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(-) Description

Title :  PENTAERYTHRITOL TETRANITRATE REDUCTASE CO-CRYSTAL STRUCTURE WITH BOUND (E)-1-(2'-HYDROXYPHENYL)-2-NITROETHENE
 
Authors :  H. S. Toogood, N. S. Scrutton
Date :  13 Oct 10  (Deposition) - 02 Mar 11  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Old Yellow Enzyme Family, Alpha, Beta Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. S. Toogood, A. Fryszkowska, M. Hulley, M. Sakuma, D. Mansell, G. M. Stephens, J. M. Gardiner, N. S. Scrutton
A Site-Saturated Mutagenesis Study Of Pentaerythritol Tetranitrate Reductase Reveals That Residues 181 And 184 Influence Ligand Binding, Stereochemistry And Reactivity.
Chembiochem V. 12 738 2011
PubMed-ID: 21374779  |  Reference-DOI: 10.1002/CBIC.201000662

(-) Compounds

Molecule 1 - PENTAERYTHRITOL TETRANITRATE REDUCTASE
    Chains: A
    EC Number: 1.6.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBLUESCRIPT II-KS(+)
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ONR, PETNR
    Organism Scientific: ENTEROBACTER CLOACAE
    Organism Taxid: 550
    Strain: PB2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2P7Y1Ligand/Ion2-[(E)-2-NITROETHENYL]PHENOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:23 , PRO A:24 , LEU A:25 , THR A:26 , ALA A:58 , GLN A:100 , HIS A:181 , HIS A:184 , ARG A:233 , LEU A:275 , ALA A:302 , PHE A:322 , GLY A:323 , ARG A:324 , TYR A:351 , HOH A:398 , P7Y A:402 , HOH A:758 , HOH A:773 , HOH A:781 , HOH A:886BINDING SITE FOR RESIDUE FMN A 401
2AC2SOFTWARETHR A:26 , TRP A:102 , HIS A:181 , HIS A:184 , TYR A:186 , LEU A:275 , HOH A:398 , FMN A:401 , HOH A:701BINDING SITE FOR RESIDUE P7Y A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P7Y)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:32 -Pro A:33

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P7Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P7Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3P7Y)

(-) 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:363
 aligned with P71278_ENTCL | P71278 from UniProtKB/TrEMBL  Length:365

    Alignment length:363
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
         P71278_ENTCL     3 AEKLFTPLKVGAVTAPNRVFMAPLTRLRSIEPGDIPTPLMGEYYRQRASAGLIISEATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVHAEDGRIAVQLWHTGRISHSSIQPGGQAPVSASALNANTRTSLRDENGNAIRVDTTTPRALELDEIPGIVNDFRQAVANAREAGFDLVELHSAHGYLLHQFLSPSSNQRTDQYGGSVENRARLVLEVVDAVCNEWSADRIGIRVSPIGTFQNVDNGPNEEADALYLIEELAKRGIAYLHMSETDLAGGKPYSEAFRQKVRERFHGVIIGAGAYTAEKAEDLIGKGLIDAVAFGRDYIANPDLVARLQKKAELNPQRPESFYGGGAEGYTDYPSL 365
               SCOP domains d3p7ya_ A: Pentaerythritol tetranirate reductase                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Oxidored_FMN-3p7yA01 A:4-343                                                                                                                                                                                                                                                                                                                        --------------------- Pfam domains
         Sec.struct. author .......eee..eee...eee...............hhhhhhhhhhh....eeeeeeee...............hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh..ee........eeeee.....eeeee....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.eeeee.............hhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhh..eeeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p7y A   2 AEKLFTPLKVGAVTAPNRVFMAPLTRLRSIEPGDIPTPLMGEYYRQRASAGLIISEATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVHAEDGRIAVQLWHTGRISHSSIQPGGQAPVSASALNANTRTSLRDENGNAIRVDTTTPRALELDEIPGIVNDFRQAVANAREAGFDLVELHSAHGYLLHQFLSPSSNQRTDQYGGSVENRARLVLEVVDAVCNEWSADRIGIRVSPIGTFQNVDNGPNEEADALYLIEELAKRGIAYLHMSETDLAGGKPYSEAFRQKVRERFHGVIIGAGAYTAEKAEDLIGKGLIDAVAFGRDYIANPDLVARLQKKAELNPQRPESFYGGGAEGYTDYPSL 364
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P7Y)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P71278_ENTCL | P71278)
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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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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 Related Entries

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

UniProtKB/TrEMBL
        P71278_ENTCL | P71278: 1gvo 1gvq 1gvr 1gvs 1h50 1h51 1h60 1h61 1h62 1h63 1vyp 1vyr 1vys 2aba 2abb 3f03 3kft 3p62 3p67 3p74 3p80 3p81 3p82 3p84 3p8i 3p8j 5lgx 5lgz

(-) Related Entries Specified in the PDB File

3p62
3p67
3p74 PENTAERYTHRITOL TETRANITRATE REDUCTASE H181N MUTANT
3p80 PENTAERYTHRITOL TETRANITRATE REDUCTASE WITH BOUND (E)-1-(3' -HYDROXYPHENYL)-2-NITROETHENE
3p81 PENTAERYTHRITOL TETRANITRATE REDUCTASE WITH BOUND (E)-1-(4' -HYDROXYPHENYL)-2-NITROETHENE
3p82 H184N MUTANT OF PENTAERYTHRITOL TETRANITRATE REDUCTASE WITH BOUND ACETATE
3p84 Y351A MUTANT OF PENTAERYTHRITOL TETRANITRATE REDUCTASE WITH BOUND ACETATE
3p8i Y351F MUTANT OF PENTAERYTHRITOL TETRANITRATE REDUCTASE WITH BOUND ACETATE
3p8j Y351S MUTANT OF PENTAERYTHRITOL TETRANITRATE REDUCTASE WITH BOUND ACETATE