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(-) Description

Title :  CRYSTAL STRUCTURE OF OXYR FROM PORPHYROMONAS GINGIVALIS
 
Authors :  D. V. Svintradze, H. T. Wright, J. P. Lewis
Date :  01 Jun 09  (Deposition) - 09 Jun 10  (Release) - 08 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Alpha-Barrels, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. V. Svintradze, D. L. Peterson, E. A. Collazo-Santiago, J. P. Lewis, H. T. Wright
Structures Of The Porphyromonas Gingivalis Oxyr Regulatory Domain Explain Differences In Expression Of The Oxyr Regulo In Escherichia Coli And P. Gingivalis.
Acta Crystallogr. , Sect. D V. 69 2091 2013
PubMed-ID: 24100327  |  Reference-DOI: 10.1107/S0907444913019471

(-) Compounds

Molecule 1 - OXYR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentREGULATORY DOMAIN
    GeneOXYR, PG_0270
    Organism CommonBACTEROIDES GINGIVALIS
    Organism ScientificPORPHYROMONAS GINGIVALIS
    Organism Taxid837
    StrainATCC 33277 / DSM 20709 / JCM 12257
    SynonymREDOX-SENSITIVE TRANSCRIPTIONAL ACTIVATOR OXYR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3HO7)

(-) Sites  (0, 0)

(no "Site" information available for 3HO7)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:199 -A:208
2B:199 -B:208

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:262 -Pro A:263
2Met B:262 -Pro B:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HO7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HO7)

(-) Exons   (0, 0)

(no "Exon" information available for 3HO7)

(-) 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:220
 aligned with Q7MXD3_PORGI | Q7MXD3 from UniProtKB/TrEMBL  Length:308

    Alignment length:220
                                                                                                                                                                                                                                                    308 
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        |-
         Q7MXD3_PORGI    90 TGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCFRDQLVRFCQMKGLHERQTAYSGGSMEAFMRLVESGQGITFIPQLTVEQLSPSQKELVRPFGMPRPVREVRLAVRQDYSRRKLREQLIGLLRSAVPSDMHKLQTGQHLA-   -
               SCOP domains d3ho7a_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhh...eeee........eeeeeeeeeeeeeee...hhhhhh...hhhhhhhhhh............hhhhhh........eeee..hhhhhhhhhhh...eeeee.hhhhhhhhhhhh.ee.....eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ho7 A  90 TGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCFRDQLVRFCQMKGLHERQTAYSGGSMEAFMRLVESGQGITFIPQLTVEQLSPSQKELVRPFGMPRPVREVRLAVRQDYSRRKLREQLIGLLRSAVPSDMHKLQTGQHLAH 309
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with Q7MXD3_PORGI | Q7MXD3 from UniProtKB/TrEMBL  Length:308

    Alignment length:220
                                                                                                                                                                                                                                                    308 
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299        |-
         Q7MXD3_PORGI    90 TGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCFRDQLVRFCQMKGLHERQTAYSGGSMEAFMRLVESGQGITFIPQLTVEQLSPSQKELVRPFGMPRPVREVRLAVRQDYSRRKLREQLIGLLRSAVPSDMHKLQTGQHLA-   -
               SCOP domains d3ho7b_ B: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhh...eeee........eeeeeeeeeeeeeee...hhhhhh...hhhhhhhhhh.......hhhhhhhhhhh........eeee..hhhhhhhhhhh...eeeee.hhhhhhhhhhhh.ee.....eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ho7 B  90 TGRLNIAVLPTIAPYLLPRVFPIWKKELAGLEIHVSEMQTSRCLASLLSGEIDMAIIASKAETEGLEDDLLYYEEFLGYVSRCEPLFEQDVIRTTEVNPHRLWLLDEGHCFRDQLVRFCQMKGLHERQTAYSGGSMEAFMRLVESGQGITFIPQLTVEQLSPSQKELVRPFGMPRPVREVRLAVRQDYSRRKLREQLIGLLRSAVPSDMHKLQTGQHLAH 309
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HO7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HO7)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7MXD3_PORGI | Q7MXD3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  Cis Peptide Bonds
    Met A:262 - Pro A:263   [ RasMol ]  
    Met B:262 - Pro B:263   [ RasMol ]  
 

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