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(-) Description

Title :  CRYSTAL STRUCTURE OF A REX-FAMILY REPRESSOR/DNA/NAD+ COMPLEX FROM THERMUS AQUATICUS
 
Authors :  K. J. Mclaughlin, C. L. Kielkopf
Date :  06 Aug 09  (Deposition) - 09 Jun 10  (Release) - 16 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Redox-Sensing, Winged Helix, Rossmann Fold, Nicotinamide Adenine Dinucleotide, Nad, Rex, Thermus Aquaticus, Dna Binding Protein, Cytoplasm, Dna-Binding, Repressor, Transcription, Transcription Regulation, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Mclaughlin, C. M. Strain-Damerell, K. Xie, D. Brekasis, A. S. Soares, M. S. Paget, C. L. Kielkopf
Structural Basis For Nadh/Nad+ Redox Sensing By A Rex Family Repressor.
Mol. Cell V. 38 563 2010
PubMed-ID: 20513431  |  Reference-DOI: 10.1016/J.MOLCEL.2010.05.006

(-) Compounds

Molecule 1 - REDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX
    Atcc: BAA-163
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: REX, TT_C1293
    Organism Scientific: THERMUS THERMOPHILUS HB27
    Organism Taxid: 262724
    Strain: HB27 / DSM 7039
 
Molecule 2 - REX OPERATOR DNA
    Chains: C, D
    Engineered: YES
    Other Details: THE MINIMAL CONSENSUS BINDING SITE OF SOME REX FAMILY MEMBERS
    Other Details - Source: SYNTHETIC 22BP DSDNA OBTAINED FROM IDT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:87 , GLY A:89 , ARG A:90 , LEU A:91 , ASP A:112 , VAL A:113 , LYS A:117 , VAL A:130 , THR A:147 , VAL A:148 , PRO A:149 , ALA A:152 , PHE A:171 , ALA A:172 , PRO A:173 , PHE A:189 , HOH A:211 , HOH A:213 , ALA B:94 , LEU B:95 , TYR B:98 , HOH B:225 , HOH B:314BINDING SITE FOR RESIDUE NAD A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IKT)

(-) 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:204
 aligned with REX_THET2 | Q72I39 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:207
                             1                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
            REX_THET2     - -MKVPEAAISRLITYLRILEELEAQGVHRTSSEQLGELAQVTAFQVRKDLSYFGSYGTRGVGYTVPVLKRELRHILGLNRKWGLCIVGMGRLGSALADYPGFGESFELRGFFDVDPEKVGRPVRGGVIEHVDLLPQRVPGRIEIALLTVPREAAQKAADLLVAAGIKGILNFAPVVLEVPKEVAVENVDFLAGLTRLSFAILNPKWR 206
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3iktA01 A:0-73 'winged helix' repressor DNA binding domain                3iktA02 A:74-206 NAD(P)-binding Rossmann-like Domain                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhh.hhhhhhhhhhh......---.eehhhhhhhhhhhh.....eeeeee..hhhhhhhhh.......eeeeeeee........ee..eeeee.hhhhhh......eeee..hhhhhhhhhhhhhhh...eeee............eeee.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ikt A   0 GMKVPEAAISRLITYLRILEELEAQGVHRTSSEQLGELAQVTAFQVRKDLSYFGSYGT---GYTVPVLKRELRHILGLNRKWGLCIVGMGRLGSALADYPGFGESFELRGFFDVDPEKVGRPVRGGVIEHVDLLPQRVPGRIEIALLTVPREAAQKAADLLVAAGIKGILNFAPVVLEVPKEVAVENVDFLAGLTRLSFAILNPKWR 206
                                     9        19        29        39        49       | - |      69        79        89        99       109       119       129       139       149       159       169       179       189       199       
                                                                                    57  61                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with REX_THET2 | Q72I39 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
            REX_THET2     1 MKVPEAAISRLITYLRILEELEAQGVHRTSSEQLGELAQVTAFQVRKDLSYFGSYGTRGVGYTVPVLKRELRHILGLNRKWGLCIVGMGRLGSALADYPGFGESFELRGFFDVDPEKVGRPVRGGVIEHVDLLPQRVPGRIEIALLTVPREAAQKAADLLVAAGIKGILNFAPVVLEVPKEVAVENVDFLAGLTRLSFAILNPKWR 206
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3iktB01 B:1-73 'winged helix' repressor DNA binding domain               3iktB02 B:74-206 NAD(P)-binding Rossmann-like Domain                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhh..........eehhhhhhhhhhhh.....eeeeee....hhhhhhhh......eeeeeeee........ee..ee.ee.hhh.........eeee..hhhhhhhhhhhhhhh...eeee............eeee.hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ikt B   1 MKVPEAAISRLITYLRILEELEAQGVHRTSSEQLGELAQVTAFQVRKDLSYFGSYGTRGVGYTVPVLKRELRHILGLNRKWGLCIVGMGRLGSALADYPGFGESFELRGFFDVDPEKVGRPVRGGVIEHVDLLPQRVPGRIEIALLTVPREAAQKAADLLVAAGIKGILNFAPVVLEVPKEVAVENVDFLAGLTRLSFAILNPKWR 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      


Chain C from PDB  Type:DNA  Length:22
                                                      
                 3ikt C   1 CGCTGTGAACGCGTTCACAGCG  22
                                    10        20  


Chain D from PDB  Type:DNA  Length:22
                                                      
                 3ikt D   1 CGCTGTGAACGCGTTCACAGCG  22
                                    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 3IKT)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (REX_THET2 | Q72I39)
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

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

UniProtKB/Swiss-Prot
        REX_THET2 | Q72I39: 3ikv 3il2

(-) Related Entries Specified in the PDB File

1xcb CRYSTAL STRUCTURE OF A REX-FAMILY REPRESSOR/NADH COMPLEX FROM THERMUS AQUATICUS
3ikv CRYSTAL STRUCTURE OF A REX-FAMILY REPRESSOR R90D MUTANT FROM THERMUS AQUATICUS
3il2 CRYSTAL STRUCTURE OF A REX-FAMILY REPRESSOR R90D MUTANT/DNA COMPLEX FROM THERMUS AQUATICUS