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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REDUCED FORM OF OXYR
 
Authors :  H. Choi, S. Kim, S. Ryu
Date :  02 Mar 01  (Deposition) - 02 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxyr Regulatory Domain, Reduced Form, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Choi, S. Kim, P. Mukhopadhyay, S. Cho, J. Woo, G. Storz, S. Ryu
Structural Basis Of The Redox Switch In The Oxyr Transcription Factor.
Cell(Cambridge, Mass. ) V. 105 103 2001
PubMed-ID: 11301006  |  Reference-DOI: 10.1016/S0092-8674(01)00300-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYDROGEN PEROXIDE-INDUCIBLE GENES ACTIVATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: REGULATORY DOMAIN
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: OXYR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BEZ1Ligand/IonBENZOIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 1I69)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I69)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:261 -Pro A:262
2Lys B:1261 -Pro B:1262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I69)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I69)

(-) Exons   (0, 0)

(no "Exon" information available for 1I69)

(-) 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:206
 aligned with OXYR_ECOLI | P0ACQ4 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:212
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296  
          OXYR_ECOLI     87 ETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCVILALVKESEAFIEVPLFDEPMLLAIYEDHPWANRECVPMADLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPCIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGHFD  298
               SCOP domains d1i69a_ A: Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain                                                                                                                             SCOP domains
               CATH domains 1i69A01 A:87-163,A:268-297 Periplasmic binding protein-like II               1i69A02 A:164-267 Periplasmic binding protein-      like II                                             1i69A01 A:87-163,A:268-297    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...hhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhh..........hhhhh.eeeeeeeeeeeeeee..hhhhhh..eehhhhhh...........hhhhh.....------.......hhhhhhhhhhh....eeee.hhh....ee..eeee.......eeeeeeee.....hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1i69 A   87 ETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALVKESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLMLEDGHSLRDQAMGFCF------DTHFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPAIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGHFD  298
                                    96       106       116       126       136       146       156       166       176       186       196       206  |    216       226       236       246       256       266       276       286       296  
                                                                                                                                                    209    216                                                                                  


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with OXYR_ECOLI | P0ACQ4 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:212
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296  
          OXYR_ECOLI     87 ETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCVILALVKESEAFIEVPLFDEPMLLAIYEDHPWANRECVPMADLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPCIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGHFD  298
               SCOP domains d1i69b_ B: Hydrogen peroxide-inducible genes LysR-type activator OxyR, regulatory domain                                                                                                                             SCOP domains
               CATH domains 1i69B01 B:1087-1163,B:1268-1297 Periplasmic binding protein-like II          1i69B02 B:1164-1267 Periplasmic binding protein      -like II                                           1i69B01                       - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...hhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhh..........hhhhh.eeeeeeeeeeeeeee..hhhhhh..ee.hhhh.......................------......hhhhhhhhhhh....eeee.hhh....ee..eeee.......eeeeeeee.....hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1i69 B 1087 ETMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDAVILALVKESEAFIEVPLFDEPMLLAIYEDHPWANREAVPMADLAGEKLLMLEDGHSLRDQAMGFCFE------THFRATSLETLRNMVAAGSGITLLPALAVPPERKRDGVVYLPAIKPEPRRTIGLVYRPGSPLRSRYEQLAEAIRARMDGHFD 1298
                                  1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206   |     -|     1226      1236      1246      1256      1266      1276      1286      1296  
                                                                                                                                                    1210   1217
   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) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I69)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (OXYR_ECOLI | P0ACQ4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000986    bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
    GO:0001131    transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:2000142    regulation of DNA-templated transcription, initiation    Any process that modulates the frequency, rate or extent of DNA-templated transcription initiation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051409    response to nitrosative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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.

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    Lys A:261 - Pro A:262   [ RasMol ]  
    Lys B:1261 - Pro B:1262   [ RasMol ]  
 

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  1i69
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 Related Entries

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

UniProtKB/Swiss-Prot
        OXYR_ECOLI | P0ACQ4: 1i6a

(-) Related Entries Specified in the PDB File

1i6a 1I6A IS THE OXIDIZED FORM OF OXYR