:   → Mismatch (orange background)
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  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  (2, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRXB1_ARATH | Q39243)
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:0004791    thioredoxin-disulfide reductase activity    Catalysis of the reaction: NADP(+) + thioredoxin = H(+) + NADPH + thioredoxin disulfide.
biological process
    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:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
cellular component
    GO:0009941    chloroplast envelope    The double lipid bilayer enclosing the chloroplast and separating its contents from the rest of the cytoplasm; includes the intermembrane space.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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