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(-) Description

Title :  SOLUTION STRUCTURE OF THE CARBOXY-TERMINAL DOMAIN OF HUMAN TFIIH P44 SUBUNIT
 
Authors :  E. Kellenberger, C. Dominguez, S. Fribourg, E. Wasielewski, D. Moras, A. Poterszman, R. Boelens, B. Kieffer
Date :  21 Mar 05  (Deposition) - 12 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Basic Transcription Factor, Zinc Binding Protein, Ring Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Kellenberger, C. Dominguez, S. Fribourg, E. Wasielewski, D. Moras, A. Poterszman, R. Boelens, B. Kieffer
Solution Structure Of The C-Terminal Domain Of Tfiih P44 Subunit Reveals A Novel Type Of C4C4 Ring Domain Involved In Protein-Protein Interactions.
J. Biol. Chem. V. 280 20785 2005
PubMed-ID: 15790571  |  Reference-DOI: 10.1074/JBC.M412999200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P44 SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TFIIH P44 SUBUNIT, BASIC TRANSCRIPTION FACTOR 2 44 KDA SUBUNIT, BTF2-P44, GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 2

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:345 , CYS A:348 , CYS A:368 , ASP A:370 , CYS A:371BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWARECYS A:360 , CYS A:363 , CYS A:382 , CYS A:385BINDING SITE FOR RESIDUE ZN A 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z60)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z60)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z60)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z60)

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1hENST000002744001hENSE00002129657chr5:70363428-70363321108TF2H2_HUMAN-00--
1.4dENST000002744004dENSE00002186585chr5:70358623-7035853589TF2H2_HUMAN1-19190--
1.5bENST000002744005bENSE00001653789chr5:70357592-7035751578TF2H2_HUMAN19-45270--
1.6ENST000002744006ENSE00001626854chr5:70357135-7035709937TF2H2_HUMAN45-57130--
1.7aENST000002744007aENSE00001692511chr5:70356757-7035667187TF2H2_HUMAN58-86290--
1.8ENST000002744008ENSE00001724482chr5:70355997-7035594751TF2H2_HUMAN87-103170--
1.9ENST000002744009ENSE00001621998chr5:70355571-7035551755TF2H2_HUMAN104-122190--
1.11aENST0000027440011aENSE00001621067chr5:70351284-70351179106TF2H2_HUMAN122-157360--
1.13aENST0000027440013aENSE00001728075chr5:70344985-7034489591TF2H2_HUMAN157-187310--
1.13cENST0000027440013cENSE00001660523chr5:70344676-7034458988TF2H2_HUMAN188-217300--
1.13fENST0000027440013fENSE00001760916chr5:70343940-70343833108TF2H2_HUMAN217-253370--
1.14ENST0000027440014ENSE00001703422chr5:70341334-7034127164TF2H2_HUMAN253-274220--
1.15ENST0000027440015ENSE00001770367chr5:70338111-70338008104TF2H2_HUMAN274-309360--
1.16ENST0000027440016ENSE00001610077chr5:70337451-70337349103TF2H2_HUMAN309-343351A:328-34316
1.17ENST0000027440017ENSE00001647256chr5:70333373-7033333440TF2H2_HUMAN343-356141A:343-35614
1.18eENST0000027440018eENSE00002111686chr5:70331623-70330784840TF2H2_HUMAN357-395391A:357-38630

(-) 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:59
 aligned with TF2H2_HUMAN | Q13888 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:59
                                   337       347       357       367       377         
          TF2H2_HUMAN   328 LDAFQEIPLEEYNGERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHCCPGCI 386
               SCOP domains d1z60a1 A:328-386 TFIIH p44 subunit cysteine-rich domain    SCOP domains
               CATH domains 1z60A00 A:328-386                                           CATH domains
               Pfam domains ----------------C1_4-1z60A01 A:344-386                      Pfam domains
         Sec.struct. author .....eeehhhhh...ee....ee....eee.........hhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.16       -------------Exon 1.18e  PDB: A:357-386     Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.17     ------------------------------ Transcript 1 (2)
                 1z60 A 328 LDAFQEIPLEEYNGERFCYGCQGELKDQHVYVCAVCQNVFCVDCDVFVHDSLHSCPGCI 386
                                   337       347       357       367       377
   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: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: C1 (13)

(-) Gene Ontology  (38, 38)

NMR Structure(hide GO term definitions)
Chain A   (TF2H2_HUMAN | Q13888)
molecular function
    GO:0008094    DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
    GO:0008353    RNA polymerase II carboxy-terminal domain kinase activity    Catalysis of the reaction: ATP + (DNA-directed RNA polymerase II) = ADP + phospho-(DNA-directed RNA polymerase II); phosphorylation occurs on residues in the carboxy-terminal domain (CTD) repeats.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    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.
    GO:0008135    translation factor activity, RNA binding    Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    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:0002031    G-protein coupled receptor internalization    The process that results in the uptake of a G-protein coupled receptor into an endocytic vesicle.
    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:0070911    global genome nucleotide-excision repair    The nucleotide-excision repair process in which DNA lesions are removed from nontranscribed strands and from transcriptionally silent regions over the entire genome.
    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:0000717    nucleotide-excision repair, DNA duplex unwinding    The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.
    GO:0033683    nucleotide-excision repair, DNA incision    A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
    GO:0006295    nucleotide-excision repair, DNA incision, 3'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 3' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision precedes the incision formed 5' to the site of damage.
    GO:0006296    nucleotide-excision repair, DNA incision, 5'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
    GO:0006294    nucleotide-excision repair, preincision complex assembly    The aggregation, arrangement and bonding together of proteins on DNA to form the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage. This assembly occurs before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
    GO:0006293    nucleotide-excision repair, preincision complex stabilization    The stabilization of the multiprotein complex involved in damage recognition, DNA helix unwinding, and endonucleolytic cleavage at the site of DNA damage as well as the unwound DNA. The stabilization of the protein-DNA complex ensures proper positioning of the preincision complex before the phosphodiester backbone of the damaged strand is cleaved 3' and 5' of the site of DNA damage.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009411    response to UV    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 an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0006363    termination of RNA polymerase I transcription    The process in which the synthesis of an RNA molecule by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit.
    GO:0006362    transcription elongation from RNA polymerase I promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I.
    GO:0006368    transcription elongation from RNA polymerase II promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
    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:0006361    transcription initiation from RNA polymerase I promoter    Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0006283    transcription-coupled nucleotide-excision repair    The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
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: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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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  1z60
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 Related Entries

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

UniProtKB/Swiss-Prot
        TF2H2_HUMAN | Q13888: 5ivw 5iy6 5iy7 5iy8 5iy9

(-) Related Entries Specified in the PDB File

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