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(-) Description

Title :  THE STRUCTURE OF TRANSCRIPTIONAL FACTOR ARAR FROM BACTEROIDES THETAIOTAOMICRON VPI IN COMPLEX WITH TARGET DOUBLE STRAND DNA
 
Authors :  C. Chang, C. Tesar, D. Rodionov, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  24 Aug 15  (Deposition) - 09 Sep 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.06
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Arar, Dna Binding, Transcriptional Regulator, Bacteroides Thetaiotaomicron, Helix-Turn-Helix Motif, Nudix Fold, Transcription Regulator-Dna Complex (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 FACTOR ARAR
    Chains: A, B
    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
    Synonym: NUDIX FAMILY HYDROLASE
 
Molecule 2 - DNA (27-MER)
    Chains: C
    Engineered: YES
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON VPI-5482
    Organism Taxid: 226186
    Synthetic: YES
 
Molecule 3 - DNA (27-MER)
    Chains: D
    Engineered: YES
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON VPI-5482
    Organism Taxid: 226186
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric/Biological Unit (3, 21)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2MLA2Ligand/IonMALONIC ACID
3MSE17Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:16 , ARG A:86 , ASP A:87 , VAL A:92 , HIS A:131binding site for residue MLA A 301
2AC2SOFTWARELYS A:137binding site for residue FMT A 302
3AC3SOFTWAREASP A:57 , LYS B:137binding site for residue FMT B 301
4AC4SOFTWAREASP B:16 , ARG B:86 , ASP B:87 , VAL B:92 , HIS B:131binding site for residue MLA B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:37 -Pro A:38
2Glu B:37 -Pro B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DDG)

(-) 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh....eeeeeeeeeeee..eeeeeeee.........ee.eeee.....hhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeee......hhhhhhhh.eeeee.hhh.....hhhhhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeeeeee.......eeeeeehhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ddg A   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 B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...eeeeeeeeeeee..eeeeeeee.........ee.eeee.....hhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeee......hhhhhhhhheeeee.........hhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhh..eeeeeeee.......eeeeeehhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ddg B   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 C from PDB  Type:DNA  Length:27
                                                           
                 5ddg C   1 GCAAAAGTGTTACTTTTACACCCATGC  27
                                    10        20       


Chain D from PDB  Type:DNA  Length:27
                                                           
                 5ddg D   1 GCATGGGTGTAAAAGTAACACTTTTGC  27
                                    10        20
   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 5DDG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DDG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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    Glu A:37 - Pro A:38   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8AAV8_BACTN | Q8AAV8: 5bs6 5dd4 5deq

(-) Related Entries Specified in the PDB File

5dd4 RELATED ID: MCSG-APC111381 RELATED DB: TARGETTRACK