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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SIGMA-54-DEPENDENT TRANSCRIPTIONAL REGULATOR DOMAIN FROM CHLOROBIUM TEPIDUM TLS
 
Authors :  R. Wu, S. Clancy, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  30 Sep 09  (Deposition) - 19 Jan 10  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sigma-54-Dependent Transcriptional Regulator Domain, Chlorobium Tepidum Tls, Crystal Structure, Psi-2, Protein Structure Initiative, Structural Genomics, Midwest Center For Structural Genomics (Mcsg), Atp-Binding, Dna-Binding, Nucleotide-Binding, Transcription, Transcription Regulation, Two-Component Regulatory System, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Wu, S. Clancy, A. Joachimiak
The Crystal Structure Of Sigma-54-Dependent Transcriptional Regulator Domain From Chlorobium
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIGMA-54-DEPENDENT TRANSCRIPTIONAL REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: CT0108, GAF
    Organism Scientific: CHLOROBIUM TEPIDUM TLS
    Organism Taxid: 194439

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3K2N)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K2N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K2N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K2N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K2N)

(-) Exons   (0, 0)

(no "Exon" information available for 3K2N)

(-) 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:177
 aligned with Q8KG60_CHLTE | Q8KG60 from UniProtKB/TrEMBL  Length:723

    Alignment length:186
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197      
         Q8KG60_CHLTE    18 RNPPMNATTLPEALKLMQYIGDAIGTIRDPQELFRTVTDKLRLLFAFDSAVIITIDRERREASVFFEMLRFELPEQLRHQTRSIAGTWLEGHLDDRTVTVASIARDIPSFGADGAPLLWTLHELGMRQIVLSPLRSGGRVIGFLSFVSAEEKLWSDGDKSLLSGVSSSIAIAVSNALAYEELRQRE 203
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hh---------hhhhhhhhhhhhhh...hhhhhhhhhhhhhh......eeeeeeee....eeeeeeee............eee...hhhhhhh.....eeee............hhhhhhhhhhh..eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k2n A  -2 SN---------AALKLmQYIGDAIGTIRDPQELFRTVTDKLRLLFAFDSAVIITIDRERREASVFFEmLRFELPEQLRHQTRSIAGTWLEGHLDDRTVTVASIARDIPSFGADGAPLLWTLHELGmRQIVLSPLRSGGRVIGFLSFVSAEEKLWSDGDKSLLSGVSSSIAIAVSNALAYEELRQRE 174
                             |       - |    |  8        18        28        38        48       |58        68        78        88        98       108     | 118       128       138       148       158       168      
                             |         0    |                                                 56-MSE                                                   114-MSE                                                        
                            -1              5-MSE                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with Q8KG60_CHLTE | Q8KG60 from UniProtKB/TrEMBL  Length:723

    Alignment length:186
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197      
         Q8KG60_CHLTE    18 RNPPMNATTLPEALKLMQYIGDAIGTIRDPQELFRTVTDKLRLLFAFDSAVIITIDRERREASVFFEMLRFELPEQLRHQTRSIAGTWLEGHLDDRTVTVASIARDIPSFGADGAPLLWTLHELGMRQIVLSPLRSGGRVIGFLSFVSAEEKLWSDGDKSLLSGVSSSIAIAVSNALAYEELRQRE 203
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------------GAF-3k2nB01 B:17-161                                                                                                                             ------------- Pfam domains (1)
           Pfam domains (2) ----------------------------GAF-3k2nB02 B:17-161                                                                                                                             ------------- Pfam domains (2)
         Sec.struct. author hh---------hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......eeeeeeee....eeeeeeee.....hhhhh..eee.....hhhhh.....eeee............hhhhhhhhhh...eeeeeeeee..eeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k2n B  -2 SN---------AALKLmQYIGDAIGTIRDPQELFRTVTDKLRLLFAFDSAVIITIDRERREASVFFEmLRFELPEQLRHQTRSIAGTWLEGHLDDRTVTVASIARDIPSFGADGAPLLWTLHELGmRQIVLSPLRSGGRVIGFLSFVSAEEKLWSDGDKSLLSGVSSSIAIAVSNALAYEELRQRE 174
                             |       - |    |  8        18        28        38        48       |58        68        78        88        98       108     | 118       128       138       148       158       168      
                            -1         0    |                                                 56-MSE                                                   114-MSE                                                        
                                            5-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3K2N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K2N)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GAF (44)
(-)
Family: GAF (30)
(-)
Chlorobium tepidum (1)
1aGAF-3k2nB01B:17-161
1bGAF-3k2nB02B:17-161

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8KG60_CHLTE | Q8KG60)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
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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 Related Entries

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