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(-) Description

Title :  NITROREDUCTASE FROM E-COLI IN COMPLEX WITH THE DINITROBENZAMIDE PRODRUG SN23862
 
Authors :  E. Johansson, G. N. Parkinson, W. A. Denny, S. Neidle
Date :  03 Mar 03  (Deposition) - 08 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nad(P)H-Quinone Reductase, Fmn, Nitroreductase, Flavoprotein, Sn23862, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Johansson, G. N. Parkinson, W. A. Denny, S. Neidle
Studies On The Nitroreductase Prodrug-Activating System. Crystal Structures Of Complexes With The Inhibitor Dicoumarol And Dinitrobenzamide Prodrugs And Of The Enzyme Active Form
J. Med. Chem. V. 46 4009 2003
PubMed-ID: 12954054  |  Reference-DOI: 10.1021/JM030843B
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
    Chains: A, B
    EC Number: 1.6.99.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI K12
    Expression System Strain: K12
    Expression System Taxid: 83333
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FMN-DEPENDENT NITROREDUCTASE, DIHYDROPTERIDINE REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2SN22Ligand/Ion5-[BIS-2(CHLORO-ETHYL)-AMINO]-2,4-DINTRO-BENZAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:10 , HIS A:11 , SER A:12 , LYS A:14 , ASN A:71 , PRO A:163 , ILE A:164 , GLU A:165 , GLY A:166 , LYS A:205 , ARG A:207 , SN2 A:221 , HOH A:270 , HOH A:276 , HOH A:285 , HOH A:315 , PRO B:38 , SER B:39 , SER B:40 , THR B:41 , ASN B:42 , GLN B:142 , LEU B:145BINDING SITE FOR RESIDUE FMN A 218
2AC2SOFTWARETHR A:41 , ALA A:116 , LYS A:119 , GLY A:120 , PHE A:124 , LYS B:14 , LYS B:74 , FMN B:220BINDING SITE FOR RESIDUE SN2 A 219
3AC3SOFTWAREPRO A:38 , SER A:39 , SER A:40 , ASN A:42 , GLN A:142 , LEU A:145 , SN2 A:219 , HOH A:248 , ARG B:10 , HIS B:11 , SER B:12 , LYS B:14 , LYS B:74 , PRO B:163 , ILE B:164 , GLU B:165 , GLY B:166 , LYS B:205 , ARG B:207 , HOH B:236BINDING SITE FOR RESIDUE FMN B 220
4AC4SOFTWARELYS A:14 , PHE A:70 , ASN A:71 , LYS A:74 , PHE A:199 , FMN A:218 , HOH A:301 , HOH A:315BINDING SITE FOR RESIDUE SN2 A 221

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OO6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OO6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OO6)

(-) Exons   (0, 0)

(no "Exon" information available for 1OO6)

(-) 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:217
 aligned with NFSB_ECOLI | P38489 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
           NFSB_ECOLI     1 MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
               SCOP domains d1oo6a_ A: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                      SCOP domains
               CATH domains 1oo6A00 A:1-217 NADH Oxidase                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh............hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oo6 A   1 MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with NFSB_ECOLI | P38489 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
           NFSB_ECOLI     1 MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
               SCOP domains d1oo6b_ B: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                      SCOP domains
               CATH domains 1oo6B00 B:1-217 NADH Oxidase                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh............hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhh......eeeeeeeeee.....hhhhh......hhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oo6 B   1 MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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, 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 1OO6)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NFSB_ECOLI | P38489)
molecular function
    GO:0004155    6,7-dihydropteridine reductase activity    Catalysis of the reaction: NADP+ + 5,6,7,8-tetrahydropteridine = NADPH + H+ + 6,7-dihydropteridine.
    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:0018545    NAD(P)H nitroreductase activity    Catalysis of the conversion of a nitrate group to an amino or hydroxylamino group on toluene or a toluene derivative.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0046256    2,4,6-trinitrotoluene catabolic process    The chemical reactions and pathways resulting in the breakdown of 2,4,6-trinitrotoluene, 1-methyl-2,4,6-trinitrobenzene, a highly explosive pale yellow crystalline solid.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NFSB_ECOLI | P38489: 1ds7 1icr 1icu 1icv 1idt 1oo5 1oon 1ooq 1yki 1ylr 1ylu 3x21 3x22

(-) Related Entries Specified in the PDB File

1idt THE SAME PROTEIN COMPLEXED WITH CB1954
1oo5 THE SAME PROTEIN UNCOMPLEXED BUT WITH REDUCED FMN
1oon THE SAME PROTEIN COMPLEXED WITH SN27217
1ooq THE SAME PROTEIN COMPLEXED WITH DICOUMAROL