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(-) Description

Title :  CRYSTAL STRUCTURES OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 QUINONE OXIDOREDUCTASE COMPLEXED WITH NADPH
 
Authors :  X. Pan, H. Zhang, Y. Gao, M. Li, W. Chang
Date :  22 Sep 09  (Deposition) - 12 Jan 10  (Release) - 12 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossmann Fold, Protein-Nadph Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Pan, H. Zhang, Y. Gao, M. Li, W. Chang
Crystal Structures Of Pseudomonas Syringae Pv. Tomato Dc3000 Quinone Oxidoreductase And Its Complex With Nadph
Biochem. Biophys. Res. Commun. V. 390 597 2009
PubMed-ID: 19818736  |  Reference-DOI: 10.1016/J.BBRC.2009.10.012
(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
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS SYRINGAE PV. TOMATO
    Organism Taxid: 323
    Strain: DC3000

 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:42 , TYR A:46 , LEU A:123 , LYS A:124 , THR A:127 , TYR A:130 , GLY A:151 , GLY A:152 , VAL A:153 , VAL A:172 , SER A:173 , LYS A:177 , TYR A:192 , GLY A:216 , PHE A:238 , GLY A:239 , ASN A:240 , ALA A:241 , SER A:242 , ARG A:263 , PRO A:264 , THR A:265 , LEU A:266 , LEU A:312 , SER A:313 , ARG A:315 , HOH A:327 , HOH A:331 , HOH A:346 , HOH A:347 , HOH A:352 , HOH A:354 , HOH A:374 , HOH A:394 , HOH A:403 , HOH A:462 , HOH A:582 , HOH A:584BINDING SITE FOR RESIDUE NDP A 350

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JYN)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:57 -Pro A:58

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JYN)

(-) Exons   (0, 0)

(no "Exon" information available for 3JYN)

(-) 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:325
 aligned with Q88B47_PSESM | Q88B47 from UniProtKB/TrEMBL  Length:325

    Alignment length:325
                                    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       310       320     
         Q88B47_PSESM     1 MAKRIQFSTVGGPEVLEYVDFEPEAPGPQAVVVRNKAIGLNFIDTYYRSGLYPAPFLPSGLGAEGAGVVEAVGDEVTRFKVGDRVAYGTGPLGAYSEVHVLPEANLVKLADSVSFEQAAALMLKGLTVQYLLRQTYQVKPGEIILFHAAAGGVGSLACQWAKALGAKLIGTVSSPEKAAHAKALGAWETIDYSHEDVAKRVLELTDGKKCPVVYDGVGQDTWLTSLDSVAPRGLVVSFGNASGPVSGVNLGILAQKDSVYVTRPTLGSYANNAQNLQTMADELFDMLASGKLKVDGIEQYALKDAAKAQIELSARRTTGSTILIP 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------ADH_N-3jynA01 A:28-91                                           ------------------------------------------------------------ADH_zinc_N-3jynA02 A:152-285                                                                                                          ---------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhheeeee........eeeeeeeeee.hhhhhhhhh...............eeeeeeee...........eeee..........eeeee...eee.....hhhhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhh..eeee....hhhhhhhhhh....eeeeee..hhhhhhhhhh.eeeeeeeee............hhhhhhh...eee..hhhhhh...hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jyn A   1 MAKRIQFSTVGGPEVLEYVDFEPEAPGPQAVVVRNKAIGLNFIDTYYRSGLYPAPFLPSGLGAEGAGVVEAVGDEVTRFKVGDRVAYGTGPLGAYSEVHVLPEANLVKLADSVSFEQAAALMLKGLTVQYLLRQTYQVKPGEIILFHAAAGGVGSLACQWAKALGAKLIGTVSSPEKAAHAKALGAWETIDYSHEDVAKRVLELTDGKKCPVVYDGVGQDTWLTSLDSVAPRGLVVSFGNASGPVSGVNLGILAQKDSVYVTRPTLGSYANNAQNLQTMADELFDMLASGKLKVDGIEQYALKDAAKAQIELSARRTTGSTILIP 325
                                    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       310       320
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3JYN)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: GroES (70)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q88B47_PSESM | Q88B47)
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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        Q88B47_PSESM | Q88B47: 3jyl

(-) Related Entries Specified in the PDB File

3jyl