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(-) Description

Title :  PROPOSED STRUCTURE FOR THE DNA-BINDING DOMAIN OF THE HELIX-LOOP-HELIX FAMILY OF EUKARYOTIC GENE REGULATORY PROTEINS
 
Authors :  T. J. Gibson, J. D. Thompson, R. A. Abagyan
Date :  10 Dec 92  (Deposition) - 31 Jan 94  (Release) - 31 Jan 94  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B
Keywords :  Dna-Binding Regulatory Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Gibson, J. D. Thompson, R. A. Abagyan
Proposed Structure For The Dna-Binding Domain Of The Helix-Loop-Helix Family Of Eukaryotic Gene Regulatory Proteins.
Protein Eng. V. 6 41 1993
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E47 PROTEIN PRODUCT OF THE E2A GENE
    Chains: A, B
    Engineered: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1HLH)

(-) Sites  (2, 2)

Theoretical Model (2, 2)
No.NameEvidenceResiduesDescription
1BRAnot definedASP A:1 , ARG A:2 , GLU A:3 , ARG A:4 , ARG A:5 , MET A:6 , ALA A:7 , ASN A:8 , ASN A:9 , ALA A:10 , ARG A:11 , GLU A:12 , ARG A:13 , VAL A:14 , ARG A:15 , VAL A:16 , ARG A:17 , ASP A:18
2BRBnot definedASP B:1 , ARG B:2 , GLU B:3 , ARG B:4 , ARG B:5 , MET B:6 , ALA B:7 , ASN B:8 , ASN B:9 , ALA B:10 , ARG B:11 , GLU B:12 , ARG B:13 , VAL B:14 , ARG B:15 , VAL B:16 , ARG B:17 , ASP B:18

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Theoretical Model (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BHLHPS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile.TFE2_HUMAN549-602
 		  2A:3-56
B:3-56

(-) Exons   (2, 4)

Theoretical Model (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002629651ENSE00001724128chr19:1652326-165229928TFE2_HUMAN-00--
1.2ENST000002629652ENSE00001376842chr19:1650286-1650176111TFE2_HUMAN1-24240--
1.3ENST000002629653ENSE00000651461chr19:1646426-164635473TFE2_HUMAN25-49250--
1.4ENST000002629654ENSE00000336287chr19:1632404-163233174TFE2_HUMAN49-73250--
1.5ENST000002629655ENSE00000651464chr19:1632115-163203779TFE2_HUMAN74-100270--
1.6ENST000002629656ENSE00001151945chr19:1627425-162735868TFE2_HUMAN100-122230--
1.7ENST000002629657ENSE00000651466chr19:1625707-1625575133TFE2_HUMAN123-167450--
1.8ENST000002629658ENSE00001151938chr19:1623999-162395050TFE2_HUMAN167-183170--
1.9ENST000002629659ENSE00000651469chr19:1622414-1622312103TFE2_HUMAN184-218350--
1.10ENST0000026296510ENSE00001151931chr19:1622222-1622053170TFE2_HUMAN218-274570--
1.11ENST0000026296511ENSE00000651472chr19:1621969-1621837133TFE2_HUMAN275-319450--
1.12ENST0000026296512ENSE00001151926chr19:1621190-162113259TFE2_HUMAN319-338200--
1.13ENST0000026296513ENSE00000651474chr19:1621045-162096779TFE2_HUMAN339-365270--
1.14ENST0000026296514ENSE00001151915chr19:1619852-161977974TFE2_HUMAN365-389250--
1.15ENST0000026296515ENSE00000873563chr19:1619473-1619315159TFE2_HUMAN390-442530--
1.16ENST0000026296516ENSE00000873564chr19:1619233-1619110124TFE2_HUMAN443-484420--
1.17aENST0000026296517aENSE00000651478chr19:1615820-1615685136TFE2_HUMAN484-529460--
1.17cENST0000026296517cENSE00000651479chr19:1615519-1615284236TFE2_HUMAN529-608802A:1-62
B:1-62		62
62
1.19bENST0000026296519bENSE00001152057chr19:1611848-16092932556TFE2_HUMAN608-654472A:62-64
B:62-64		3
3

(-) Sequences/Alignments

Theoretical Model
   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:64
 aligned with TFE2_HUMAN | P15923 from UniProtKB/Swiss-Prot  Length:654

    Alignment length:64
                                   556       566       576       586       596       606    
           TFE2_HUMAN   547 EKERRVANNARERLRVRDINEAFKELGRMCQLHLNSEKPQTKLLILHQAVSVILNLEQQVRERN 610
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --BHLH  PDB: A:3-56 UniProt: 549-602                    -------- PROSITE
           Transcript 1 (1) Exon 1.17c  PDB: A:1-62 UniProt: 529-608 [INCOMPLETE]         -- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------1.1 Transcript 1 (2)
                 1hlh A   1 DRERRMANNARERVRVRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN  64
                                    10        20        30        40        50        60    


Chain B from PDB  Type:PROTEIN  Length:64
 aligned with TFE2_HUMAN | P15923 from UniProtKB/Swiss-Prot  Length:654

    Alignment length:64
                                   556       566       576       586       596       606    
           TFE2_HUMAN   547 EKERRVANNARERLRVRDINEAFKELGRMCQLHLNSEKPQTKLLILHQAVSVILNLEQQVRERN 610
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --BHLH  PDB: B:3-56 UniProt: 549-602                    -------- PROSITE
           Transcript 1 (1) Exon 1.17c  PDB: B:1-62 UniProt: 529-608 [INCOMPLETE]         -- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------1.1 Transcript 1 (2)
                 1hlh B   1 DRERRMANNARERVRVRDINEAFRELGRMCQMHLKSDKAQTKLLILQQAVQVILGLEQQVRERN  64
                                    10        20        30        40        50        60
   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 1HLH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1HLH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (41, 41)

Theoretical Model(hide GO term definitions)
Chain A,B   (TFE2_HUMAN | P15923)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070888    E-box binding    Interacting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues.
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0043425    bHLH transcription factor binding    Interacting selectively and non-covalently with any of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors, important regulatory components in transcriptional networks of many developmental pathways.
    GO:0035326    enhancer binding    Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
    GO:0031435    mitogen-activated protein kinase kinase kinase binding    Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase kinase, any protein that can phosphorylate a MAP kinase kinase.
    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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    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: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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0001078    transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0070644    vitamin D response element binding    Interacting selectively and non-covalently with the vitamin D response element (VDRE), a short sequence with dyad symmetry found in the promoters of some of the cellular immediate-early genes, regulated by serum.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0002326    B cell lineage commitment    The process in which a lymphoid progenitor cell becomes committed to become any type of B cell.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0033152    immunoglobulin V(D)J recombination    The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0030890    positive regulation of B cell proliferation    Any process that activates or increases the rate or extent of B cell proliferation.
    GO:0045787    positive regulation of cell cycle    Any process that activates or increases the rate or extent of progression through the cell cycle.
    GO:0051149    positive regulation of muscle cell differentiation    Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
    GO:0045666    positive regulation of neuron differentiation    Any process that activates or increases the frequency, rate or extent of neuron differentiation.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    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:2000045    regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that controls the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated 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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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  1hlh
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 Related Entries

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

UniProtKB/Swiss-Prot
        TFE2_HUMAN | P15923: 2mh0 2ypa 2ypb 3u5v

(-) Related Entries Specified in the PDB File

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