2GE9 - JenaLib

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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURES OF THE SH2 DOMAIN OF BRUTON'S TYROSINE KINASE

Authors :   J. -W. Cheng, K. -C. Huang

Date :   18 Mar 06 (Deposition) - 24 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Sh2 Domain, Btk, Structure, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. -C. Huang, H. -T. Cheng, M. -T. Pai, S. -R. Tzeng, J. -W. Cheng
Solution Structure And Phosphopeptide Binding Of The Sh2 Domain From The Human Bruton'S Tyrosine Kinase
J. Biomol. Nmr V. 36 73 2006
PubMed-ID: 16969585 | Reference-DOI: 10.1007/S10858-006-9064-3
(for further references see the PDB file header)

Molecule 1 - TYROSINE-PROTEIN KINASE BTK
	Chains	:	A
	EC Number	:	2.7.1.112
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SH2 DOMAIN
	Gene	:	BTK, AGMX1, ATK, BPK
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BRUTON'S TYROSINE KINASE, AGAMMAGLOBULINAEMIA TYROSINE KINASE, ATK, B CELL PROGENITOR KINASE, BPK


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2GE9)

(no "Site" information available for 2GE9)

(no "SS Bond" information available for 2GE9)

(no "Cis Peptide Bond" information available for 2GE9)

NMR Structure (19, 19)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_008305	R	288	Q	BTK_HUMAN	Disease (XLA)	---	A	R	19	Q
02	UniProt	VAR_006227	R	288	W	BTK_HUMAN	Disease (XLA)	128621194	A	R	19	W
03	UniProt	VAR_006228	L	295	P	BTK_HUMAN	Disease (XLA)	---	A	L	26	P
04	UniProt	VAR_006230	G	302	E	BTK_HUMAN	Disease (XLA)	---	A	G	33	E
05	UniProt	VAR_008306	G	302	R	BTK_HUMAN	Disease (XLA)	---	A	G	33	R
06	UniProt	VAR_006231	R	307	G	BTK_HUMAN	Disease (XLA)	128621195	A	R	38	G
07	UniProt	VAR_008307	R	307	T	BTK_HUMAN	Disease (XLA)	---	A	R	38	T
08	UniProt	VAR_008308	D	308	E	BTK_HUMAN	Disease (XLA)	---	A	D	39	E
09	UniProt	VAR_008309	V	319	A	BTK_HUMAN	Disease (XLA)	---	A	V	50	A
10	UniProt	VAR_006232	Y	334	S	BTK_HUMAN	Disease (XLA)	128621196	A	Y	65	S
11	UniProt	VAR_006233	L	358	F	BTK_HUMAN	Disease (XLA)	---	A	L	89	F
12	UniProt	VAR_006234	Y	361	C	BTK_HUMAN	Disease (XLA)	28935478	A	Y	92	C
13	UniProt	VAR_006235	H	362	Q	BTK_HUMAN	Disease (XLA)	---	A	H	93	Q
14	UniProt	VAR_006236	H	364	P	BTK_HUMAN	Disease (XLA)	---	A	H	95	P
15	UniProt	VAR_006237	N	365	Y	BTK_HUMAN	Disease (XLA)	---	A	N	96	Y
16	UniProt	VAR_008310	S	366	F	BTK_HUMAN	Disease (XLA)	---	A	S	97	F
17	UniProt	VAR_008311	L	369	F	BTK_HUMAN	Disease (XLA)	---	A	L	100	F
18	UniProt	VAR_006238	I	370	M	BTK_HUMAN	Disease (XLA)	---	A	I	101	M
19	UniProt	VAR_008312	R	372	G	BTK_HUMAN	Disease (XLA)	---	A	R	103	G

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH2	PS50001	Src homology 2 (SH2) domain profile.	BTK_HUMAN	281-377	1	A:12-108

NMR Structure (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000308731	1b	ENSE00001821870	X:100641183-100641050	134	BTK_HUMAN	-	0	0	-	-
1.3	ENST00000308731	3	ENSE00002149458	X:100630302-100630132	171	BTK_HUMAN	1-47	47	0	-	-
1.4a	ENST00000308731	4a	ENSE00001643950	X:100629622-100629524	99	BTK_HUMAN	48-80	33	0	-	-
1.5	ENST00000308731	5	ENSE00001646803	X:100626689-100626621	69	BTK_HUMAN	81-103	23	0	-	-
1.6	ENST00000308731	6	ENSE00001698702	X:100625067-100624986	82	BTK_HUMAN	104-131	28	0	-	-
1.7b	ENST00000308731	7b	ENSE00001643964	X:100617677-100617549	129	BTK_HUMAN	131-174	44	0	-	-
1.8b	ENST00000308731	8b	ENSE00001601394	X:100617228-100617161	68	BTK_HUMAN	174-196	23	0	-	-
1.9	ENST00000308731	9	ENSE00001608013	X:100615743-100615556	188	BTK_HUMAN	197-259	63	0	-	-
1.10	ENST00000308731	10	ENSE00001712685	X:100615138-100615076	63	BTK_HUMAN	259-280	22	1	A:1-11	11
1.11	ENST00000308731	11	ENSE00001801955	X:100614335-100614281	55	BTK_HUMAN	280-298	19	1	A:11-29	19
1.12	ENST00000308731	12	ENSE00000673984	X:100613684-100613605	80	BTK_HUMAN	299-325	27	1	A:30-56	27
1.13b	ENST00000308731	13b	ENSE00000673983	X:100613425-100613298	128	BTK_HUMAN	325-368	44	1	A:56-99	44
1.14b	ENST00000308731	14b	ENSE00000673982	X:100612571-100612497	75	BTK_HUMAN	368-393	26	1	A:99-118	20
1.15a	ENST00000308731	15a	ENSE00000673981	X:100611943-100611772	172	BTK_HUMAN	393-450	58	0	-	-
1.16b	ENST00000308731	16b	ENSE00000673980	X:100611256-100611040	217	BTK_HUMAN	450-522	73	0	-	-
1.17	ENST00000308731	17	ENSE00000673977	X:100609682-100609618	65	BTK_HUMAN	523-544	22	0	-	-
1.18b	ENST00000308731	18b	ENSE00001780523	X:100608976-100608858	119	BTK_HUMAN	544-584	41	0	-	-
1.19b	ENST00000308731	19b	ENSE00001702496	X:100608339-100608182	158	BTK_HUMAN	584-636	53	0	-	-
1.20b	ENST00000308731	20b	ENSE00001855631	X:100604944-100604438	507	BTK_HUMAN	637-659	23	0	-	-

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:118
 aligned with BTK_HUMAN | Q06187 from UniProtKB/Swiss-Prot  Length:659

    Alignment length:118
                                   279       289       299       309       319       329       339       349       359       369       379        
            BTK_HUMAN   270 TEAEDSIEMYEWYSKHMTRSQAEQLLKQEGKEGGFIVRDSSKAGKYTVSVFAKSTGDPQGVIRHYVVCSTPQSQYYLAEKHLFSTIPELINYHQHNSAGLISRLKYPVSQQNKNAPST 387
               SCOP domains d2ge9a_ A: automated matches                                                                                           SCOP domains
               CATH domains 2ge9A00 A:1-118 SHC Adaptor Protein                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhh...eeeeee......eeeeeee........eeeeee.eee...eeeee..eee.hhhhhhhhhhh..........ee........... Sec.struct. author
             SAPs(SNPs) (1) ------------------Q------P------E----GE----------A--------------S-----------------------F--CQ-PYF--FM-G--------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------W-------------R----T-------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------SH2  PDB: A:12-108 UniProt: 281-377                                                              ---------- PROSITE
           Transcript 1 (1) Exon 1.10  ------------------Exon 1.12  PDB: A:30-56    ------------------------------------------Exon 1.14b           Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.11          --------------------------Exon 1.13b  PDB: A:56-99 UniProt: 325-368   ------------------- Transcript 1 (2)
                 2ge9 A   1 TEAEDSIEMYEWYSKHMTRSQAEQLLKQEGKEGGFIVRDSSKAGKYTVSVFAKSTGDPQGVIRHYVVCSTPQSQYYLAEKHLFSTIPELINYHQHNSAGLISRLKYPVSQQNKNAPST 118
                                    10        20        30        40        50        60        70        80        90       100       110

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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: SH2-like (260)

Superfamily: SH2 domain (260)

Family: automated matches (35)

Protein domain: automated matches (35)

Human (Homo sapiens) [TaxId: 9606] (30)

d2ge9a_

NMR Structure

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: SHC Adaptor Protein (206)

Homologous Superfamily: SHC Adaptor Protein (206)

Human (Homo sapiens) (147)

2ge9A00

A:1-118

(no "Pfam Domain" information available for 2GE9)

NMR Structure(hide GO term definitions)

Chain A (BTK_HUMAN | Q06187)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004715	non-membrane spanning protein tyrosine kinase activity	Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005547	phosphatidylinositol-3,4,5-trisphosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions.
	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:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0042113	B cell activation	The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0038095	Fc-epsilon receptor signaling pathway	A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
	GO:0007249	I-kappaB kinase/NF-kappaB signaling	The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
	GO:0002755	MyD88-dependent toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor where the MyD88 adaptor molecule mediates transduction of the signal. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0097190	apoptotic signaling pathway	A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
	GO:0019722	calcium-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
	GO:0048469	cell maturation	A developmental process, independent of morphogenetic (shape) change, that is required for a cell to attain its fully functional state.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0007498	mesoderm development	The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.
	GO:0001818	negative regulation of cytokine production	Any process that stops, prevents, or reduces the rate of production of a cytokine.
	GO:0038083	peptidyl-tyrosine autophosphorylation	The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0045579	positive regulation of B cell differentiation	Any process that activates or increases the frequency, rate or extent of B cell differentiation.
	GO:0051092	positive regulation of NF-kappaB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0002902	regulation of B cell apoptotic process	Any process that modulates the frequency, rate, or extent of B cell apoptotic process.
	GO:0002721	regulation of B cell cytokine production	Any process that modulates the frequency, rate, or extent of B cell cytokine production.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	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.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

NMR Structure
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