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(-) Description

Title :  STRUCTURE AND SITE-DIRECTED MUTAGENESIS OF A FLAVOPROTEIN FROM ESCHERICHIA COLI THAT REDUCES NITROCOMPOUNDS. ALTERATION OF PYRIDINE NUCLEOTIDE BINDING BY A SINGLE AMINO ACID SUBSTITUTION
 
Authors :  T. Kobori, H. Sasaki, W. C. Lee, S. Zenno, K. Saigo, M. E. P. Murphy, M. Tanokura
Date :  17 Jun 00  (Deposition) - 14 Feb 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nitroreductase, Flavoprotein, Escherichia Coli, Oxidoreduction, Nitrocompound, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kobori, H. Sasaki, W. C. Lee, S. Zenno, K. Saigo, M. E. Murphy, M. Tanokura
Structure And Site-Directed Mutagenesis Of A Flavoprotein From Escherichia Coli That Reduces Nitrocompounds: Alteration Of Pyridine Nucleotide Binding By A Single Amino Acid Substitution.
J. Biol. Chem. V. 276 2816 2001
PubMed-ID: 11034992  |  Reference-DOI: 10.1074/JBC.M002617200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OXYGEN-INSENSITIVE NADPH NITROREDUCTASE
    Chains: A, B
    EC Number: 1.6.99.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAJ102
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:11 , SER A:13 , ARG A:15 , GLN A:67 , VAL A:127 , TYR A:128 , ILE A:129 , GLY A:130 , GLY A:131 , LYS A:167 , ARG A:169 , HOH A:367 , HOH A:380 , HOH A:403 , HOH A:475 , SER B:38 , SER B:39 , SER B:40 , PHE B:42 , VAL B:106 , ASP B:107 , HOH B:504BINDING SITE FOR RESIDUE FMN A 360
2AC2SOFTWARESER A:38 , SER A:39 , SER A:40 , PHE A:42 , VAL A:106 , ASP A:107 , HIS B:11 , ARG B:12 , SER B:13 , ARG B:15 , GLN B:67 , VAL B:127 , TYR B:128 , ILE B:129 , GLY B:130 , GLY B:131 , LYS B:167 , ARG B:169 , HOH B:381 , HOH B:416 , HOH B:425 , HOH B:427 , HOH B:498BINDING SITE FOR RESIDUE FMN B 361

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F5V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F5V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F5V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F5V)

(-) Exons   (0, 0)

(no "Exon" information available for 1F5V)

(-) Sequences/Alignments

Asymmetric/Biological 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:240
 aligned with NFSA_ECOLI | P17117 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
           NFSA_ECOLI     1 MTPTIELICGHRSIRHFTDEPISEAQREAIINSARATSSSSFLQCSSIIRITDKALREELVTLTGGQKHVAQAAEFWVFCADFNRHLQICPDAQLGLAEQLLLGVVDTAMMAQNALIAAESLGLGGVYIGGLRNNIEAVTKLLKLPQHVLPLFGLCLGWPADNPDLKPRLPASILVHENSYQPLDKGALAQYDEQLAEYYLTRGSNNRRDTWSDHIRRTIIKESRPFILDYLHKQGWATR 240
               SCOP domains d1f5va_ A: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                                             SCOP domains
               CATH domains 1f5vA00 A:1-240 NADH Oxidase                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeee..hhhhhhhhhhhh...hhhhhh.eeeeeeeehhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....eeeeeeeeee............hhhhheee......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f5v A   1 MTPTIELICGHRSIRHFTDEPISEAQREAIINSARATSSSSFLQCSSIIRITDKALREELVTLTGGQKHVAQAAEFWVFCADFNRHLQICPDAQLGLAEQLLLGVVDTAMMAQNALIAAESLGLGGVYIGGLRNNIEAVTKLLKLPQHVLPLFGLCLGWPADNPDLKPRLPASILVHENSYQPLDKGALAQYDEQLAEYYLTRGSNNRRDTWSDHIRRTIIKESRPFILDYLHKQGWATR 240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with NFSA_ECOLI | P17117 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:240
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
           NFSA_ECOLI     1 MTPTIELICGHRSIRHFTDEPISEAQREAIINSARATSSSSFLQCSSIIRITDKALREELVTLTGGQKHVAQAAEFWVFCADFNRHLQICPDAQLGLAEQLLLGVVDTAMMAQNALIAAESLGLGGVYIGGLRNNIEAVTKLLKLPQHVLPLFGLCLGWPADNPDLKPRLPASILVHENSYQPLDKGALAQYDEQLAEYYLTRGSNNRRDTWSDHIRRTIIKESRPFILDYLHKQGWATR 240
               SCOP domains d1f5vb_ B: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                                             SCOP domains
               CATH domains 1f5vB00 B:1-240 NADH Oxidase                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeee..hhhhhhhhhhhh...hhhhhh.eeeeeeeehhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.....eeeeeeeeee............hhhhheee......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f5v B   1 MTPTIELICGHRSIRHFTDEPISEAQREAIINSARATSSSSFLQCSSIIRITDKALREELVTLTGGQKHVAQAAEFWVFCADFNRHLQICPDAQLGLAEQLLLGVVDTAMMAQNALIAAESLGLGGVYIGGLRNNIEAVTKLLKLPQHVLPLFGLCLGWPADNPDLKPRLPASILVHENSYQPLDKGALAQYDEQLAEYYLTRGSNNRRDTWSDHIRRTIIKESRPFILDYLHKQGWATR 240
                                    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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F5V)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NFSA_ECOLI | P17117)
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:0034567    chromate reductase activity    Catalysis of the reaction: chromate = chromium (III).
    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:0016657    oxidoreductase activity, acting on NAD(P)H, nitrogenous group as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a nitrogenous group.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.
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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 Related Entries

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