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(-) Description

Title :  CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN YXAF
 
Authors :  J. Seetharaman, S. Swaminathan, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  24 Feb 04  (Deposition) - 17 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Seetharaman, D. Kumaran, J. B. Bonanno, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Hth-Type Transcriptional Regulator Yxaf From Bacillus Subtilis.
Proteins V. 63 1087 2006
PubMed-ID: 16475182  |  Reference-DOI: 10.1002/PROT.20924
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR YXAF
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneYXAF, S14F, BSU39990
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423

 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 1SGM)

(-) Sites  (0, 0)

(no "Site" information available for 1SGM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_TETR_2PS50977 TetR-type HTH domain profile.YXAF_BACSU5-65
 
  2A:5-65
B:5-65

(-) Exons   (0, 0)

(no "Exon" information available for 1SGM)

(-) 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:184
 aligned with YXAF_BACSU | P42105 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:184
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
           YXAF_BACSU     5 GDSREKILHTASRLFQLQGYHATGLNQIVKESGAPKGSLYHFFPNGKEELAIEAVTYTGKIVEHLIQQSMDESSDPVEAIQLFIKKTASQFDNTESIKGIPVGLLASETALISEPLRTVCMKVFKSWEAVFARKLMENGFAEEEANQLGTLINSMIEGGIMLSLTNKDKTPLLLIAEQIPVLVR 188
               SCOP domains d1sgma1 A:5-77 Putative transcriptional regulator YxaF                   d1sgma2 A:78-188 Putative transcriptional regulator YxaF                                                        SCOP domains
               CATH domains 1sgmA00 A:5-188 Tetracycline Repressor, domain 2                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_TETR_2  PDB: A:5-65 UniProt: 5-65                        --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sgm A   5 GDSREKILHTASRLSQLQGYHATGLNQIVKESGAPKGSLYHFFPNGKEELAIEAVTYTGKIVEHLIQQSMDESSDPVEAIQLFIKKTASQFDNTESIKGIPVGLLASETALISEPLRTVCMKVFKSWEAVFARKLMENGFAEEEANQLGTLINSMIEGGIMLSLTNKDKTPLLLIAEQIPVLVR 188
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with YXAF_BACSU | P42105 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:184
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    
           YXAF_BACSU     5 GDSREKILHTASRLFQLQGYHATGLNQIVKESGAPKGSLYHFFPNGKEELAIEAVTYTGKIVEHLIQQSMDESSDPVEAIQLFIKKTASQFDNTESIKGIPVGLLASETALISEPLRTVCMKVFKSWEAVFARKLMENGFAEEEANQLGTLINSMIEGGIMLSLTNKDKTPLLLIAEQIPVLVR 188
               SCOP domains d1sgmb1 B:5-77 Putative transcriptional regulator YxaF                   d1sgmb2 B:78-188 Putative transcriptional regulator YxaF                                                        SCOP domains
               CATH domains 1sgmB00 B:5-188 Tetracycline Repressor, domain 2                                                                                                                                         CATH domains
           Pfam domains (1) ------TetR_N-1sgmB01 B:11-58                          ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------TetR_N-1sgmB02 B:11-58                          ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_TETR_2  PDB: B:5-65 UniProt: 5-65                        --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sgm B   5 GDSREKILHTASRLSQLQGYHATGLNQIVKESGAPKGSLYHFFPNGKEELAIEAVTYTGKIVEHLIQQSMDESSDPVEAIQLFIKKTASQFDNTESIKGIPVGLLASETALISEPLRTVCMKVFKSWEAVFARKLMENGFAEEEANQLGTLINSMIEGGIMLSLTNKDKTPLLLIAEQIPVLVR 188
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    

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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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (YXAF_BACSU | P42105)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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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