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(-) Description

Title :  STRUCTURE AND FUNCTIONAL PROPERTIES OF THE BACILLUS SUBTILIS TRANSCRIPTIONAL REPRESSOR REX
 
Authors :  E. Wang, M. C. Bauer, A. Rogstam, S. Linse, D. T. Logan, C. Von Wachenfe
Date :  08 May 08  (Deposition) - 09 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcriptional Regulation, Redox Poise, Dna-Binding, Transcription, Repressor, Dna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Wang, M. C. Bauer, A. Rogstam, S. Linse, D. T. Logan, C. Von Wachenfeldt
Structure And Functional Properties Of The Bacillus Subtilis Transcriptional Repressor Rex.
Mol. Microbiol. V. 69 466 2008
PubMed-ID: 18485070  |  Reference-DOI: 10.1111/J.1365-2958.2008.06295.X

(-) Compounds

Molecule 1 - REDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET101
    Expression System Strain: TURNER(DE3)
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 1A1
    Synonym: REX

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:44 , GLY B:92 , VAL B:93 , GLY B:94 , ASN B:95 , ASP B:118 , ILE B:119 , LEU B:136 , THR B:152 , VAL B:153 , PRO B:154 , ALA B:157 , ILE B:161 , HOH B:2077 , HOH B:2078 , HOH B:2079BINDING SITE FOR RESIDUE NAD B1214
2AC2SOFTWAREGLY A:92 , VAL A:93 , GLY A:94 , ASN A:95 , ASP A:118 , ILE A:119 , LYS A:123 , LEU A:136 , THR A:152 , VAL A:153 , PRO A:154 , ALA A:157 , ILE A:161 , HOH A:2054 , HOH A:2055BINDING SITE FOR RESIDUE NAD A1210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VT2)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1His A:102 -Tyr A:103
2Lys B:7 -Ile B:8
3Glu B:212 -Glu B:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VT2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VT2)

(-) Exons   (0, 0)

(no "Exon" information available for 2VT2)

(-) 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 REX_BACSU | O05521 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:199
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
            REX_BACSU    11 ATAKRLPLYYRFLKNLHASGKQRVSSAELSDAVKVDSATIRRDFSYFGALGKKGYGYNVDYLLSFFRKTLDQDEMTDVILIGVGNLGTAFLHYNFTKNNNTKISMAFDINESKIGTEVGGVPVYNLDDLEQHVKDESVAILTVPAVAAQSITDRLVALGIKGILNFTPARLNVPEHIRIHHIDLAVELQSLVYFLKHYS 209
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhh...-----.eehhhhhhhhhhhhhhh---.eeee..hhhhhhhh..-------..eeeeee.......eee..eeeee..hhhhhh....eeee..hhhhhhhhhhhhhhh...eeee............eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vt2 A  11 ATAKRLPLYYRFLKNLHASGKQRVSSAELSDAVKVDSATIRRDFSYFGAL-----GYNVDYLLSFFRKTLDQD---DVILIGVGNLGTAFLHY-------TKISMAFDINESKIGTEVGGVPVYNLDDLEQHVKDESVAILTVPAVAAQSITDRLVALGIKGILNFTPARLNVPEHIRIHHIDLAVELQSLVYFLKHYS 209
                                    20        30        40        50        60     |  70        80  |   | 90       100  |      -|      120       130       140       150       160       170       180       190       200         
                                                                            60    66               83  87             103     111                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with REX_BACSU | O05521 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:207
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       
            REX_BACSU     7 KIPQATAKRLPLYYRFLKNLHASGKQRVSSAELSDAVKVDSATIRRDFSYFGALGKKGYGYNVDYLLSFFRKTLDQDEMTDVILIGVGNLGTAFLHYNFTKNNNTKISMAFDINESKIGTEVGGVPVYNLDDLEQHVKDESVAILTVPAVAAQSITDRLVALGIKGILNFTPARLNVPEHIRIHHIDLAVELQSLVYFLKHYSVLEE 213
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Put_DNA-bind_N-2vt2B01 B:7-55                    ---------------------------CoA_binding-2vt2B03 B:83-179                                                                     ---------------------------------- Pfam domains (1)
           Pfam domains (2) Put_DNA-bind_N-2vt2B02 B:7-55                    ---------------------------CoA_binding-2vt2B04 B:83-179                                                                     ---------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhhh....---.eehhhhhhhhhhhhhhhhheeeeee..hhhhhhhhh........eeeeeeee........ee..eeeee..hhhhhh....eeee..hhhhhhhhhhhhhhh...eeee............eeee.hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vt2 B   7 KIPQATAKRLPLYYRFLKNLHASGKQRVSSAELSDAVKVDSATIRRDFSYFGALGK---GYNVDYLLSFFRKTLDQDEMTDVILIGVGNLGTAFLHYNFTKNNNTKISMAFDINESKIGTEVGGVPVYNLDDLEQHVKDESVAILTVPAVAAQSITDRLVALGIKGILNFTPARLNVPEHIRIHHIDLAVELQSLVYFLKHYSVLEE 213
                                    16        26        36        46        56     |  66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       
                                                                                  62  66
   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 2VT2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VT2)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (REX_BACSU | O05521)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051775    response to redox state    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating redox state. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.
    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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 Related Entries

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        REX_BACSU | O05521: 2vt3

(-) Related Entries Specified in the PDB File

2vt3 STRUCTURE AND FUNCTIONAL PROPERTIES OF THE BACILLUS SUBTILIS TRANSCRIPTIONAL REPRESSOR REX