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(-) Description

Title :  CRYSTAL STRUCTURE OF DEINOCOCCUS RADIODURANS THIOREDOXIN REDUCTASE
 
Authors :  D. A. R. Sanders, J. Obiero, S. A. Bonderoff, M. M. Goertzen
Date :  07 Jun 07  (Deposition) - 08 Jul 08  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Fad, Flavoprotein, Oxidoreductase, Redox-Active Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Obiero, V. Pittet, S. A. Bonderoff, D. A. Sanders
Thioredoxin System From Deinococcus Radiodurans.
J. Bacteriol. V. 192 494 2010
PubMed-ID: 19933368  |  Reference-DOI: 10.1128/JB.01046-09

(-) Compounds

Molecule 1 - THIOREDOXIN REDUCTASE
    Chains: A, B
    EC Number: 1.8.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET-30B
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRXB
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Strain: R1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:15 , GLY A:17 , PRO A:18 , ALA A:19 , LEU A:37 , GLU A:38 , LYS A:39 , GLY A:44 , GLN A:45 , ILE A:46 , ASN A:54 , ASP A:85 , GLU A:86 , ALA A:118 , THR A:119 , GLY A:120 , CYS A:145 , GLY A:283 , ASP A:284 , ARG A:291 , GLN A:292 , LEU A:293 , SER A:296BINDING SITE FOR RESIDUE FAD A 348
2AC2SOFTWARETYR A:26 , GLY B:15 , GLY B:17 , PRO B:18 , ALA B:19 , LEU B:37 , GLU B:38 , LYS B:39 , GLY B:44 , GLN B:45 , ILE B:46 , SER B:49 , ASN B:54 , ASP B:85 , GLU B:86 , ALA B:118 , THR B:119 , GLY B:120 , CYS B:145 , GLY B:283 , ASP B:284 , ARG B:291 , GLN B:292 , LEU B:293 , SER B:296BINDING SITE FOR RESIDUE FAD B 448

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:142 -A:145
2B:142 -B:145

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:97 -Pro A:98
2His B:97 -Pro B:98

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q7V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q7V)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q7V)

(-) 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:313
 aligned with Q9RSY7_DEIRA | Q9RSY7 from UniProtKB/TrEMBL  Length:325

    Alignment length:313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311   
         Q9RSY7_DEIRA     2 TAPTAHDYDVVIIGGGPAGLTAAIYTGRAQLSTLILEKGMPGGQIAWSEEVENFPGFPEPIAGMELAQRMHQQAEKFGAKVEMDEVQGVQHDATSHPYPFTVRGYNGEYRAKAVILATGADPRKLGIPGEDNFWGKGVSTCATCDGFFYKGKKVVVIGGGDAAVEEGMFLTKFADEVTVIHRRDTLRANKVAQARAFANPKMKFIWDTAVEEIQGADSVSGVKLRNLKTGEVSELATDGVFIFIGHVPNTAFVKDTVSLRDDGYVDVRDEIYTNIPMLFAAGDVSDYIYRQLATSVGAGTRAAMMTERQLAAL 314
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------2q7vA02 A:124-246  [code=3.50.50.60, no name defined]                                                                      -------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhh.............hhhhhhhhhhhhhhhh..eeee..eeeeee........eeeee...eeeeeeeee...eee...............ee.hhhhhhhhhh..eeeee..hhhhhhhhhhhh....eeeee........hhhhhhhhhh...eeee..eeeeeeee...eeeeeeee.....eeeee..eeee...eee.hhhhh.......................eee..........hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q7v A   2 TAPTAHDYDVVIIGGGPAGLTAAIYTGRAQLSTLILEKGMPGGQIAWSEEVENFPGFPEPIAGMELAQRMHQQAEKFGAKVEMDEVQGVQHDATSHPYPFTVRGYNGEYRAKAVILATGADPRKLGIPGEDNFWGKGVSTCATCDGFFYKGKKVVVIGGGDAAVEEGMFLTKFADEVTVIHRRDTLRANKVAQARAFANPKMKFIWDTAVEEIQGADSVSGVKLRNLKTGEVSELATDGVFIFIGHVPNTAFVKDTVSLRDDGYVDVRDEIYTNIPMLFAAGDVSDYIYRQLATSVGAGTRAAMMTERQLAAL 314
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311   


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with Q9RSY7_DEIRA | Q9RSY7 from UniProtKB/TrEMBL  Length:325

    Alignment length:309
                                    15        25        35        45        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         
         Q9RSY7_DEIRA     6 AHDYDVVIIGGGPAGLTAAIYTGRAQLSTLILEKGMPGGQIAWSEEVENFPGFPEPIAGMELAQRMHQQAEKFGAKVEMDEVQGVQHDATSHPYPFTVRGYNGEYRAKAVILATGADPRKLGIPGEDNFWGKGVSTCATCDGFFYKGKKVVVIGGGDAAVEEGMFLTKFADEVTVIHRRDTLRANKVAQARAFANPKMKFIWDTAVEEIQGADSVSGVKLRNLKTGEVSELATDGVFIFIGHVPNTAFVKDTVSLRDDGYVDVRDEIYTNIPMLFAAGDVSDYIYRQLATSVGAGTRAAMMTERQLAAL 314
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------2q7vB02 B:124-246  [code=3.50.50.60, no name defined]                                                                      -------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-2q7vB01 B:154-232                                                    ---------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-2q7vB02 B:154-232                                                    ---------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----Pyr_redox_2-2q7vB03 B:10-290                                                                                                                                                                                                                                                             ------------------------ Pfam domains (3)
           Pfam domains (4) ----Pyr_redox_2-2q7vB04 B:10-290                                                                                                                                                                                                                                                             ------------------------ Pfam domains (4)
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhh.............hhhhhhhhhhhhhhhh..eeee..eeeeee........eeeee...eeeeeeeee...eee...............ee.hhhhhhhhhh..eeeee..hhhhhhhhhhhh....eeeee........hhhhhhhhhhh..eeee..eeeeeeee...eeeeeeee.....eeeee..eeee...eee.hhhhh.......................eee..........hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q7v B   6 AHDYDVVIIGGGPAGLTAAIYTGRAQLSTLILEKGMPGGQIAWSEEVENFPGFPEPIAGMELAQRMHQQAEKFGAKVEMDEVQGVQHDATSHPYPFTVRGYNGEYRAKAVILATGADPRKLGIPGEDNFWGKGVSTCATCDGFFYKGKKVVVIGGGDAAVEEGMFLTKFADEVTVIHRRDTLRANKVAQARAFANPKMKFIWDTAVEEIQGADSVSGVKLRNLKTGEVSELATDGVFIFIGHVPNTAFVKDTVSLRDDGYVDVRDEIYTNIPMLFAAGDVSDYIYRQLATSVGAGTRAAMMTERQLAAL 314
                                    15        25        35        45        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
   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 2Q7V)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9RSY7_DEIRA | Q9RSY7)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2q7v
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 Related Entries

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