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(-) Description

Title :  NMR STRUCTURE OF A COMPLEX FORMED BY THE C-TERMINAL DOMAIN OF HUMAN RAP74 AND A PHOSPHORYLATED PEPTIDE FROM THE CENTRAL DOMAIN OF THE FCP1
 
Authors :  A. Yang, K. L. Abbott, A. Desjardins, P. Di Lello, J. G. Omichinski, P. Legault
Date :  13 Aug 08  (Deposition) - 02 Jun 09  (Release) - 09 Jun 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (21x)
Keywords :  Tfiif, Fcp1, Phosphorylation, Ck2, Rap74, Nucleus, Phosphoprotein, Polymorphism, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Yang, K. L. Abbott, A. Desjardins, P. Di Lello, J. G. Omichinski, P. Legault
Nmr Structure Of A Complex Formed By The Carboxyl-Terminal Domain Of Human Rap74 And A Phosphorylated Peptide From The Central Domain Of The Fcp1 Phosphatase
Biochemistry V. 48 1964 2009
PubMed-ID: 19215094  |  Reference-DOI: 10.1021/BI801549M
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CENTFCP1-T584PO4 PEPTIDE
    Chains: B
    Engineered: YES
    Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 451 TO 517)
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED BY THE SOLID-PHASE METHOD
    Synthetic: YES
 
Molecule 2 - GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TOPP2
    Gene: GTF2F1, RAP74
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ALPHA, TFIIF-ALPHA, TRANSCRIPTION INITIATION FACTOR RAP74, GENERAL TRANSCRIPTION FACTOR IIF POLYPEPTIDE 1 74 KDA SUBUNIT PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (21x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (0, 0)

(no "Site" information available for 2K7L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K7L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K7L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2K7L)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003944561ENSE00002168237chr19:6393291-6392995297T2FA_HUMAN1-440--
1.2ENST000003944562ENSE00001664061chr19:6392914-639286847T2FA_HUMAN5-20160--
1.3ENST000003944563ENSE00001720340chr19:6391985-639191373T2FA_HUMAN20-44250--
1.4ENST000003944564ENSE00000666056chr19:6389648-6389455194T2FA_HUMAN45-109650--
1.5ENST000003944565ENSE00000666058chr19:6387570-6387400171T2FA_HUMAN109-166580--
1.6ENST000003944566ENSE00000666060chr19:6383506-6383322185T2FA_HUMAN166-228630--
1.7ENST000003944567ENSE00001060029chr19:6381861-6381708154T2FA_HUMAN228-279520--
1.8ENST000003944568ENSE00001060032chr19:6381626-638156562T2FA_HUMAN279-300220--
1.9ENST000003944569ENSE00001060028chr19:6381489-6381370120T2FA_HUMAN300-340410--
1.10ENST0000039445610ENSE00000666066chr19:6381206-638113374T2FA_HUMAN340-364250--
1.11ENST0000039445611ENSE00000666068chr19:6381053-6380915139T2FA_HUMAN365-411470--
1.12ENST0000039445612ENSE00000666070chr19:6380701-6380584118T2FA_HUMAN411-450400--
1.13ENST0000039445613ENSE00001518517chr19:6380496-6379580917T2FA_HUMAN450-517681A:451-51767

(-) 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:67
 aligned with T2FA_HUMAN | P35269 from UniProtKB/Swiss-Prot  Length:517

    Alignment length:67
                                   460       470       480       490       500       510       
           T2FA_HUMAN   451 DVQVTEDAVRRYLTRKPMTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRLNPERKMINDKMHFSLKE 517
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains 2k7lA00 A:451-517 'winged helix' repressor DNA binding domain       CATH domains
               Pfam domains TFIIF_alpha-2k7lA01 A:451-517                                       Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.eeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.13  PDB: A:451-517 UniProt: 450-517 [INCOMPLETE]             Transcript 1
                 2k7l A 451 DVQVTEDAVRRYLTRKPMTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRLNPERKMINDKMHFSLKE 517
                                   460       470       480       490       500       510       


Chain B from PDB  Type:PROTEIN  Length:19
 aligned with CTDP1_HUMAN | Q9Y5B0 from UniProtKB/Swiss-Prot  Length:961

    Alignment length:19
                                   591         
          CTDP1_HUMAN   582 EDTDEDDHLIYLEEILVRV 600
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 2k7l B 582 EDtDEDDHLIYLEEILVRV 600
                              |    591         
                              |                
                            584-TPO
   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 2K7L)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: TFIIF_alpha] (3)

(-) Gene Ontology  (45, 51)

NMR Structure(hide GO term definitions)
Chain A   (T2FA_HUMAN | P35269)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0019211    phosphatase activator activity    Increases the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
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:0008543    fibroblast growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
    GO:0010467    gene expression    The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0032968    positive regulation of transcription elongation from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0050434    positive regulation of viral transcription    Any process that activates or increases the frequency, rate or extent of viral transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009615    response to virus    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 from a virus.
    GO:0042795    snRNA transcription from RNA polymerase II promoter    The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
    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: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.
cellular component
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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.
    GO:0005674    transcription factor TFIIF complex    A general transcription initiation factor which in humans consists of a heterodimer of an alpha and a beta subunit. Helps recruit RNA polymerase II to the initiation complex and promotes translation elongation.

Chain B   (CTDP1_HUMAN | Q9Y5B0)
molecular function
    GO:0008420    CTD phosphatase activity    Catalysis of the reaction: phospho-(DNA-directed RNA polymerase) + H2O = (DNA-directed RNA polymerase) + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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).
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0070940    dephosphorylation of RNA polymerase II C-terminal domain    The process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form.
    GO:0010458    exit from mitosis    The cell cycle transition where a cell leaves M phase and enters a new G1 phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
    GO:0061052    negative regulation of cell growth involved in cardiac muscle cell development    Any process that decreases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
    GO:0050434    positive regulation of viral transcription    Any process that activates or increases the frequency, rate or extent of viral transcription.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    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).
cellular component
    GO:0016591    DNA-directed RNA polymerase II, holoenzyme    A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters.
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    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.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
    GO:0051233    spindle midzone    The area in the center of the spindle where the spindle microtubules from opposite poles overlap.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CTDP1_HUMAN | Q9Y5B0: 1j2x 1onv
        T2FA_HUMAN | P35269: 1f3u 1i27 1j2x 1nha 1onv 5iy6 5iy7 5iy8 5iy9 5iya 5iyb 5iyc 5iyd

(-) Related Entries Specified in the PDB File

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