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(-) Description

Title :  STRUCTURE OF THE HYPOTHETICAL OXIDOREDUCTASE YCND FROM BACILLUS SUBTILIS
 
Authors :  A. Morokutti, A. Lyskowski, S. Sollner, E. Pointner, T. B. Fitzpatrick C. Kratky, K. Gruber, P. Macheroux
Date :  12 Apr 05  (Deposition) - 01 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nitroreductase, Nadh-Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Morokutti, A. Lyskowski, S. Sollner, E. Pointner, T. B. Fitzpatrick, C. Kratky, K. Gruber, P. Macheroux
Structure And Function Of Ycnd From Bacillus Subtilis, A Flavin-Containing Oxidoreductase(, ).
Biochemistry V. 44 13724 2005
PubMed-ID: 16229462  |  Reference-DOI: 10.1021/BI0510835

(-) Compounds

Molecule 1 - HYPOTHETICAL OXIDOREDUCTASE YCND
    Chains: A
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YCND
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 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, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:41 , FMN A:301BINDING SITE FOR RESIDUE CL A 302
2AC2SOFTWAREGLU A:25 , GLU A:150 , ASN A:189 , HOH A:440 , HOH A:475 , HOH A:552BINDING SITE FOR RESIDUE CA A 303
3AC3SOFTWAREHIS A:11 , ARG A:12 , SER A:13 , ARG A:15 , PRO A:38 , SER A:39 , SER A:40 , ASN A:42 , GLN A:67 , TRP A:69 , ILE A:116 , VAL A:133 , PRO A:134 , ILE A:135 , GLY A:136 , ALA A:137 , LYS A:173 , ARG A:175 , CL A:302 , HOH A:417 , HOH A:432 , HOH A:465BINDING SITE FOR RESIDUE FMN A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZCH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZCH)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:249
 aligned with NFRA2_BACSU | P94424 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
          NFRA2_BACSU     1 MNEVIKSLTDHRSIRSYTDEPVAQEQLDQIIEAVQSAPSSINGQQVTVITVQDKERKKKISELAGGQPWIDQAPVFLLFCADFNRAKIALEDLHDFKMEITNGLESVLVGAVDAGIALGTATAAAESLGLGTVPIGAVRGNPQELIELLELPKYVFPLSGLVIGHPADRSAKKPRLPQEAVNHQETYLNQDELTSHIQAYDEQMSEYMNKRTNGKETRNWSQSIASYYERLYYPHIREMLEKQGFKVEK 249
               SCOP domains d1zcha1 A:1-249 Hypothetical oxidoreductase YcnD                                                                                                                                                                                                          SCOP domains
               CATH domains 1zchA00 A:1-249 NADH Oxidase                                                                                                                                                                                                                              CATH domains
               Pfam domains -------Nitroreductase-1zchA01 A:8-165                                                                                                                                ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh............hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhh..hhhhhhh.eeeeeeeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....eeeeeeeeee............hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zch A   1 MNEVIKSLTDHRSIRSYTDEPVAQEQLDQIIEAVQSAPSSINGQQVTVITVQDKERKKKISELAGGQPWIDQAPVFLLFCADFNRAKIALEDLHDFKMEITNGLESVLVGAVDAGIALGTATAAAESLGLGTVPIGAVRGNPQELIELLELPKYVFPLSGLVIGHPADRSAKKPRLPQEAVNHQETYLNQDELTSHIQAYDEQMSEYMNKRTNGKETRNWSQSIASYYERLYYPHIREMLEKQGFKVEK 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   Legend:   → Mismatch (orange background)
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  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) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Nitroreductase] (9)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (NFRA2_BACSU | P94424)
molecular function
    GO:0052874    FMN reductase (NADH) activity    Catalysis of the reaction: FMNH2 + NAD+ = FMN + NADH + 2 H+.
    GO:0052873    FMN reductase (NADPH) activity    Catalysis of the reaction: FMNH2 + NADP+ = FMN + NADPH + 2 H+.
    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.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    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:0009636    response to toxic substance    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 a toxic stimulus.

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  1zch
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