1A25 - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   C2 DOMAIN FROM PROTEIN KINASE C (BETA)

Authors :   R. B. Sutton, S. R. Sprang

Date :   16 Jan 98 (Deposition) - 06 May 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Calcium++/Phospholipid Binding Protein, Calcium-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. B. Sutton, S. R. Sprang
Structure Of The Protein Kinase Cbeta Phospholipid-Binding C2 Domain Complexed With Ca2+.
Structure V. 6 1395 1998
PubMed-ID: 9817842 | Reference-DOI: 10.1016/S0969-2126(98)00139-7
(for further references see the PDB file header)

Molecule 1 - PROTEIN KINASE C (BETA)
	Cell Line	:	BL21
	Chains	:	A, B
	EC Number	:	2.7.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX-KG
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	BACTERIAL
	Fragment	:	CALCIUM/PHOSPHOLIPID BINDING DOMAIN
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	CALB

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 7)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	PSE	1	Ligand/Ion	O-PHOSPHOETHANOLAMINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:187 , ASP A:193 , ASP A:246 , TRP A:247 , ASP A:248	BINDING SITE FOR RESIDUE CA A 290
2	AC2	SOFTWARE	MET A:186 , ASP A:187 , ASP A:246 , ASP A:248 , ASP A:254 , GLU B:281	BINDING SITE FOR RESIDUE CA A 291
3	AC3	SOFTWARE	ASP A:248 , SER A:251 , ARG A:252 , ASP A:254 , GLU B:281	BINDING SITE FOR RESIDUE CA A 292
4	AC4	SOFTWARE	ASP B:187 , ASP B:193 , ASP B:246 , TRP B:247 , ASP B:248 , HOH B:299	BINDING SITE FOR RESIDUE CA B 290
5	AC5	SOFTWARE	GLU A:281 , MET B:186 , ASP B:187 , ASP B:246 , ASP B:248 , ASP B:254	BINDING SITE FOR RESIDUE CA B 291
6	AC6	SOFTWARE	GLU A:281 , ASP B:248 , SER B:251 , ARG B:252 , ASP B:254	BINDING SITE FOR RESIDUE CA B 292
7	AC7	SOFTWARE	TYR B:195 , LYS B:197 , LYS B:209 , LYS B:211 , TRP B:245 , ASN B:253	BINDING SITE FOR RESIDUE PSE B 1
8	CLB	UNKNOWN	MET A:186 , ASP A:187 , ASP A:193 , TRP A:247 , ASP A:246 , ASP A:248 , ASN A:253 , ASP A:254 , GLU B:281	CA BINDING SITE.

(no "SS Bond" information available for 1A25)

Asymmetric/Biological Unit

No.	Residues
1	Ile A:201	-	Pro A:202
2	Ile B:201	-	Pro B:202

(no "SAP(SNP)/Variant" information available for 1A25)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C2	PS50004	C2 domain profile.	KPCB_RAT	173-260	2	A:173-260 B:173-260

(no "Exon" information available for 1A25)

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:132
 aligned with KPCB_RAT | P68403 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:132
                                   166       176       186       196       206       216       226       236       246       256       266       276       286  
             KPCB_RAT   157 ERRGRIYIQAHIDREVLIVVVRDAKNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKCSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAGVDGWFKLLSQEEGEYFNV 288
               SCOP domains d1a25a_ A: C2 domain from protein kinase c (beta)                                                                                    SCOP domains
               CATH domains 1a25A00 A:157-288 C2- domain Calcium/lipid binding domain                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeee...eeeeee................eeeeeeee.......................eeeeee...hhhh.eeeeeeee.......eeeeeeeeehhhh....eeeeee...hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------C2  PDB: A:173-260 UniProt: 173-260                                                     ---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a25 A 157 ERRGRIYIQAHIDREVLIVVVRDAKNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKCSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAGVDGWFKLLSQEEGEYFNV 288
                                   166       176       186       196       206       216       226       236       246       256       266       276       286

Chain B from PDB  Type:PROTEIN  Length:132
 aligned with KPCB_RAT | P68403 from UniProtKB/Swiss-Prot  Length:671

    Alignment length:132
                                   166       176       186       196       206       216       226       236       246       256       266       276       286  
             KPCB_RAT   157 ERRGRIYIQAHIDREVLIVVVRDAKNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKCSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAGVDGWFKLLSQEEGEYFNV 288
               SCOP domains d1a25b_ B: C2 domain from protein kinase c (beta)                                                                                    SCOP domains
               CATH domains 1a25B00 B:157-288 C2- domain Calcium/lipid binding domain                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeee...eeeeee................eeeeeeee.......................eeeeee...hhhh.eeeeeeee.......eeeeeeeeehhhh....eeeeee...hhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------C2  PDB: B:173-260 UniProt: 173-260                                                     ---------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a25 B 157 ERRGRIYIQAHIDREVLIVVVRDAKNLVPMDPNGLSDPYVKLKLIPDPKSESKQKTKTIKCSLNPEWNETFRFQLKESDKDRRLSVEIWDWDLTSRNDFMGSLSFGISELQKAGVDGWFKLLSQEEGEYFNV 288
                                   166       176       186       196       206       216       226       236       246       256       266       276       286

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: C2 domain-like (198)

Superfamily: C2 domain (Calcium/lipid-binding domain, CaLB) (148)

Family: Synaptotagmin-like (S variant) (38)

Protein domain: C2 domain from protein kinase c (beta) (1)

Norway rat (Rattus norvegicus) [TaxId: 10116] (1)

1a	d1a25a_	A:
1b	d1a25b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: C2- domain Calcium/lipid binding domain (78)

Norway rat (Rattus norvegicus) (20)

1a	1a25A00	A:157-288
1b	1a25B00	B:157-288

(no "Pfam Domain" information available for 1A25)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KPCB_RAT | P68403)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0050681	androgen receptor binding	Interacting selectively and non-covalently with an androgen receptor.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	GO:0035403	histone kinase activity (H3-T6 specific)	Catalysis of the transfer of a phosphate group to the threonine-6 residue of the N-terminal tail of histone H3.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0030374	ligand-dependent nuclear receptor transcription coactivator activity	The function of a transcription cofactor that activates transcription in conjuction with a ligand-dependent nuclear receptor from a RNA polymerase II promoter; does not bind DNA itself.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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: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:0018894	dibenzo-p-dioxin metabolic process	The chemical reactions and pathways involving dibenzo-p-dioxin, a substance composed of two benzene rings linked by two ether bonds. Dibenzo-p-dioxins are generated as by-products in the manufacturing of herbicides, insecticides, fungicides, paper pulp bleaching, and in incineration, and can accumulate in milk and throughout the food chain, creating significant health concern.
	GO:0035408	histone H3-T6 phosphorylation	The modification of histone H3 by the addition of an phosphate group to a threonine residue at position 6 of the histone.
	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:0010829	negative regulation of glucose transport	Any process that decreases the frequency, rate or extent of glucose transport. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0046627	negative regulation of insulin receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling.
	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:0050861	positive regulation of B 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 B cell.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	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:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0042488	positive regulation of odontogenesis of dentin-containing tooth	Any process that activates or increases the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages that are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates.
	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:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0014059	regulation of dopamine secretion	Any process that modulates the frequency, rate or extent of the regulated release of dopamine.
	GO:0040008	regulation of growth	Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0045471	response to ethanol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
	GO:0009749	response to glucose	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
	GO:0033280	response to vitamin D	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin D stimulus.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0031526	brush border membrane	The portion of the plasma membrane surrounding the brush border.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Asymmetric/Biological Unit
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	1a25
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(no "Related Entries Specified in the PDB File" available for 1A25)

Description

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Ligands, Modified Residues, Ions (2, 7)

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