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(-) Description

Title :  SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE KAP-1 COREPRESSOR
 
Authors :  A. D. Capili, D. C. Schultz, F. J. Rauscher Iii, K. L. B. Borden
Date :  29 Aug 00  (Deposition) - 24 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Phd Domain, C3Hc4 Type Zinc Binding Domain, Nmr-Structure, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. D. Capili, D. C. Schultz, F. J. Rauscheriii, K. L. Borden
Solution Structure Of The Phd Domain From The Kap-1 Corepressor: Structural Determinants For Phd, Ring And Lim Zinc-Binding Domains.
Embo J. V. 20 165 2001
PubMed-ID: 11226167  |  Reference-DOI: 10.1093/EMBOJ/20.1.165
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KAP-1 COREPRESSOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE50
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PHD DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRANSCRIPTION INTERMEDIARY FACTOR 1-BETA, NUCLEAR COREPRESSOR, KAP-1, KRAB-ASSOCIATED PROTEIN 1

 Structural Features

(-) Chains, Units

  
NMR Structure : 

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:40 , GLN A:42 , CYS A:43 , CYS A:66 , CYS A:69BINDING SITE FOR RESIDUE ZN A 89
2AC2SOFTWARECYS A:28 , VAL A:30 , CYS A:31 , PHE A:47 , HIS A:48 , CYS A:51BINDING SITE FOR RESIDUE ZN A 90

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1FP0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FP0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FP0)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.TIF1B_HUMAN625-672  1A:25-72
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.TIF1B_HUMAN628-669  1A:28-69

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002530241ENSE00001469551chr19:59055836-59056464629TIF1B_HUMAN1-1141140--
1.2ENST000002530242ENSE00000655831chr19:59056792-59056904113TIF1B_HUMAN114-151380--
1.3ENST000002530243ENSE00000655830chr19:59057131-59057263133TIF1B_HUMAN152-196450--
1.4ENST000002530244ENSE00000655828chr19:59058743-59058878136TIF1B_HUMAN196-241460--
1.5ENST000002530245ENSE00000655827chr19:59058964-59059080117TIF1B_HUMAN241-280400--
1.6ENST000002530246ENSE00000655826chr19:59059159-59059273115TIF1B_HUMAN280-318390--
1.7ENST000002530247ENSE00000655825chr19:59059401-59059547147TIF1B_HUMAN319-367490--
1.8ENST000002530248ENSE00000655824chr19:59059661-59059775115TIF1B_HUMAN368-406390--
1.9ENST000002530249ENSE00000655823chr19:59059853-59059959107TIF1B_HUMAN406-441360--
1.10ENST0000025302410ENSE00000655822chr19:59060107-5906014337TIF1B_HUMAN442-454130--
1.11ENST0000025302411ENSE00000655820chr19:59060229-5906027749TIF1B_HUMAN454-470170--
1.12ENST0000025302412ENSE00000655819chr19:59060355-59060607253TIF1B_HUMAN470-554851A:1-16 (gaps)73
1.13ENST0000025302413ENSE00000655818chr19:59060698-59061017320TIF1B_HUMAN555-6611071A:17-61 (gaps)107
1.14ENST0000025302414ENSE00000655817chr19:59061104-59061227124TIF1B_HUMAN661-702421A:61-88 (gaps)37
1.15ENST0000025302415ENSE00000655816chr19:59061316-5906140287TIF1B_HUMAN703-731290--
1.16ENST0000025302416ENSE00000655815chr19:59061514-59061651138TIF1B_HUMAN732-777460--
1.17ENST0000025302417ENSE00001391650chr19:59061744-59062082339TIF1B_HUMAN778-835580--

(-) 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:88
 aligned with TIF1B_HUMAN | Q13263 from UniProtKB/Swiss-Prot  Length:835

    Alignment length:216
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691      
          TIF1B_HUMAN   482 MRKVPRVSLERLDLDLTADSQPPVFKVFPGSTTEDYNLIVIERGAAAAATGQPGTAPAGTPGAPPLAGMAIVKEEETEAAIGAPPTATEGPETKPVLMALAEGPGAEGPRLASPSGSTSSGLEVVAPEGTSAPGGGPGTLDDSATICRVCQKPGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEEDGSLSLDGADSTGVVAKLS 697
               SCOP domains -----------------------------------------------------------------------------------------------------------------------------------------d1fp0a1 A:19-88 Nuclear corepressor KAP-1 (TIF-1beta)                           SCOP domains
               CATH domains 1f                           p0A00 A                              :1-88 Zin                                                              c/RING finger domain, C3HC4 (zinc finger)                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..---------------------------.......------------------------------.........--------------------------------------------------------------...................eee....eee................eeee............--....-------..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------ZF_PHD_2  PDB: A:25-72 UniProt: 625-672         ------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------ZF_PHD_1  PDB: A:28-69 UniProt: 628-669   ---------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.12  PDB: A:1-16 (gaps) UniProt: 470-554 [INCOMPLETE]              Exon 1.13  PDB: A:17-61 (gaps) UniProt: 555-661                                                            ------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:61-88 (gaps)        Transcript 1 (2)
                 1fp0 A   1 MR---------------------------GSHHHHH------------------------------HGSDIIDEF--------------------------------------------------------------GTLDDSATICRVCQKPGDLVMCNQCEFCFHLDCHLPALQDVPGEEWSCSLCHVLPDLKEED--VDLQ-------ACKLN  88
                             |       -         -         3     |   -         -         -      | 13    |    -         -         -         -         -         -       |21        31        41        51        61        71       | -|  |     - |    
                             2                           3     9                             10      18                                                             19                                                          79 80 83      84
   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  (0, 0)

(no "Pfam Domain" information available for 1FP0)

(-) Gene Ontology  (50, 50)

NMR Structure(hide GO term definitions)
Chain A   (TIF1B_HUMAN | Q13263)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0035851    Krueppel-associated box domain binding    Interacting selectively and non-covalently with a Krueppel-associated box (KRAB) domain of a protein. The approximately 75 amino acid KRAB domain is enriched in charged amino acids, and is found in the N-terminal regions of many zinc finger-containing transcription factors.
    GO:0001105    RNA polymerase II transcription coactivator activity    Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
    GO:0070087    chromo shadow domain binding    Interacting selectively and non-covalently with a chromo shadow domain, a protein domain that is distantly related, and found in association with, the chromo domain.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:1990841    promoter-specific chromatin binding    Interacting selectively and non-covalently with a section of chromatin that is associated with gene promoter sequences of 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: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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0043045    DNA methylation involved in embryo development    The covalent transfer of a methyl group to C-5 of cytosine that contributes to the epigenetic regulation of embryonic gene expression.
    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:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    GO:0060028    convergent extension involved in axis elongation    The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis contributing to the lengthening of the axis of an organism.
    GO:0007566    embryo implantation    Attachment of the blastocyst to the uterine lining.
    GO:0060669    embryonic placenta morphogenesis    The process in which the embryonic placenta is generated and organized.
    GO:0001837    epithelial to mesenchymal transition    A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:1901536    negative regulation of DNA demethylation    Any process that stops, prevents or reduces the frequency, rate or extent of DNA demethylation.
    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: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:1902187    negative regulation of viral release from host cell    Any process that stops, prevents or reduces the frequency, rate or extent of viral release from host cell.
    GO:0045739    positive regulation of DNA repair    Any process that activates or increases the frequency, rate or extent of DNA repair.
    GO:0090309    positive regulation of methylation-dependent chromatin silencing    Any process that increases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
    GO:0042993    positive regulation of transcription factor import into nucleus    Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:2000653    regulation of genetic imprinting    Any process that modulates the frequency, rate or extent of genetic imprinting.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated 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.
cellular component
    GO:0090575    RNA polymerase II transcription factor complex    A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005719    nuclear euchromatin    The dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, a some being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin.
    GO:0005720    nuclear heterochromatin    A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        TIF1B_HUMAN | Q13263: 2ro1 2yvr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1FP0)