2VY1 - JenaLib

Title :   STRUCTURE OF LEAFY TRANSCRIPTION FACTOR FROM ARABIDOPSIS THALIANA IN COMPLEX WITH DNA FROM AP1 PROMOTER

Authors :   C. Hames, D. Ptchelkine, C. Grimm, E. Thevenon, E. Moyroud, F. Gerard, J. L. Martiel, R. Benlloch, F. Parcy, C. W. Muller

Date :   16 Jul 08 (Deposition) - 23 Sep 08 (Release) - 07 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,W
Biol. Unit 1: A,W  (2x)

Keywords :   Dna-Binding, Polymorphism, Transcription, Developmental Protein, Transcription Regulation, Homeotic Genes, Flowering, Nucleus, Differentiation, Flower Development, Activator, Coiled Coil (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Hames, D. Ptchelkine, C. Grimm, E. Thevenon, E. Moyroud, F. Gerard, J. L. Martiel, R. Benlloch, F. Parcy, C. W. Muller
Structural Basis For Leafy Floral Switch Function And Similarity With Helix-Turn-Helix Proteins.
Embo J. V. 27 2628 2008
PubMed-ID: 18784751 | Reference-DOI: 10.1038/EMBOJ.2008.184

Compounds

Molecule 1 - PROTEIN LEAFY
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM-11
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTABLUE PLYS
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA BINDING DOMAIN, RESIDUES 231-424
	Organ	:	FLOWER
	Organism Common	:	MOUSE-EAR CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Other Details	:	NONE
	Synonym	:	LEAFY
	Tissue	:	FLOWER MERISTEM

*Molecule 2 - 5'-D(TPTPAPCPGPGPAPCPCPAP CPTPGPGPTPCPCPTPTPCP)-3'*
	Chains	:	W
	Organism Common	:	MOUSE-EAR CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	DNA AP1 SITE
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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:164
 aligned with LFY_ARATH | Q00958 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:164
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392    
            LFY_ARATH   233 REHPFIVTEPGEVARGKKNGLDYLFHLYEQCREFLLQVQTIAKDRGEKCPTKVTNQVFRYAKKSGASYINKPKMRHYVHCYALHCLDEEASNALRRAFKERGENVGSWRQACYKPLVNIACRHGWDIDAVFNAHPRLSIWYVPTKLRQLCHLERNNAVAAAAAL 396
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains FLO_LFY-2vy1A01 A:237-395                                                                                                                                      ----- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vy1 A 237 REHPFIVTEPGEVARGKKNGLDYLFHLYEQCREFLLQVQTIAKDRGEKCPTKVTNQVFRYAKKSGASYINKPKMRHYVHCYALHCLDEEASNALRRAFKERGENVGSWRQACYKPLVNIACRHGWDIDAVFNAHPRLSIWYVPTKLRQLCHLERNNAVAAAAAL 400
                                   246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396

Chain W from PDB  Type:DNA  Length:26
                                                          
                 2vy1 W   1 ATGTAACGGACCAGCTGGTCCGTTAC  20
                                     7        16

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)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (16, 16)

Asymmetric Unit(hide GO term definitions)

Chain A (LFY_ARATH | Q00958)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0031490	chromatin DNA binding	Interacting selectively and non-covalently with DNA that is assembled into chromatin.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0043621	protein self-association	Interacting selectively and non-covalently with a domain within the same polypeptide.
	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.
biological process
	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:0010582	floral meristem determinacy	The process in which a floral meristem becomes determinate (i.e. ceases to produce lateral organs and may or may not terminally differentiate).
	GO:0009908	flower development	The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem.
	GO:0009740	gibberellic acid mediated signaling pathway	A series of molecular signals mediated by the detection of gibberellic acid.
	GO:0010077	maintenance of inflorescence meristem identity	The process in which an organism retains a population of inflorescence meristem cells, preventing the commitment of all stem cell progeny to a differentiated cell fate.
	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: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: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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