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(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE EXTENDED PBX HOMEODOMAIN BOUND TO DNA
 
Authors :  T. Sprules, N. Green, M. Featherstone, K. Gehring
Date :  12 Apr 02  (Deposition) - 14 Jan 03  (Release) - 01 Feb 17  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,P  (20x)
NMR Structure *:  A,B,P  (1x)
Keywords :  Protein-Dna Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Sprules, N. Green, M. Featherstone, K. Gehring
Lock And Key Binding Of The Hox Ypwm Peptide To The Pbx Homeodomain
J. Biol. Chem. V. 278 1053 2003
PubMed-ID: 12409300  |  Reference-DOI: 10.1074/JBC.M207504200

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*GP*CP*AP*TP*GP*AP*TP*TP*GP*CP*CP*C)-3'
    ChainsA
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'-D(*GP*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*CP*GP*C)-3'
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - HOMEOBOX PROTEIN PBX1
    ChainsP
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET 11A
    Expression System StrainBL21(DE3)GOLD
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHOMEODOMAIN AND CONSERVED C-TERMINUS
    GenePBX1
    MutationYES
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymPBX, PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR-1

 Structural Features

(-) Chains, Units

  123
NMR Structure (20x)ABP
NMR Structure * (1x)ABP

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1LFU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.PBX1_MOUSE269-292  1P:34-57
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.PBX1_MOUSE269-292  1P:34-57

(-) Exons   (0, 0)

(no "Exon" information available for 1LFU)

(-) 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:DNA  Length:14
                                              
                 1lfu A   1 GCGCATGATTGCCC  14
                                    10    

Chain B from PDB  Type:DNA  Length:14
                                              
                 1lfu B  15 GGGCAATCATGCGC  28
                                    24    

Chain P from PDB  Type:PROTEIN  Length:82
 aligned with PBX1_MOUSE | P41778 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:82
                                   241       251       261       271       281       291       301       311  
           PBX1_MOUSE   232 DARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTA 313
               SCOP domains d1lfup_ P: pbx1                                                                    SCOP domains
               CATH domains 1lfuP00 P:0-78 Homeodomain-like                                                    CATH domains
               Pfam domains --Homeobox-1lfuP01 P:2-58                                     -------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------HOMEOBOX_1  PDB: P:34-57--------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1lfu P   0 MARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTAVTA  78
                                     9        19    ||| 26        36        46        56        66        76  
                                                  23A||                                                       
                                                   23B|                                                       
                                                    23C                                                       

   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

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HTH (544)

(-) Gene Ontology  (38, 38)

NMR Structure(hide GO term definitions)
Chain P   (PBX1_MOUSE | P41778)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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: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:0001077    transcriptional activator 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 activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0030325    adrenal gland development    The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0001658    branching involved in ureteric bud morphogenesis    The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.
    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:0035162    embryonic hemopoiesis    The stages of blood cell formation that take place within the embryo.
    GO:0030326    embryonic limb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
    GO:0048568    embryonic organ development    Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0048706    embryonic skeletal system development    The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045665    negative regulation of neuron differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0010971    positive regulation of G2/M transition of mitotic cell cycle    Any process that increases the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    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:0009954    proximal/distal pattern formation    The regionalization process in which specific areas of cell differentiation are determined along a proximal/distal axis. The proximal/distal axis is defined by a line that runs from main body (proximal end) of an organism outward (distal end).
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0030278    regulation of ossification    Any process that modulates the frequency, rate or extent of bone formation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007548    sex differentiation    The establishment of the sex of an organism by physical differentiation.
    GO:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0048538    thymus development    The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
    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.
    GO:0001655    urogenital system development    The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        PBX1_MOUSE | P417781du6

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