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(-) Description

Title :  THE CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR YAIJ
 
Authors :  A. Bochkarev, V. V. Lunin, A. Ezersky, E. Evdokimova, T. Skarina, X. Xu, A. M. Edwards, A. Joachimiak, A. Savchenko, Midwest Center For Str Genomics (Mcsg)
Date :  08 Feb 05  (Deposition) - 22 Mar 05  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcriptional Regulator, Yaij, Iclr, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bochkarev, V. V. Lunin, A. Ezersky, E. Evdokimova, T. Skarina, X. Xu D. Borek, A. M. Edwards, A. Savchenko
Structural Study Of Effector Binding Specificity In Iclr Transcriptional Regulators
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR YIAJ
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YIAJ
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:60 , SER A:65 , ALA A:66 , MET A:67 , SER A:147 , HOH A:359 , HOH A:425BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWAREGLU A:25 , GLY A:48 , MET A:49 , LEU A:50 , SER A:151 , ARG A:154BINDING SITE FOR RESIDUE PO4 A 302
3AC3SOFTWAREARG A:32 , TYR A:71 , PHE A:74 , GLY A:75 , VAL A:142 , HOH A:332 , HOH A:365 , HOH A:423BINDING SITE FOR RESIDUE PO4 A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YSQ)

(-) 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    
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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:181
 aligned with YIAJ_ECOLI | P37671 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:187
                                                                                                                                                                                                                   282 
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276     | 
           YIAJ_ECOLI    97 SLNIIHIAAPHLEALNIATGETINFSSREDDHAILIYKLEPTTGMLRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESHQHEIQPLTRNTITELPAMFDELAHIRESGAAMDREENELGVSCIAVPVFDIHGRVPYAVSISLSTSRLKQVGEKNLLKPLRETAQAISNELGFTVRDDLGAIT-   -
               SCOP domains d1ysqa_ A: automated matches                                                                                                                                                                SCOP domains
               CATH domains 1ysqA00 A:5-191  [code=3.30.450.40, no name defined]                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------IclR-1ysqA01 A:50-177                                                                                                           -------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeee...............eee...hhhhhhhhhh.hhhhhhhhhhhh.............hhhhhhhhhhhhhhhh.eeee......eeeeeeee........eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ysq A   5 SLNIIHIAAPHLEALNIATGETINFSSREDDHAILIYKLEPTTGMLRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESHQHEIQPLTRNTITELPAMFDELAHIRESGAAMDREENELGVSCIAVPVFDIHGRVPYAVSISLSTSRLKQVGEKNLLKPLRETAQAISNELGFT------AITG 191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174      |  -   |   
                                                                                                                                                                                                          181    188
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  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) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: GAF (44)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YIAJ_ECOLI | P37671)
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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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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