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(-) Description

Title :  THE STRUCTURE OF ESCHERICHIA COLI NITROREDUCTASE COMPLEXED WITH NICOTINIC ACID
 
Authors :  A. L. Lovering, E. I. Hyde, P. F. Searle, S. A. White
Date :  02 Apr 01  (Deposition) - 18 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alpha-Beta, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Lovering, E. I. Hyde, P. F. Searle, S. A. White
The Structure Of Escherichia Coli Nitroreductase Complexed With Nicotinic Acid: Three Crystal Forms At 1. 7 A, 1. 8 A And 2. 4 A Resolution.
J. Mol. Biol. V. 309 203 2001
PubMed-ID: 11491290  |  Reference-DOI: 10.1006/JMBI.2001.4653
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
    Chains: A, B, C, D
    EC Number: 1.6.99.7
    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: NFSB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
2NIO4Ligand/IonNICOTINIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2NIO2Ligand/IonNICOTINIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
2NIO2Ligand/IonNICOTINIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG 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 , ASN A:200 , LYS A:205 , ARG A:207 , HOH A:227 , HOH A:241 , HOH A:242 , PRO B:38 , SER B:39 , SER B:40 , ASN B:42 , LEU B:145 , NIO B:219BINDING SITE FOR RESIDUE FMN A 218
2AC2SOFTWAREPHE A:70 , GLY A:166 , FMN A:218 , SER B:40 , THR B:41 , PHE B:124BINDING SITE FOR RESIDUE NIO B 219
3AC3SOFTWAREPRO A:38 , SER A:39 , SER A:40 , ASN A:42 , GLN A:142 , LEU A:145 , NIO A:221 , 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 , HOH B:226 , HOH B:241 , HOH B:248BINDING SITE FOR RESIDUE FMN B 220
4AC4SOFTWARESER A:40 , THR A:41 , PHE A:124 , PHE B:70 , GLY B:166 , FMN B:220BINDING SITE FOR RESIDUE NIO A 221
5AC5SOFTWAREARG 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 , ASN C:200 , LYS C:205 , ARG C:207 , HOH C:234 , HOH C:237 , HOH C:242 , PRO D:38 , SER D:39 , SER D:40 , ASN D:42 , GLN D:142 , LEU D:145 , NIO D:223BINDING SITE FOR RESIDUE FMN C 222
6AC6SOFTWAREPHE C:70 , GLY C:166 , FMN C:222 , SER D:40 , THR D:41 , PHE D:124BINDING SITE FOR RESIDUE NIO D 223
7AC7SOFTWAREPRO C:38 , SER C:39 , SER C:40 , ASN C:42 , LEU C:145 , NIO C:225 , 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 , HOH D:237 , HOH D:239 , HOH D:250BINDING SITE FOR RESIDUE FMN D 224
8AC8SOFTWARESER C:40 , THR C:41 , PHE C:124 , FMN D:224BINDING SITE FOR RESIDUE NIO C 225

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ICU)

(-) 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 d1icua_ A: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1icuA00 A:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhhh.....hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1icu 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 d1icub_ B: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                      SCOP domains
               CATH domains 1icuB00 B: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
                 1icu 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 d1icuc_ C: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                     SCOP domains
               CATH domains 1icuC00 C:2-217 NADH Oxidase                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhh.....hhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhhh.....hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1icu 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 d1icud_ D: Oxygen-insensitive NAD(P)H nitroreductase                                                                                                                                                                      SCOP domains
               CATH domains 1icuD00 D:1-217 NADH Oxidase                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh............hhhhhhhhhhhhhh..hhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh..ee......hhhhhhhhhhhhhhheeeeeeeeee.....hhhhhh.....hhhhheee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1icu 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)
    → 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, 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 1ICU)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        NFSB_ECOLI | P38489: 1ds7 1icr 1icv 1idt 1oo5 1oo6 1oon 1ooq 1yki 1ylr 1ylu 3x21 3x22

(-) Related Entries Specified in the PDB File

1icr 1ICR WAS SOLVED USING THE TETRAGONAL CRYSTAL FORM.
1icv 1ICV WAS SOLVED USING THE ORTHORHOMBIC CRYSTAL FORM.