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Title :   SOLUTION STRUCTURE OF THE PH DOMAIN OF PROTEIN KINASE C, D2 TYPE FROM HUMAN

Authors :   H. Li, K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   17 May 05 (Deposition) - 17 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Protein Kinase D2, Ph Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Li, K. Saito, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Ph Domain Of Protein Kinase C, D2 Type From Human
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTEIN KINASE C, D2 TYPE
	Chains	:	A
	EC Number	:	2.7.1.-
	Engineered	:	YES
	Expression System Plasmid	:	P041129-04
	Expression System Vector Type	:	PLASMID
	Fragment	:	PH DOMAIN
	Gene	:	PKD2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	NPKC-D2, PROTEIN KINASE D2, HSPC187


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2COA)

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

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

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_042331	A	496	V	KPCD2_HUMAN	Polymorphism	55716765	A	A	106	V

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PH_DOMAIN	PS50003	PH domain profile.	KPCD2_HUMAN	397-509	1	A:8-119

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000291281	1c	ENSE00001134098	chr19:47220384-47219388	997	KPCD2_HUMAN	1-80	80	0	-	-
1.2	ENST00000291281	2	ENSE00000953051	chr19:47217258-47217120	139	KPCD2_HUMAN	81-127	47	0	-	-
1.3	ENST00000291281	3	ENSE00000953052	chr19:47214295-47214164	132	KPCD2_HUMAN	127-171	45	0	-	-
1.4	ENST00000291281	4	ENSE00000953053	chr19:47207906-47207752	155	KPCD2_HUMAN	171-222	52	0	-	-
1.5	ENST00000291281	5	ENSE00000953054	chr19:47207648-47207426	223	KPCD2_HUMAN	223-297	75	0	-	-
1.6	ENST00000291281	6	ENSE00001225255	chr19:47204369-47204292	78	KPCD2_HUMAN	297-323	27	0	-	-
1.7	ENST00000291281	7	ENSE00000858298	chr19:47204209-47204056	154	KPCD2_HUMAN	323-374	52	1	A:1-4	4
1.8	ENST00000291281	8	ENSE00000714320	chr19:47201107-47200990	118	KPCD2_HUMAN	374-413	40	1	A:5-23	19
1.9	ENST00000291281	9	ENSE00000714319	chr19:47200491-47200414	78	KPCD2_HUMAN	414-439	26	1	A:24-49	26
1.10	ENST00000291281	10	ENSE00000714317	chr19:47197390-47197132	259	KPCD2_HUMAN	440-526	87	1	A:50-125 (gaps)	82
1.11	ENST00000291281	11	ENSE00000858297	chr19:47195242-47195190	53	KPCD2_HUMAN	526-543	18	0	-	-
1.12	ENST00000291281	12	ENSE00000714316	chr19:47195064-47194992	73	KPCD2_HUMAN	544-568	25	0	-	-
1.13	ENST00000291281	13	ENSE00000714315	chr19:47193963-47193857	107	KPCD2_HUMAN	568-603	36	0	-	-
1.14	ENST00000291281	14	ENSE00000576607	chr19:47192955-47192794	162	KPCD2_HUMAN	604-657	54	0	-	-
1.15	ENST00000291281	15	ENSE00001606568	chr19:47185005-47184907	99	KPCD2_HUMAN	658-690	33	0	-	-
1.16a	ENST00000291281	16a	ENSE00000714306	chr19:47181920-47181653	268	KPCD2_HUMAN	691-780	90	0	-	-
1.17	ENST00000291281	17	ENSE00000714304	chr19:47178375-47178290	86	KPCD2_HUMAN	780-808	29	0	-	-
1.18	ENST00000291281	18	ENSE00001134090	chr19:47177992-47177574	419	KPCD2_HUMAN	809-878	70	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:125
 aligned with KPCD2_HUMAN | Q9BZL6 from UniProtKB/Swiss-Prot  Length:878

    Alignment length:155
                                   376       386       396       406       416       426       436       446       456       466       476       486       496       506       516     
          KPCD2_HUMAN   367 GEGGKAQSSLGYIPLMRVVQSVRHTTRKSSTTLREGWVVHYSNKDTLRKRHYWRLDCKCITLFQNNTTNRYYKEIPLSEILTVESAQNFSLVPPGTNPHCFEIVTANATYFVGEMPGGTPGGPSGQGAEAARGWETAIRQALMPVILQDAPSAPG 521
               SCOP domains -------------------------------d2coaa1 A:8-119 Protein kinase c, d2 type                                                                       ------------ SCOP domains
               CATH domains -------------------------------2coaA01 A:8-125 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....------------------------.....eeeeeee........eeeeeee...eeeee.........eeee.....eeee.............eeeeee.......ee...............hhhhhhhhhhhhhhhh-----....-. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------V------------------------- SAPs(SNPs)
                    PROSITE ------------------------------PH_DOMAIN  PDB: A:8-119 UniProt: 397-509                                                                         ------------ PROSITE
           Transcript 1 (1) Exon 1.7---------------------------------------Exon 1.9  PDB: A:24-49    Exon 1.10  PDB: A:50-125 (gaps) UniProt: 440-526 [INCOMPLETE]                      Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.8  PDB: A:5-23 UniProt: 374-413  ------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2coa A   1 GSSG------------------------SSGTLREGWVVHYSNKDTLRKRHYWRLDCKCITLFQNNTTNRYYKEIPLSEILTVESAQNFSLVPPGTNPHCFEIVTANATYFVGEMPGGTPGGPSGQGAEAARGWETAIRQALMS-----GPSS-G 125
                               |     -         -        |6        16        26        36        46        56        66        76        86        96       106       116   |   121  | |
                               4                        5                                                                                                                120   121  | |
                                                                                                                                                                                  124 |
                                                                                                                                                                                    125

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( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: PH domain-like barrel (258)

Superfamily: PH domain-like (257)

Family: Pleckstrin-homology domain (PH domain) (102)

Protein domain: Protein kinase c, d2 type (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2coaa1

A:8-119

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: PH-domain like (150)

Homologous Superfamily: Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) (147)

Human (Homo sapiens) (85)

2coaA01

A:8-125

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

NMR Structure(hide GO term definitions)

Chain A (KPCD2_HUMAN | Q9BZL6)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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:0004697	protein kinase C activity	Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires diacylglycerol.
	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:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	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:0050852	T cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
	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:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0008219	cell death	Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
	GO:0035924	cellular response to vascular endothelial growth factor 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 vascular endothelial growth factor stimulus.
	GO:0061154	endothelial tube morphogenesis	The process in which the anatomical structures of a tube are generated and organized from an endothelium. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells.
	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: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:0018105	peptidyl-serine phosphorylation	The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
	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:0032793	positive regulation of CREB transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of the transcription factor CREB.
	GO:2000573	positive regulation of DNA biosynthetic process	Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	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:0050862	positive regulation of T cell receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0043536	positive regulation of blood vessel endothelial cell migration	Any process that activates or increases the frequency, rate or extent of the migration of the endothelial cells of blood vessels.
	GO:0045785	positive regulation of cell adhesion	Any process that activates or increases the frequency, rate or extent of cell adhesion.
	GO:2001028	positive regulation of endothelial cell chemotaxis	Any process that activates or increases the frequency, rate or extent of endothelial cell chemotaxis.
	GO:0038033	positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway	A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a VEGFR on the surface of a cell, which activates or increases the frequency, rate or extent of endothelial cell chemotaxis.
	GO:0010595	positive regulation of endothelial cell migration	Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
	GO:0001938	positive regulation of endothelial cell proliferation	Any process that activates or increases the rate or extent of endothelial cell proliferation.
	GO:0045743	positive regulation of fibroblast growth factor receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of fibroblast growth factor receptor signaling pathway activity.
	GO:1901727	positive regulation of histone deacetylase activity	Any process that activates or increases the frequency, rate or extent of histone deacetylase activity.
	GO:0032743	positive regulation of interleukin-2 production	Any process that activates or increases the frequency, rate, or extent of interleukin-2 production.
	GO:0032757	positive regulation of interleukin-8 production	Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
	GO:1902533	positive regulation of intracellular signal transduction	Any process that activates or increases the frequency, rate or extent of intracellular signal transduction.
	GO:0098779	positive regulation of macromitophagy in response to mitochondrial depolarization	The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
	GO:0033138	positive regulation of peptidyl-serine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	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:0030949	positive regulation of vascular endothelial growth factor receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0089700	protein kinase D signaling	A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase D, which occurs as a result of a single trigger reaction or compound.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0048010	vascular endothelial growth factor receptor signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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: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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