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(-) Description

Title :  STRUCTURE OF NITROREDUCTASE FROM E. CLOACAE BOUND WITH 2E-REDUCED FLAVIN MONONUCLEOTIDE (FMN)
 
Authors :  C. A. Haynes, R. L. Koder, A. F. Miller, D. W. Rodgers
Date :  04 Jan 02  (Deposition) - 13 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Nitroreductase, Reduced Hydroquinone, Flavin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Haynes, R. L. Koder, A. F. Miller, D. W. Rodgers
Structures Of Nitroreductase In Three States: Effects Of Inhibitor Binding And Reduction.
J. Biol. Chem. V. 277 11513 2002
PubMed-ID: 11805110  |  Reference-DOI: 10.1074/JBC.M111334200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
    Chains: A, B, C, D
    EC Number: 1.6.6.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24D(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROBACTER CLOACAE
    Organism Taxid: 550

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:10 , HIS A:11 , SER A:12 , LYS A:14 , ASN A:71 , LYS A:74 , TYR A:144 , PRO A:163 , ILE A:164 , GLU A:165 , GLY A:166 , LYS A:205 , ARG A:207 , HOH A:547 , HOH A:565 , HOH A:571 , HOH A:576 , PRO B:38 , SER B:39 , SER B:40 , THR B:41 , ASN B:42 , GLN B:142 , LEU B:145 , HOH B:632BINDING SITE FOR RESIDUE FMN A 518
2AC2SOFTWAREPRO A:38 , SER A:39 , SER A:40 , ASN A:42 , GLN A:142 , LEU A:145 , HOH A:605 , ARG B:10 , HIS B:11 , SER B:12 , LYS B:14 , ASN B:71 , LYS B:74 , TYR B:144 , PRO B:163 , ILE B:164 , GLU B:165 , GLY B:166 , LYS B:205 , ARG B:207 , HOH B:527 , HOH B:552 , HOH B:555 , HOH B:556 , HOH B:631BINDING SITE FOR RESIDUE FMN B 519
3AC3SOFTWAREARG 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 , HOH C:541 , HOH C:556 , HOH C:561 , HOH C:564 , PRO D:38 , SER D:39 , SER D:40 , ASN D:42 , GLN D:142 , LEU D:145 , HOH D:643 , HOH D:644BINDING SITE FOR RESIDUE FMN C 520
4AC4SOFTWAREPRO 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 , TYR D:144 , PRO D:163 , ILE D:164 , GLU D:165 , GLY D:166 , ASN D:200 , LYS D:205 , ARG D:207 , HOH D:537 , HOH D:538 , HOH D:541 , HOH D:572 , HOH D:645BINDING SITE FOR RESIDUE FMN D 521

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KQD)

(-) 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_ENTCL | Q01234 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_ENTCL     2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
               SCOP domains d1kqda_ A: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1kqdA00 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......hhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kqd A   2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 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:216
 aligned with NFSB_ENTCL | Q01234 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_ENTCL     2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
               SCOP domains d1kqdb_ B: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1kqdB00 B:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kqd B   2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      


Chain C from PDB  Type:PROTEIN  Length:216
 aligned with NFSB_ENTCL | Q01234 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_ENTCL     2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
               SCOP domains d1kqdc_ C: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1kqdC00 C:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee................hhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kqd C   2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 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:216
 aligned with NFSB_ENTCL | Q01234 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_ENTCL     2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
               SCOP domains d1kqdd_ D: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1kqdD00 D:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhh......hhhhheeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1kqd D   2 DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTEC 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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, 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 1KQD)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (NFSB_ENTCL | Q01234)
molecular function
    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: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.

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  1kqd
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  1.6.6.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        NFSB_ENTCL | Q01234: 1kqb 1kqc 1nec 5j8d 5j8g

(-) Related Entries Specified in the PDB File

1kqb STRUCTURE OF NITROREDUCTASE FROM E. CLOACAE COMPLEX WITH INHIBITOR BENZOATE
1kqc STRUCTURE OF NITROREDUCTASE FROM E. CLOACAE COMPLEX WITH INHIBITOR ACETATE