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(-) Description

Title :  NMR STRUCTURE OF THE COMPLEX BETWEEN THE PH DOMAIN OF THE TFB1 SUBUNIT FROM TFIIH AND RAD4
 
Authors :  J. Lafrance-Vanasse, G. Arseneault, L. Cappadocia, P. Legault, J. G. O
Date :  16 Nov 12  (Deposition) - 23 Jan 13  (Release) - 06 Mar 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Tfb1, Ph Domain, Transcription-Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lafrance-Vanasse, G. Arseneault, L. Cappadocia, P. Legault, J. G. Omichinski
Structural And Functional Evidence That Rad4 Competes With Rad2 For Binding To The Tfb1 Subunit Of Tfiih In Ner.
Nucleic Acids Res. V. 41 2736 2013
PubMed-ID: 23295669  |  Reference-DOI: 10.1093/NAR/GKS1321

(-) Compounds

Molecule 1 - RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PGEX-2TK
    Fragment: UNP RESIDUES 2-115
    Gene: TFB1, YDR311W, D9740.3
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH SUBUNIT TFB1, TFIIH SUBUNIT TFB1, RNA POLYMERASE II TRANSCRIPTION FACTOR B 73 KDA SUBUNIT, RNA POLYMERASE II TRANSCRIPTION FACTOR B P73 SUBUNIT
 
Molecule 2 - DNA REPAIR PROTEIN RAD4
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PGEX-2TK
    Fragment: UNP RESIDUES 76-115
    Gene: RAD4, YER162C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2M14)

(-) Sites  (0, 0)

(no "Site" information available for 2M14)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M14)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M14)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M14)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2M14)

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR311W1YDR311W.1IV:1085063-10869911929TFB1_YEAST1-6426421A:1-115115
2.1YER162C1YER162C.1V:502889-5006252265RAD4_YEAST1-7547541B:90-10415

(-) Sequences/Alignments

NMR Structure
   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:115
 aligned with TFB1_YEAST | P32776 from UniProtKB/Swiss-Prot  Length:642

    Alignment length:115
                                    10        20        30        40        50        60        70        80        90       100       110     
           TFB1_YEAST     1 MSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDAD 115
               SCOP domains d2m14a_ A: RNA polymerase II transcription factor B 73 kDa, TFB1                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..ee..eeeeeeee......eeeeee.....eeeee.....eeee.........eeee......................eee....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-115 UniProt: 1-642 [INCOMPLETE]                                                                  Transcript 1
                 2m14 A   1 PSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDAD 115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain B from PDB  Type:PROTEIN  Length:15
 aligned with RAD4_YEAST | P14736 from UniProtKB/Swiss-Prot  Length:754

    Alignment length:15
                                    99     
           RAD4_YEAST    90 YDSEEFEDVTDGNEV 104
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ............... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
               Transcript 2 Exon 2.1        Transcript 2
                 2m14 B  90 YDSEEFEDVTDGNEV 104
                                    99
   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  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M14)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M14)

(-) Gene Ontology  (28, 34)

NMR Structure(hide GO term definitions)
Chain A   (TFB1_YEAST | P32776)
molecular function
    GO:0032266    phosphatidylinositol-3-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position.
    GO:0010314    phosphatidylinositol-5-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-5-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 5' position.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0000990    transcription factor activity, core RNA polymerase binding    Interacting selectively and non-covalently with an RNA polymerase in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0070816    phosphorylation of RNA polymerase II C-terminal domain    The process of introducing a phosphate group on to an amino acid residue in the C-terminal domain of RNA polymerase II. Typically, this occurs during the transcription cycle and results in production of an RNA polymerase II enzyme where the carboxy-terminal domain (CTD) of the largest subunit is extensively phosphorylated, often referred to as hyperphosphorylated or the II(0) form. Specific types of phosphorylation within the CTD are usually associated with specific regions of genes, though there are exceptions. The phosphorylation state regulates the association of specific complexes such as the capping enzyme or 3'-RNA processing machinery to the elongating RNA polymerase complex.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006360    transcription from RNA polymerase I promoter    The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000439    core TFIIH complex    The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005675    holo TFIIH complex    A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex.
    GO:0000112    nucleotide-excision repair factor 3 complex    One of several protein complexes involved in nucleotide-excision repair; possesses endodeoxynuclease and DNA helicase activities. In S. cerevisiae, it is composed of Rad2p and the core TFIIH-Ssl2p complex (core TFIIH is composed of Rad3p, Tfb1p, Tfb2p, Ssl1p, Tfb4p and Tfb5p. Note that Ssl2p is also called Rad25p).
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B   (RAD4_YEAST | P14736)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:1990165    single-strand break-containing DNA binding    Interacting selectively and non-covalently with damaged DNA containing single-strand breaks (SSBs).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
cellular component
    GO:0071942    XPC complex    A nucleotide-excision repair complex that is involved in damage sensing during global genome nucleotide excision repair (GG-NER). It is part of the pre-incision (or initial recognition) complex bound to sites of DNA damage. In human, it is composed of XPC, RAD23B and CETN2.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0000111    nucleotide-excision repair factor 2 complex    One of several protein complexes involved in nucleotide-excision repair; possesses damaged DNA binding activity. In S. cerevisiae, it is composed of Rad4p and Rad23p.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  TFB1_YEAST | P32776
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 Related Entries

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

UniProtKB/Swiss-Prot
        RAD4_YEAST | P14736: 2qsf 2qsg 2qsh 4yir
        TFB1_YEAST | P32776: 1y5o 2gs0 2k2u 2l2i 2lox 2mkr 2n0y 2n23 5urn

(-) Related Entries Specified in the PDB File

1y5o
2gs0
2k2u
2l2i
2lox RELATED ID: 18842 RELATED DB: BMRB