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(-) Description

Title :  THE CRYSTAL STRUCTURE OF AZOR (AZOREDUCTASE) FROM ESCHERICHIA COLI: OXIDIZED AZOR IN TETRAGONAL CRYSTALS (THE RESOLUTION HAS IMPROVED FROM 1.8 (1V4B) TO 1.4 ANGSTROM)
 
Authors :  K. Ito
Date :  18 Sep 07  (Deposition) - 11 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Azoreductase, Flavoprotein, Fmn, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ito, M. Nakanishi, W. C. Lee, Y. Zhi, H. Sasaki, S. Zenno, K. Saigo, Y. Kitade, M. Tanokura
Expansion Of Substrate Specificity And Catalytic Mechanism Of Azoreductase By X-Ray Crystallography And Site-Directed Mutagenesis
J. Biol. Chem. V. 283 13889 2008
PubMed-ID: 18337254  |  Reference-DOI: 10.1074/JBC.M710070200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FMN-DEPENDENT NADH-AZOREDUCTASE
    Chains: A
    EC Number: 1.7.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AZOR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FMN-DEPENDENT NADH-AZO COMPOUND OXIDOREDUCTASE, AZO-DYE REDUCTASE

 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:9 , LEU A:11 , SER A:15 , GLN A:16 , SER A:17 , LEU A:50 , PRO A:94 , MET A:95 , TYR A:96 , ASN A:97 , PHE A:98 , SER A:139 , ARG A:140 , GLY A:141 , GLY A:142 , HIS A:144 , HOH A:233 , HOH A:258BINDING SITE FOR RESIDUE FMN A 201
2AC2SOFTWAREPHE A:98 , ASN A:99 , LEU A:151 , TYR A:155BINDING SITE FOR RESIDUE EDO A 202
3AC3SOFTWAREPHE A:170 , PHE A:172 , ASP A:189BINDING SITE FOR RESIDUE EDO A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z98)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z98)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z98)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z98)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z98)

(-) 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:194
 aligned with AZOR_ECOLI | P41407 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:200
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
           AZOR_ECOLI     2 SKVLVLKSSILAGYSQSNQLSDYFVEQWREKHSADEITVRDLAANPIPVLDGELVGALRPSDAPLTPRQQEALALSDELIAELKAHDVIVIAAPMYNFNISTQLKNYFDLVARAGVTFRYTENGPEGLVTGKKAIVITSRGGIHKDGPTDLVTPYLSTFLGFIGITDVKFVFAEGIAYGPEMAAKAQSDAKAAIDSIVSA 201
               SCOP domains d2z98a_ A: ACP phosphodiesterase AcpD                                                                                                                                                                    SCOP domains
               CATH domains 2z98A00 A:1-200  [code=3.40.50.360, no name defined]                                                                                                                                                     CATH domains
               Pfam domains Flavodoxin_2-2z98A01 A:1-198                                                                                                                                                                          -- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhh------.hhhhhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhhh.....eeee..eeee.....eeeeeee...........hhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z98 A   1 SKVLVLKSSILAGYSQSNQLSDYFVEQWREKHSADEITVRDLAANPIPVLDGELVGAL------LTPRQQEALALSDELIAELKAHDVIVIAAPMYNFNISTQLKNYFDLVARAGVTFRYTENGPEGLVTGKKAIVITSRGGIHKDGPTDLVTPYLSTFLGFIGITDVKFVFAEGIAYGPEMAAKAQSDAKAAIDSIVSA 200
                                    10        20        30        40        50       | -    |   70        80        90       100       110       120       130       140       150       160       170       180       190       200
                                                                                    58     65
   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  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Flavoprotein (71)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (AZOR_ECOLI | P41407)
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:0008752    FMN reductase activity    Catalysis of the reaction: FMNH2 + NAD(P)+ = FMN + NAD(P)H + H+.
    GO:0050446    azobenzene reductase activity    Catalysis of the reaction: N,N-dimethyl-1,4-phenylenediamine + aniline + NADP+ = 4-(dimethylamino)azobenzene + NADPH + H+.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    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:0016652    oxidoreductase activity, acting on NAD(P)H, NAD(P) as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    GO:0016655    oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
    GO:0016661    oxidoreductase activity, acting on other nitrogenous compounds as donors    Catalysis of an oxidation-reduction (redox) reaction in which a nitrogenous group, excluding NH and NH2 groups, acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
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:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  2z98
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  AZOR_ECOLI | P41407
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  1.7.1.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        AZOR_ECOLI | P41407: 1tik 1v4b 2d5i 2z9b 2z9c 2z9d

(-) Related Entries Specified in the PDB File

1v4b SAME PROTEIN, THE HIGH RESOLUTION WAS 1.8 ANGSTROM.
2z9b
2z9c
2z9d