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(-) Description

Title :  XENOBIOTIC REDUCTASE A IN COMPLEX WITH 8-HYDROXYCOUMARIN
 
Authors :  H. Dobbek
Date :  08 Jun 06  (Deposition) - 29 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Beta-Alpha Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Griese, R. P. Jakob, S. Schwarzinger, H. Dobbek
Xenobiotic Reductase A In The Degradation Of Quinoline By Pseudomonas Putida 86: Physiological Function, Structure And Mechanism Of 8-Hydroxycoumarin Reduction.
J. Mol. Biol. V. 361 140 2006
PubMed-ID: 16822524  |  Reference-DOI: 10.1016/J.JMB.2006.06.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - XENOBIOTIC REDUCTASE A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: XENA
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
18CM3Ligand/Ion8-HYDROXYCOUMARIN
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3SO410Ligand/IonSULFATE ION
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
18CM6Ligand/Ion8-HYDROXYCOUMARIN
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3SO420Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:346 , ALA A:347 , SER A:348 , HOH A:1709BINDING SITE FOR RESIDUE SO4 A 1501
02AC2SOFTWARETYR A:8 , ARG A:18 , HOH A:1606 , HOH A:1611 , HOH A:1684 , HOH A:1875BINDING SITE FOR RESIDUE SO4 A 1502
03AC3SOFTWAREARG A:291 , LYS A:295 , LEU A:296 , PRO A:297 , HOH A:1641 , HOH A:1834BINDING SITE FOR RESIDUE SO4 A 1503
04AC4SOFTWARETRP A:278 , GLY A:279 , PRO A:280 , TRP A:302 , HOH A:1667BINDING SITE FOR RESIDUE SO4 A 1504
05AC5SOFTWAREASP A:205 , ARG A:209 , ARG A:254 , HOH A:1624 , HOH A:1748 , HOH A:1763 , HOH A:1773BINDING SITE FOR RESIDUE SO4 A 1505
06AC6SOFTWAREHIS A:181 , ARG A:231 , SER A:266 , ALA A:301 , 8CM A:801 , FMN A:1401BINDING SITE FOR RESIDUE SO4 A 1506
07AC7SOFTWAREARG A:155 , ARG A:168 , ASP A:169 , HOH A:1701 , HOH A:1719BINDING SITE FOR RESIDUE SO4 A 1507
08AC8SOFTWAREPHE A:189 , GLU A:191 , ARG A:207 , ARG A:240 , GLU A:247 , HOH A:1549BINDING SITE FOR RESIDUE SO4 A 1508
09AC9SOFTWAREARG A:111 , ARG A:125 , HOH A:1797BINDING SITE FOR RESIDUE SO4 A 1509
10BC1SOFTWAREILE A:34 , ASN A:35 , ALA A:81 , HOH A:1636 , HOH A:1752 , HOH A:1918BINDING SITE FOR RESIDUE SO4 A 1510
11BC2SOFTWAREPRO A:22 , PRO A:23 , MET A:24 , CYS A:25 , ALA A:57 , GLN A:99 , HIS A:178 , HIS A:181 , ARG A:231 , ALA A:301 , TRP A:302 , GLY A:303 , GLY A:325 , ARG A:326 , TRP A:358 , 8CM A:801 , SO4 A:1506 , HOH A:1543 , HOH A:1588 , HOH A:1902 , HOH A:1978BINDING SITE FOR RESIDUE FMN A 1401
12BC3SOFTWARECYS A:25 , TYR A:27 , ILE A:66 , HIS A:178 , HIS A:181 , TYR A:183 , PHE A:269 , FMN A:1401 , SO4 A:1506 , HOH A:1880BINDING SITE FOR RESIDUE 8CM A 801
13BC4SOFTWAREARG A:65 , THR A:124 , ARG A:125 , TRP A:127 , ARG A:168 , GLU A:220 , VAL A:221 , TRP A:222 , PRO A:223 , 8CM A:803 , HOH A:1650 , HOH A:1697 , HOH A:1717BINDING SITE FOR RESIDUE 8CM A 802
14BC5SOFTWAREASP A:31 , GLU A:224 , 8CM A:802 , HOH A:1717 , HOH A:1989BINDING SITE FOR RESIDUE 8CM A 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H8Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H8Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H8Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H8Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2H8Z)

(-) 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:359
 aligned with Q88NF7_PSEPK | Q88NF7 from UniProtKB/TrEMBL  Length:363

    Alignment length:359
                                    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       321       331       341       351         
         Q88NF7_PSEPK     2 SALFEPYTLKDVTLRNRIAIPPMCQYMAEDGMINDWHHVHLAGLARGGAGLLVVEATAVAPEGRITPGCAGIWSDAHAQAFVPVVQAIKAAGSVPGIQIAHAGRKASANRPWEGDDHIAADDARGWETIAPSAIAFGAHLPKVPREMTLDDIARVKQDFVDAARRARDAGFEWIELHFAHGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLAAVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTIPDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLADPHWAYFAAKELGVEKASWTLPAPYAHWLE 360
               SCOP domains d2h8za_ A: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eee..eee...eee.............hhhhhhhhhhhhhh...eeeeeeee.hhhhh.....ee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh...hhhhh..............ee..............ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhh.......eeeeee......hhhhhhhhhhhhhhhhhhh...eeeee................hhhhhhhhhhhhh..eee.....hhhhhhhhhhh....eee.hhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8z A   2 SALFEPYTLKDVTLRNRIAIPPMCQYMAEDGMINDWHHVHLAGLARGGAGLLVVEATAVAPEGRITPGCAGIWSDAHAQAFVPVVQAIKAAGSVPGIQIAHAGRKASANRPWEGDDHIAADDTRGWETIAPSAIAFGAHLPKVPREMTLDDIARVKQDFVDAARRARDAGFEWIELHFAHGYLGQSFFSEHSNKRTDAYGGSFDNRSRFLLETLAAVREVWPENLPLTARFGVLEYDGRDEQTLEESIELARRFKAGGLDLLSVSVGFTIPDTNIPWGPAFMGPIAERVRREAKLPVTSAWGFGTPQLAEAALQANQLDLVSVGRAHLADPHWAYFAAKELGVEKASWTLPAPYAHWLE 360
                                    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       321       331       341       351
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H8Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H8Z)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q88NF7_PSEPK | Q88NF7)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0003959    NADPH dehydrogenase activity    Catalysis of the reaction: NADPH + H+ + acceptor = NADP+ + reduced acceptor.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0018548    pentaerythritol trinitrate reductase activity    Catalysis of the reaction: pentaerythritol trinitrate + NADPH = NADP+ + nitrate + pentaerythritol dinitrate.
    GO:0052690    trichloro-p-hydroquinone reductive dehalogenase activity    Catalysis of the reaction: 2,3,6-trichlorohydroquinone + 2 glutathione = 2,6-dichlorohydroquinone + glutathione disulfide + HCl.
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

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

UniProtKB/TrEMBL
        Q88NF7_PSEPK | Q88NF7: 2h8x 2h90

(-) Related Entries Specified in the PDB File

2h8x XENOBIOTIC REDUCTASE A-OXIDIZED
2h90 XENOBIOTIC REDUCTASE A IN COMPLEX WITH COUMARIN