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Title :   THE SOLUTION STRUCTURE OF THE HOMEOBOX DOMAIN OF HUMAN HOMEOBOX PROTEIN DLX-5

Authors :   A. Sasagawa, S. Ohnishi, N. Tochio, K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   05 Apr 06 (Deposition) - 05 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Homeobox, Dlx5, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Sasagawa, S. Ohnishi, N. Tochio, K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
The Solution Structure Of The Homeobox Domain Of Human Homeobox Protein Dlx-5
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HOMEOBOX PROTEIN DLX-5
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CELL FREE SYNTHESIS
	Expression System Plasmid	:	P050509-13
	Expression System Vector Type	:	PLASMID
	Fragment	:	HOMEOBOX DOMAIN
	Gene	:	DLX5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2DJN)

(no "Site" information available for 2DJN)

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

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

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_067413	Q	178	P	DLX5_HUMAN	Disease (SHFM1D)	387906737	A	Q	48	P

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HOMEOBOX_2	PS50071	'Homeobox' domain profile.	DLX5_HUMAN	135-195	1	A:8-63
2	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	DLX5_HUMAN	170-193	1	A:40-63

NMR Structure (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000222598	1a	ENSE00001896696	chr7:96654409-96653581	829	DLX5_HUMAN	1-119	119	1	A:1-7	7
1.2a	ENST00000222598	2a	ENSE00000706885	chr7:96651681-96651497	185	DLX5_HUMAN	119-180	62	1	A:8-50	43
1.3b	ENST00000222598	3b	ENSE00001039779	chr7:96650377-96649708	670	DLX5_HUMAN	181-289	109	1	A:51-70 (gaps)	30

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
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Chain A from PDB  Type:PROTEIN  Length:70
 aligned with DLX5_HUMAN | P56178 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:132
                                    88        98       108       118       128       138       148       158       168       178       188       198       208  
           DLX5_HUMAN    79 GVNGSAGSYPAKAYADYSYASSYHQYGGAYNRVPSATNQPEKEVTEPEVRMVNGKPKKVRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKIMKNGEMPPEHSPSSS 210
               SCOP domains d2djna_                                                     A: automated matches                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......----------------------------------------------------.......hhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhh..---...-------.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------P-------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------HOMEOBOX_2  PDB: A:8-63 UniProt: 135-195                     --------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------HOMEOBOX_1  PDB: A:40-63----------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:1-7 UniProt: 1-119     -------------------------------------------------------------Exon 1.3b  PDB: A:51-70 (gaps) Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.2a  PDB: A:8-50 UniProt: 119-180 [INCOMPLETE]          ------------------------------ Transcript 1 (2)
                 2djn A   1 GSSGSSG----------------------------------------------------RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK---KSG-------PSSG  70
                                  |  -         -         -         -         -         8        18        28        38        48        58    |   65|       68  
                                  7                                                    8                                                     63  64 |      67   
                                                                                                                                                   66

Legend:		→ Mismatch	(orange background)
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	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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Homeodomain-like (373)

Family: automated matches (53)

Protein domain: automated matches (53)

Human (Homo sapiens) [TaxId: 9606] (19)

d2djna_

(no "CATH Domain" information available for 2DJN)

(no "Pfam Domain" information available for 2DJN)

NMR Structure(hide GO term definitions)

Chain A (DLX5_HUMAN | P56178)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0071837	HMG box domain binding	Interacting selectively and non-covalently with an HMG box domain, a protein domain that consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin.
	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: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: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: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:0030509	BMP signaling pathway	A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0048646	anatomical structure formation involved in morphogenesis	The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0007409	axonogenesis	De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
	GO:0060349	bone morphogenesis	The process in which bones are generated and organized.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0071773	cellular response to BMP stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bone morphogenetic protein (BMP) stimulus.
	GO:0043583	ear development	The process whose specific outcome is the progression of the ear over time, from its formation to the mature structure. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
	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:0001958	endochondral ossification	Replacement ossification wherein bone tissue replaces cartilage.
	GO:0030855	epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
	GO:0060325	face morphogenesis	The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head.
	GO:0060322	head development	The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body.
	GO:0042472	inner ear morphogenesis	The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
	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: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:0060166	olfactory pit development	The biological process whose specific outcome is the progression of the olfactory pit from an initial condition to its mature state. This process begins with the formation of the olfactory pit, which is an indentation of the olfactory placode, and ends when the pits hollows out to form the nasopharynx.
	GO:0001503	ossification	The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
	GO:0001649	osteoblast differentiation	The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
	GO:0060021	palate development	The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
	GO:0090263	positive regulation of canonical Wnt signaling pathway	Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
	GO:0050679	positive regulation of epithelial cell proliferation	Any process that activates or increases the rate or extent of epithelial cell proliferation.
	GO:0045669	positive regulation of osteoblast differentiation	Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
	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:1901522	positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus	Any positive regulation of transcription from RNA polymerase II promoter that is involved in cellular response to chemical stimulus.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0001501	skeletal system development	The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
	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.
cellular component
	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: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.

NMR Structure
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	2djn
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	DLX5_HUMAN \| P56178	:	4rdu

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Description

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Ligands, Modified Residues, Ions (0, 0)

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Exons (3, 3)

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