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(-) Description

Title :  THE STRUCTURE OF E. COLI NITROREDUCTASE BOUND WITH THE ANTIBIOTIC NITROFURAZONE
 
Authors :  P. R. Race, A. L. Lovering, R. M. Green, A. Ossor, S. A. White, P. F. Searle, C. J. Wrighton, E. I. Hyde
Date :  18 Jan 05  (Deposition) - 08 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Oxidoreductase, Oxygen-Insensitive Nad(P)H Nitroreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Race, A. L. Lovering, R. M. Green, A. Ossor, S. A. White, P. F. Searle, C. J. Wrighton, E. I. Hyde
Structural And Mechanistic Studies Of Escherichia Coli Nitroreductase With The Antibiotic Nitrofurazone. Reversed Binding Orientations In Different Redox States Of The Enzyme.
J. Biol. Chem. V. 280 13256 2005
PubMed-ID: 15684426  |  Reference-DOI: 10.1074/JBC.M409652200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
    Chains: A, B, C, D
    EC Number: 1.5.1.34
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET11C
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: NFNB, DPRA, NFSB, NFSI, NTR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FMN-DEPENDENT NITROREDUCTASE, DIHYDROPTERIDINE REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2DMS3Ligand/IonDIMETHYL SULFOXIDE
3FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
4NFZ4Ligand/IonNITROFURAZONE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1CIT-1Ligand/IonCITRIC ACID
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
4NFZ2Ligand/IonNITROFURAZONE
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
4NFZ2Ligand/IonNITROFURAZONE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:10 , HIS A:11 , SER A:12 , LYS A:14 , ASN A:71 , LYS A:74 , PRO A:163 , ILE A:164 , GLU A:165 , GLY A:166 , LYS A:205 , ARG A:207 , NFZ A:1219 , HOH A:1229 , HOH A:1232 , HOH A:1233 , HOH A:1266 , PRO B:38 , SER B:39 , SER B:40 , ASN B:42 , GLN B:142 , LEU B:145BINDING SITE FOR RESIDUE FMN A 1218
02AC2SOFTWAREASN A:67 , TYR A:68 , PHE A:70 , ASN A:71 , GLU A:165 , FMN A:1218 , HOH A:1251 , HOH A:1421 , THR B:41 , PHE B:124BINDING SITE FOR RESIDUE NFZ A 1219
03AC3SOFTWAREPRO A:38 , SER A:39 , SER A:40 , ASN A:42 , GLN A:142 , LEU A:145 , ARG B:10 , HIS B:11 , SER B:12 , LYS B:14 , ASN B:71 , LYS B:74 , PRO B:163 , ILE B:164 , GLU B:165 , GLY B:166 , ASN B:200 , LYS B:205 , ARG B:207 , NFZ B:2219 , HOH B:2229 , HOH B:2237 , HOH B:2239 , HOH B:2256BINDING SITE FOR RESIDUE FMN B 2218
04AC4SOFTWARETHR A:41 , PHE A:124 , ASN B:67 , TYR B:68 , PHE B:70 , ASN B:71 , LYS B:74 , GLU B:165 , FMN B:2218 , HOH B:2290 , HOH B:2342BINDING SITE FOR RESIDUE NFZ B 2219
05AC5SOFTWAREARG C:10 , HIS C:11 , SER C:12 , LYS C:14 , ASN C:71 , LYS C:74 , TYR C:144 , PRO C:163 , ILE C:164 , GLU C:165 , GLY C:166 , LYS C:205 , ARG C:207 , NFZ C:3219 , HOH C:4222 , HOH C:4233 , HOH C:4234 , HOH C:4241 , PRO D:38 , SER D:39 , SER D:40 , ASN D:42 , GLN D:142 , LEU D:145BINDING SITE FOR RESIDUE FMN C 3218
06AC6SOFTWAREASN C:67 , TYR C:68 , PHE C:70 , ASN C:71 , GLU C:165 , FMN C:3218 , CIT C:4220 , HOH C:4275 , HOH C:4289 , THR D:41 , PHE D:124BINDING SITE FOR RESIDUE NFZ C 3219
07AC7SOFTWAREPRO C:38 , SER C:39 , SER C:40 , ASN C:42 , GLN C:142 , LEU C:145 , ARG D:10 , HIS D:11 , SER D:12 , LYS D:14 , ASN D:71 , LYS D:74 , PRO D:163 , ILE D:164 , GLU D:165 , GLY D:166 , LYS D:205 , ARG D:207 , NFZ D:4219 , HOH D:4231 , HOH D:4236 , HOH D:4252 , HOH D:4261BINDING SITE FOR RESIDUE FMN D 4218
08AC8SOFTWARETHR C:41 , PHE C:124 , ASN D:67 , TYR D:68 , PHE D:70 , ASN D:71 , GLU D:165 , FMN D:4218 , HOH D:4281 , HOH D:4301BINDING SITE FOR RESIDUE NFZ D 4219
09AC9SOFTWARELYS C:14 , LYS C:74 , PHE C:199 , NFZ C:3219 , HOH C:4275 , HOH C:4279 , HOH C:4307 , ASN D:117BINDING SITE FOR RESIDUE CIT C 4220
10BC1SOFTWARELYS C:9 , ALA C:201 , LEU C:203BINDING SITE FOR RESIDUE DMS C 1223
11BC2SOFTWARESER D:52 , HOH D:4274 , HOH D:4295BINDING SITE FOR RESIDUE DMS C 1224
12BC3SOFTWAREALA B:104 , ASP B:105BINDING SITE FOR RESIDUE DMS B 1225

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YKI)

(-) 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:216
 aligned with NFSB_ECOLI | P38489 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           NFSB_ECOLI     2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
               SCOP domains d1ykia_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains 1ykiA00 A:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yki A   2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      


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 d1ykib_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains 1ykiB00 B:1-217 NADH Oxidase                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh............hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yki 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       


Chain C from PDB  Type:PROTEIN  Length:216
 aligned with NFSB_ECOLI | P38489 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
           NFSB_ECOLI     2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
               SCOP domains d1ykic_ C: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains 1ykiC00 C:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhhh.hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yki C   2 DIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      


Chain D 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 d1ykid_ D: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains 1ykiD00 D: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......hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yki D   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)
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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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  1yki
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  NFSB_ECOLI | P38489
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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 1oo6 1oon 1ooq 1ylr 1ylu 3x21 3x22

(-) Related Entries Specified in the PDB File

1icr THE SAME PROTEIN COMPLEXED WITH NICOTINIC ACID
1icu THE SAME PROTEIN COMPLEXED WITH NICOTINIC ACID
1icv THE SAME PROTEIN COMPLEXED WITH NICOTINIC ACID
1ylr
1ylu