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(-) Description

Title :  STRUCTURE OF THE EFFECTOR-BINDING DOMAIN OF ARABINOSE REPRESSOR ARAR FROM BACILLUS SUBTILIS
 
Authors :  P. Rezacova, K. Prochazkova
Date :  05 Aug 11  (Deposition) - 25 Jan 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription Regulation, Arabinose Binding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Prochazkova, K. Cermakova, P. Pachl, I. Sieglova, M. Fabry, Z. Otwinowski, P. Rezacova
Structure Of The Effector-Binding Domain Of The Arabinose Repressor Arar From Bacillus Subtilis.
Acta Crystallogr. , Sect. D V. 68 176 2012
PubMed-ID: 22281747  |  Reference-DOI: 10.1107/S090744491105414X

(-) Compounds

Molecule 1 - ARABINOSE METABOLISM TRANSCRIPTIONAL REPRESSOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET51/D-TOPO
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EFFECTOR BINDING DOMAIN (UNP RESIDUES 71-362)
    Gene: ARAC, ARAR, BSU33970, YVBS
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ARB2Ligand/IonBETA-L-ARABINOSE
2GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:92 , GLU A:142 , ASN A:170 , GLN A:214 , ARG A:218 , ASN A:273 , ASP A:301 , HIS A:318 , HOH A:524 , HOH A:579BINDING SITE FOR RESIDUE ARB A 400
2AC2SOFTWARETHR A:240 , GLU A:245 , PRO B:121 , LEU B:148 , GLN B:149 , PRO B:151 , HOH B:511BINDING SITE FOR RESIDUE GOL A 401
3AC3SOFTWARETYR B:92 , GLU B:142 , ASN B:170 , GLN B:214 , ARG B:218 , ASN B:273 , ASP B:301 , HIS B:318 , HOH B:501 , HOH B:509 , HOH B:592BINDING SITE FOR RESIDUE ARB B 400
4AC4SOFTWAREHOH A:583 , SER B:146 , ALA B:147 , LEU B:148 , GLN B:149 , THR B:150 , ALA B:174BINDING SITE FOR RESIDUE GOL B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TB6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:291 -Pro A:292
2Val B:291 -Pro B:292

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TB6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TB6)

(-) Exons   (0, 0)

(no "Exon" information available for 3TB6)

(-) 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:283
 aligned with ARAR_BACSU | P96711 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:283
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358   
           ARAR_BACSU    79 NKTIGVLTTYISDYIFPSIIRGIESYLSEQGYSMLLTSTNNNPDNERRGLENLLSQHIDGLIVEPTKSALQTPNIGYYLNLEKNGIPFAMINASYAELAAPSFTLDDVKGGMMAAEHLLSLGHTHMMGIFKADDTQGVKRMNGFIQAHRERELFPSPDMIVTFTTEEKESKLLEKVKATLEKNSKHMPTAILCYNDEIALKVIDMLREMDLKVPEDMSIVGYDDSHFAQISEVKLTSVKHPKSVLGKAAAKYVIDCLEHKKPKQEDVIFEPELIIRQSARKLN 361
               SCOP domains d3tb6a_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhh...eeee..........eeeehhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh....hhh.eeeehhhhhhhhhhhhhhhhhhhh......eee..hhhhhhhhhhhhhhh........eee.....hhhhhh.....eee..hhhhhhhhhhhhhhhhh........eee..eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tb6 A  79 NKTIGVLTTYISDYIFPSIIRGIESYLSEQGYSMLLTSTNNNPDNERRGLENLLSQHIDGLIVEPTKSALQTPNIGYYLNLEKNGIPFAMINASYAELAAPSFTLDDVKGGMMAAEHLLSLGHTHMMGIFKADDTQGVKRMNGFIQAHRERELFPSPDMIVTFTTEEKESKLLEKVKATLEKNSKHMPTAILCYNDEIALKVIDMLREMDLKVPEDMSIVGYDDSHFAQISEVKLTSVKHPKSVLGKAAAKYVIDCLEHKKPKQEDVIFEPELIIRQSARKLN 361
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358   


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with ARAR_BACSU | P96711 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:283
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359   
           ARAR_BACSU    80 KTIGVLTTYISDYIFPSIIRGIESYLSEQGYSMLLTSTNNNPDNERRGLENLLSQHIDGLIVEPTKSALQTPNIGYYLNLEKNGIPFAMINASYAELAAPSFTLDDVKGGMMAAEHLLSLGHTHMMGIFKADDTQGVKRMNGFIQAHRERELFPSPDMIVTFTTEEKESKLLEKVKATLEKNSKHMPTAILCYNDEIALKVIDMLREMDLKVPEDMSIVGYDDSHFAQISEVKLTSVKHPKSVLGKAAAKYVIDCLEHKKPKQEDVIFEPELIIRQSARKLNE 362
               SCOP domains d3tb6b_ B: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhh....eeee..........hhhhhhhhhhh...eeee..........eeeehhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh....hhh.eeeehhhhh.hhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh........eee.....hhhhhh.....ee...hhhhhhhhhhhhhhhhh........eee...ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tb6 B  80 KTIGVLTTYISDYIFPSIIRGIESYLSEQGYSMLLTSTNNNPDNERRGLENLLSQHIDGLIVEPTKSALQTPNIGYYLNLEKNGIPFAMINASYAELAAPSFTLDDVKGGMMAAEHLLSLGHTHMMGIFKADDTQGVKRMNGFIQAHRERELFPSPDMIVTFTTEEKESKLLEKVKATLEKNSKHMPTAILCYNDEIALKVIDMLREMDLKVPEDMSIVGYDDSHFAQISEVKLTSVKHPKSVLGKAAAKYVIDCLEHKKPKQEDVIFEPELIIRQSARKLNE 362
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TB6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TB6)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ARAR_BACSU | P96711)
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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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    Val A:291 - Pro A:292   [ RasMol ]  
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  3tb6
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARAR_BACSU | P96711: 4egy 4egz 4h0e 5d4r 5d4s

(-) Related Entries Specified in the PDB File

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