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(-) Description

Title :  APO STRUCTURE OF TRANSCRIPTIONAL FACTOR ARAR FROM BACTEROIDES THETAIOTAOMICRON VPI
 
Authors :  C. Chang, C. Tesar, R. Jedrzejczak, A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg)
Date :  01 Jun 15  (Deposition) - 17 Jun 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Transcriptional Regulator, Bacteroides Thetaiotaomicron, Helix-Turn-Helix Motif, Nudix Fold, Dna Binding, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, C. Tesar, X. Li, Y. Kim, D. A. Rodionov, A. Joachimiak
A Novel Transcriptional Regulator Of L-Arabinose Utilizatio In Human Gut Bacteria.
Nucleic Acids Res. V. 43 10546 2015
PubMed-ID: 26438537  |  Reference-DOI: 10.1093/NAR/GKV1005

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR ARAR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG68
    Expression System Taxid: 562
    Gene: BT_0354
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON (STRAIN ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
    Organism Taxid: 226186
    Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 39)

Asymmetric Unit (2, 39)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE35Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 19)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE17Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 20)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:16 , ARG A:86 , ASP A:87 , HIS A:131binding site for residue EDO A 301
2AC2SOFTWAREASP B:16 , ARG B:86 , ASP B:87 , VAL B:92 , HIS B:131binding site for residue EDO B 301
3AC3SOFTWAREASP C:16 , ARG C:86 , ASP C:87 , VAL C:92 , HIS C:131binding site for residue EDO C 301
4AC4SOFTWAREASP D:16 , ARG D:86 , ASP D:87 , VAL D:92 , HIS D:131binding site for residue EDO D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BS6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:37 -Pro A:38
2Glu B:37 -Pro B:38
3Glu C:37 -Pro C:38
4Glu D:37 -Pro D:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BS6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BS6)

(-) Exons   (0, 0)

(no "Exon" information available for 5BS6)

(-) Sequences/Alignments

Asymmetric 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:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeee..eeeeeeee.........ee.eeee.....hhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeee......hhhhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhh...hhhhhhhhhhh...eeeeeeeeeee..eeeeeeeehhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bs6 A   3 NYYSSNPTFYLGIDCIIFGFNEGEISLLLLKRNFEPAmGEWSLmGGFVQKDESVDDAAKRVLAELTGLENVYmEQVGAFGAIDRDPGERVVSIAYYALININEYDRELVQKHNAYWVNINELPALIFDHPEmVDKAREmmKQKASVEPIGFNLLPKLFTLSQLQSLYEAIYGEPmDKRNFRKRVAEmDFIEKTDKIDKLGSKRGAALYKFNGKAYRKDPKFKL 225
                                    12        22        32       |42   |    52        62        72  |     82        92       102       112       122       132 |     142       152       162       172    |  182      |192       202       212       222   
                                                                40-MSE |                           75-MSE                                                    134-MSE  ||                                177-MSE     189-MSE                                
                                                                      46-MSE                                                                                        141-MSE                                                                                
                                                                                                                                                                     142-MSE                                                                               


Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeeeee..eeeeeeee.........ee.eeee.....hhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeee......hhhhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh....hhhhhhhhhhh...eeeeeeeee.....eeeeeeehhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bs6 B   0 AmKNYYSSNPTFYLGIDCIIFGFNEGEISLLLLKRNFEPAmGEWSLmGGFVQKDESVDDAAKRVLAELTGLENVYmEQVGAFGAIDRDPGERVVSIAYYALININEYDRELVQKHNAYWVNINELPALIFDHPEmVDKAREmmKQKASVEPIGFNLLPKLFTLSQLQSLYEAIYGEPmDKRNFRKRVAEmDFIEKTDKIDKLGSKRGAALYKFNGKAYRKDPFKL 225
                             |       9        19        29        39|     | 49        59        69     |  79        89        99       109       119       129    |  139 ||    149       159       169       179       189       199       209       219 ||  
                             1-MSE                                 40-MSE |                           75-MSE                                                    134-MSE  ||                                177-MSE     189-MSE                         221|  
                                                                         46-MSE                                                                                        141-MSE                                                                          223  
                                                                                                                                                                        142-MSE                                                                              


Chain C from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.......eeeeeeeeeeee..eeeeeeee.........ee.eeee.....hhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeee......hhhhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeeeeeeee...eeeeeeeehhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bs6 C   0 AmKNYYSSNPTFYLGIDCIIFGFNEGEISLLLLKRNFEPAmGEWSLmGGFVQKDESVDDAAKRVLAELTGLENVYmEQVGAFGAIDRDPGERVVSIAYYALININEYDRELVQKHNAYWVNINELPALIFDHPEmVDKAREmmKQKASVEPIGFNLLPKLFTLSQLQSLYEAIYGEPmDKRNFRKRVAEmDFIEKTDKIDKLGSKRGAALYKFNGKAYRKDPKFKL 225
                             |       9        19        29        39|     | 49        59        69     |  79        89        99       109       119       129    |  139 ||    149       159       169       179       189       199       209       219      
                             |                                     40-MSE |                           75-MSE                                                    134-MSE  ||                                177-MSE     189-MSE                                
                             1-MSE                                       46-MSE                                                                                        141-MSE                                                                                
                                                                                                                                                                        142-MSE                                                                               


Chain D from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeeeeeeeee..eeeeeeee.........ee.eeee.....hhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeee......hhhhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhhh.hhhhh...eehhhhhhhhhhhhhh...hhhhhhhhhhh...eeeeeeeee.....eeeeeeehhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5bs6 D  -2 SNAmKNYYSSNPTFYLGIDCIIFGFNEGEISLLLLKRNFEPAmGEWSLmGGFVQKDESVDDAAKRVLAELTGLENVYmEQVGAFGAIDRDPGERVVSIAYYALININEYDRELVQKHNAYWVNINELPALIFDHPEmVDKAREmmKQKASVEPIGFNLLPKLFTLSQLQSLYEAIYGEPmDKRNFRKRVAEmDFIEKTDKIDKLGSKRGAALYKFNGKAYRKDPKFKL 225
                               |     7        17        27        37  |     47        57        67       |77        87        97       107       117       127      |137   ||  147       157       167       177       187 |     197       207       217        
                               1-MSE                                 40-MSE |                           75-MSE                                                    134-MSE  ||                                177-MSE     189-MSE                                
                                                                           46-MSE                                                                                        141-MSE                                                                                
                                                                                                                                                                          142-MSE
   Legend:   → Mismatch (orange background)
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    → 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 ; only for superseded entry 2FB1: 2,8)

(no "SCOP Domain" information available for 5BS6, only for superseded entry 2FB1 replaced by 5BS6)

(-) CATH Domains  (0, 0 ; only for superseded entry 2FB1: 2,8)

(no "CATH Domain" information available for 5BS6, only for superseded entry 2FB1 replaced by 5BS6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BS6)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

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        Q8AAV8_BACTN | Q8AAV8: 5dd4 5ddg 5deq

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