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(-) Description

Title :  CRYSTAL STRUCTURES OF THE QUINONE OXIDOREDUCTASE FROM THERMUS THERMOPHILUS HB8 AND ITS COMPLEX WITH NADPH
 
Authors :  Y. Shimomura, Y. Kakuta, K. Fukuyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 Sep 02  (Deposition) - 15 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Protein-Nadph Complex, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shimomura, Y. Kakuta, K. Fukuyama
Crystal Structures Of The Quinone Oxidoreductase From Thermus Thermophilus Hb8 And Its Complex With Nadph: Implication For Nadph And Substrate Recognition
J. Bacteriol. V. 185 4211 2003
PubMed-ID: 12837796  |  Reference-DOI: 10.1128/JB.185.14.4211-4218.2003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - QUINONE OXIDOREDUCTASE
    Chains: A
    EC Number: 1.6.5.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:39 , THR A:113 , ALA A:133 , GLY A:136 , ALA A:137 , ALA A:157 , SER A:158 , LYS A:162 , TYR A:177 , VAL A:196 , ILE A:217 , ALA A:220 , GLU A:221 , PHE A:242 , TRP A:243 , LEU A:244 , ARG A:292 , HIS A:294 , GLY A:296 , HOH A:381BINDING SITE FOR RESIDUE NDP A 350

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:55 -Pro A:56

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IYZ)

(-) Exons   (0, 0)

(no "Exon" information available for 1IYZ)

(-) 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:299
 aligned with Q8L3C8_THETH | Q8L3C8 from UniProtKB/TrEMBL  Length:302

    Alignment length:302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
         Q8L3C8_THETH     1 MKAWVLKRLGGPLELVDLPEPEAEEGEVVLRVEAVGLNFADHLMRLGAYLTRLHPPFIPGMEVVGVVEGRRYAALVPQGGLAERVAVPKGALLPLPEGLSPEEAAAFPVSFLTAYLALKRAQARPGEKVLVQAAAGALGTAAVQVARAMGLRVLAAASRPEKLALPLALGAEEAATYAEVPERAKAWGGLDLVLEVRGKEVEESLGLLAHGGRLVYIGAAEGEVAPIPPLRLMRRNLAVLGFWLTPLLREGALVEEALGFLLPRLGRELRPVVGPVFPFAEAEAAFRALLDRGHTGKVVVRL 302
               SCOP domains d1iyza1 A:1-98,A:270-302 Quinone oxidoreductase                                                   d1iyza2 A:99-269 Quinone oxidoreductase                                                                                                                                    d1iyza1 A:1-98,A:270-302          SCOP domains
               CATH domains -1iyzA01 A:2-109,A:271-302 Medium-chain alcohol dehydrogenases, catalytic domain                             1iyzA02 A:110-270 NAD(P)-binding Rossmann-like Domain                                                                                                            1iyzA01 A:2-109,A:271-302        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeee.........eeeeeeeeee.hhhhhhhhh...............eeeeee..eeeeee........eeeee.hhhee.....hhhhhh.hhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh..eeee..hhhhhhhhhh.eeeeee....hhhhhhh.eeeeeeeee.....---.....hhhhhh..eeee.hhhhhhhhhhhhhhhhhhhh..........eeeeee..hhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iyz A   1 MKAWVLKRLGGPLELVDLPEPEAEEGEVVLRVEAVGLNFADHLMRLGAYLTRLHPPFIPGMEVVGVVEGRRYAALVPQGGLAERVAVPKGALLPLPEGLSPEEAAAFPVSFLTAYLALKRAQARPGEKVLVQAAAGALGTAAVQVARAMGLRVLAAASRPEKLALPLALGAEEAATYAEVPERAKAWGGLDLVLEVRGKEVEESLGLLAHGGRLVYIGAAE---APIPPLRLMRRNLAVLGFWLTPLLREGALVEEALGFLLPRLGRELRPVVGPVFPFAEAEAAFRALLDRGHTGKVVVRL 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220|   |  230       240       250       260       270       280       290       300  
                                                                                                                                                                                                                                                      221 225
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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  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8L3C8_THETH | Q8L3C8)
molecular function
    GO:0003960    NADPH:quinone reductase activity    Catalysis of the reaction: NADPH + H+ + quinone = NADP+ + semiquinone.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.

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 Related Entries

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        Q8L3C8_THETH | Q8L3C8: 1iz0

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