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(-) Description

Title :  CRYSTAL STRUCTURE OF TTHA1657 (AT-RICH DNA-BINDING PROTEIN) FROM THERMUS THERMOPHILUS HB8
 
Authors :  A. Nakamura, A. Sosa, H. Komori, A. Kita, K. Miki
Date :  11 Jul 06  (Deposition) - 02 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Rex, Nadh, Nad, Rossmann Fold, Redox Sensing, Winged Helix, Thermus Themophilus, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Nakamura, A. Sosa, H. Komori, A. Kita, K. Miki
Crystal Structure Of Ttha1657 (At-Rich Dna-Binding Protein; P25) From Thermus Thermophilus Hb8 At 2. 16 A Resolution
Proteins V. 66 755 2007
PubMed-ID: 17154156  |  Reference-DOI: 10.1002/PROT.21222

(-) Compounds

Molecule 1 - AT-RICH DNA-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TTHA1657
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: REDOX SENSING REPRESSOR P25

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4SO46Ligand/IonSULFATE ION
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4SO412Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:30 , SER A:31 , ARG A:58 , GLY A:61 , HOH A:629BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWARESER B:30 , SER B:31 , ARG B:46 , TYR B:55 , THR B:57 , GLY B:59 , VAL B:60 , GLY B:61BINDING SITE FOR RESIDUE SO4 B 402
3AC3SOFTWAREARG A:72 , ASN A:78 , HOH A:690BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREARG B:120 , ARG B:123BINDING SITE FOR RESIDUE SO4 B 404
5AC5SOFTWARETYR A:98 , PRO A:99 , GLY A:100 , PHE A:101 , GLY A:102 , HOH A:723BINDING SITE FOR RESIDUE SO4 A 405
6AC6SOFTWARELYS A:155 , LEU A:159 , HOH A:676 , HOH A:683BINDING SITE FOR RESIDUE SO4 A 406
7AC7SOFTWAREGLY A:87 , MET A:88 , GLY A:89 , ARG A:90 , LEU A:91 , ASP A:112 , VAL A:113 , ASP A:114 , LYS A:117 , THR A:147 , VAL A:148 , PRO A:149 , ARG A:150 , GLU A:151 , PHE A:171 , ALA A:172 , PRO A:173 , VAL A:187 , PHE A:189 , HOH A:602 , HOH A:604 , HOH A:613 , HOH A:614 , HOH A:686 , HOH A:687 , HOH A:720 , ALA B:94 , LEU B:95 , TYR B:98 , PRO B:99 , PHE B:189 , HOH B:461BINDING SITE FOR RESIDUE NAD A 301
8AC8SOFTWAREALA A:94 , LEU A:95 , TYR A:98 , HOH A:612 , VAL B:86 , GLY B:87 , GLY B:89 , ARG B:90 , LEU B:91 , ASP B:112 , VAL B:113 , ASP B:114 , LYS B:117 , THR B:147 , VAL B:148 , PRO B:149 , ARG B:150 , ALA B:152 , PHE B:171 , ALA B:172 , PRO B:173 , VAL B:187 , PHE B:189 , HOH B:407 , HOH B:411 , HOH B:446 , HOH B:447 , HOH B:449 , HOH B:464 , HOH B:490 , HOH B:498BINDING SITE FOR RESIDUE NAD B 302
9AC9SOFTWAREGLY A:25 , VAL A:26 , HIS A:27 , ARG A:28 , HOH A:738BINDING SITE FOR RESIDUE GOL A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DT5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DT5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DT5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DT5)

(-) Exons   (0, 0)

(no "Exon" information available for 2DT5)

(-) 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:210
 aligned with REX_THET8 | Q5SHS3 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
            REX_THET8     2 KVPEAAISRLITYLRILEELEAQGVHRTSSEQLGELAQVTAFQVRKDLSYFGSYGTRGVGYTVPVLKRELRHILGLNRKWGLCIVGMGRLGSALADYPGFGESFELRGFFDVDPEKVGRPVRGGVIEHVDLLPQRVPGRIEIALLTVPREAAQKAADLLVAAGIKGILNFAPVVLEVPKEVAVENVDFLAGLTRLSFAILNPKWREEMMG 211
               SCOP domains --d2dt5a1 A:4-77 Transcriptional repressor Rex, N-terminal domain           d2dt5a2 A:78-203 Transcriptional repressor Rex, C-terminal domain                                                             -------- SCOP domains
               CATH domains 2dt5A01 A:2-73 'winged helix' repressor DNA binding domain              2dt5A02 A:74-211 NAD(P)-binding Rossmann-like Domain                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhh.........eehhhhhhhhhhhh.....eeeeee..hhhhhhhhhh......eeeeeeee........ee..eeeee..hhhhhh.....eeee..hhhhhhhhhhhhhhhh..eeee............eeee..hhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dt5 A   2 KVPEAAISRLITYLRILEELEAQGVHRTSSEQLGGLAQVTAFQVRKDLSYFGSYGTRGVGYTVPVLKRELRHILGLNRKWGLCIVGMGRLGSALADYPGFGESFELRGFFDVDPEKVGRPVRGGVIEHVDLLPQRVPGRIEIALLTVPREAAQKAADLLVAAGIKGILNFAPVVLEVPKEVAVENVDFLAGLTRLSFAILNPKWREEMMG 211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211


Chain B from PDB  Type:PROTEIN  Length:211
 aligned with REX_THET8 | Q5SHS3 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
            REX_THET8     1 MKVPEAAISRLITYLRILEELEAQGVHRTSSEQLGELAQVTAFQVRKDLSYFGSYGTRGVGYTVPVLKRELRHILGLNRKWGLCIVGMGRLGSALADYPGFGESFELRGFFDVDPEKVGRPVRGGVIEHVDLLPQRVPGRIEIALLTVPREAAQKAADLLVAAGIKGILNFAPVVLEVPKEVAVENVDFLAGLTRLSFAILNPKWREEMMG 211
               SCOP domains ---d2dt5b1 B:4-77 Transcriptional repressor Rex, N-terminal domain           d2dt5b2 B:78-203 Transcriptional repressor Rex, C-terminal domain                                                             -------- SCOP domains
               CATH domains 2dt5B01 B:1-73 'winged helix' repressor DNA binding domain               2dt5B02 B:74-211 NAD(P)-binding Rossmann-like Domain                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh...eehhhhhhhhh..hhhhhhhhhhhh.........eehhhhhhhhhhhh.....eeeeee..hhhhhhhhh.......eeeeeeee........ee..ee.ee.hhhhhh......eeee..hhhhhhhhhhhhhhhh..eeee............eeee....hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dt5 B   1 MKVPEAAISRLITYLRILEELEAQGVHRTSSEQLGGLAQVTAFQVRKDLSYFGSYGTRGVGYTVPVLKRELRHILGLNRKWGLCIVGMGRLGSALADYPGFGESFELRGFFDVDPEKVGRPVRGGVIEHVDLLPQRVPGRIEIALLTVPREAAQKAADLLVAAGIKGILNFAPVVLEVPKEVAVENVDFLAGLTRLSFAILNPKWREEMMG 211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DT5)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (REX_THET8 | Q5SHS3)
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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