2DRN - JenaLib

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NMR Structure - model 1 (Jmol Viewer)

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Title :   DOCKING AND DIMERIZATION DOMAIN (D/D) OF THE TYPE II-ALPHA REGULATORY SUBUNITY OF PROTEIN KINASE A (PKA) IN COMPLEX WITH A PEPTIDE FROM AN A-KINASE ANCHORING PROTEIN

Authors :   M. G. Newlon, M. Roy, D. Morikis, Z. E. Hausken, V. Coghlan, J. D. Scott, P. A. Jennings

Date :   11 Jun 06 (Deposition) - 29 Aug 06 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C  (13x)

Keywords :   Akap, Pka, Nmr, Signal Transduction, 4-Helix Bundle, Helix- Loop-Helix, Protein-Peptide Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. G. Newlon, M. Roy, D. Morikis, D. W. Carr, R. Westphal, J. D. Scott, P. A. Jennings
A Novel Mechanism Of Pka Anchoring Revealed By Solution Structures Of Anchoring Complexes.
Embo J. V. 20 1651 2001
PubMed-ID: 11285229 | Reference-DOI: 10.1093/EMBOJ/20.7.1651
(for further references see the PDB file header)

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY SUBUNIT
	Chains	:	A, B
	EC Number	:	2.7.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-16B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOCKING AND DIMERIZATION DOMAIN, RESIDUES 4-46
	Gene	:	RIIA(1-44)
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

Molecule 2 - 24-RESIDUES PEPTIDE FROM AN A-KINASE ANCHORING PROTEIN
	Chains	:	C
	Engineered	:	YES
	Other Details	:	THE PEPTIDE HAS BEEN GENERATED BY SOLID PHASE PEPTIDE SYNTHESIS.; THIS SEQUENCE OCCURS NATURALLY IN HUMANS.
	Synonym	:	FRAGMENT, HUMAN THYROID ANCHORING PROTEIN, HT31(493-515) PEPTIDE
	Synthetic	:	YES


NMR Structure (13x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2DRN)

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

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

(no "SAP(SNP)/Variant" information available for 2DRN)

(no "PROSITE Motif" information available for 2DRN)

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000394518	1	ENSE00001302181	chr15:85923871-85924029	159	AKP13_HUMAN	-	0	0	-	-
1.2	ENST00000394518	2	ENSE00001332196	chr15:86028941-86028984	44	AKP13_HUMAN	1-11	11	0	-	-
1.4	ENST00000394518	4	ENSE00001332207	chr15:86064659-86064806	148	AKP13_HUMAN	12-61	50	0	-	-
1.5a	ENST00000394518	5a	ENSE00001106086	chr15:86076815-86077111	297	AKP13_HUMAN	61-160	100	0	-	-
1.6	ENST00000394518	6	ENSE00001255215	chr15:86087003-86087186	184	AKP13_HUMAN	160-221	62	0	-	-
1.7	ENST00000394518	7	ENSE00001255210	chr15:86118362-86118560	199	AKP13_HUMAN	221-287	67	0	-	-
1.8	ENST00000394518	8	ENSE00000924595	chr15:86122161-86125338	3178	AKP13_HUMAN	288-1347	1060	1	C:1-24	24
1.9	ENST00000394518	9	ENSE00000924596	chr15:86128933-86129054	122	AKP13_HUMAN	1347-1387	41	0	-	-
1.12	ENST00000394518	12	ENSE00001161572	chr15:86182605-86182680	76	AKP13_HUMAN	1388-1413	26	0	-	-
1.13	ENST00000394518	13	ENSE00001183573	chr15:86189049-86189185	137	AKP13_HUMAN	1413-1458	46	0	-	-
1.14	ENST00000394518	14	ENSE00001255357	chr15:86198648-86199018	371	AKP13_HUMAN	1459-1582	124	0	-	-
1.15	ENST00000394518	15	ENSE00001183389	chr15:86201768-86201821	54	AKP13_HUMAN	1582-1600	19	0	-	-
1.17	ENST00000394518	17	ENSE00001183388	chr15:86207794-86207986	193	AKP13_HUMAN	1600-1664	65	0	-	-
1.18	ENST00000394518	18	ENSE00000924601	chr15:86212953-86213061	109	AKP13_HUMAN	1665-1701	37	0	-	-
1.20	ENST00000394518	20	ENSE00001639921	chr15:86225389-86225443	55	AKP13_HUMAN	1701-1719	19	0	-	-
1.21	ENST00000394518	21	ENSE00002188320	chr15:86227972-86228104	133	AKP13_HUMAN	1719-1763	45	0	-	-
1.22	ENST00000394518	22	ENSE00001652051	chr15:86236508-86236682	175	AKP13_HUMAN	1764-1822	59	0	-	-
1.23	ENST00000394518	23	ENSE00001711074	chr15:86251250-86251317	68	AKP13_HUMAN	1822-1844	23	0	-	-
1.24	ENST00000394518	24	ENSE00001771305	chr15:86253810-86253876	67	AKP13_HUMAN	1845-1867	23	0	-	-
1.25	ENST00000394518	25	ENSE00001719928	chr15:86259019-86259154	136	AKP13_HUMAN	1867-1912	46	0	-	-
1.26	ENST00000394518	26	ENSE00001689611	chr15:86260521-86260633	113	AKP13_HUMAN	1912-1950	39	0	-	-
1.27a	ENST00000394518	27a	ENSE00001798925	chr15:86261238-86261390	153	AKP13_HUMAN	1950-2001	52	0	-	-
1.28	ENST00000394518	28	ENSE00001697029	chr15:86262307-86262557	251	AKP13_HUMAN	2001-2084	84	0	-	-
1.29	ENST00000394518	29	ENSE00001649682	chr15:86265222-86265347	126	AKP13_HUMAN	2085-2126	42	0	-	-
1.30	ENST00000394518	30	ENSE00001612910	chr15:86265461-86265578	118	AKP13_HUMAN	2127-2166	40	0	-	-
1.31	ENST00000394518	31	ENSE00001803184	chr15:86266303-86266551	249	AKP13_HUMAN	2166-2249	84	0	-	-
1.32	ENST00000394518	32	ENSE00001753596	chr15:86269641-86269717	77	AKP13_HUMAN	2249-2274	26	0	-	-
1.33	ENST00000394518	33	ENSE00001735665	chr15:86270297-86270478	182	AKP13_HUMAN	2275-2335	61	0	-	-
1.34	ENST00000394518	34	ENSE00001678821	chr15:86270612-86270694	83	AKP13_HUMAN	2335-2363	29	0	-	-
1.35	ENST00000394518	35	ENSE00001629448	chr15:86273744-86273938	195	AKP13_HUMAN	2363-2428	66	0	-	-
1.36	ENST00000394518	36	ENSE00001734761	chr15:86278223-86278381	159	AKP13_HUMAN	2428-2481	54	0	-	-
1.37	ENST00000394518	37	ENSE00001762863	chr15:86278791-86278861	71	AKP13_HUMAN	2481-2504	24	0	-	-
1.38	ENST00000394518	38	ENSE00001747445	chr15:86279321-86279365	45	AKP13_HUMAN	2505-2519	15	0	-	-
1.39	ENST00000394518	39	ENSE00001637119	chr15:86283453-86283503	51	AKP13_HUMAN	2520-2536	17	0	-	-
1.40	ENST00000394518	40	ENSE00001776231	chr15:86284277-86284726	450	AKP13_HUMAN	2537-2686	150	0	-	-
1.41	ENST00000394518	41	ENSE00001594809	chr15:86286723-86287056	334	AKP13_HUMAN	2687-2798	112	0	-	-
1.42b	ENST00000394518	42b	ENSE00001390831	chr15:86287859-86292586	4728	AKP13_HUMAN	2798-2813	16	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
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Chain A from PDB  Type:PROTEIN  Length:46
 aligned with KAP2_RAT | P12368 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:46
                             1                                            
                             |       9        19        29        39      
            KAP2_RAT      - -MSHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR   45
               SCOP domains d2drna1 A:1-46                                 SCOP domains
               CATH domains 2drnA00 A:1-46                                 CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                2drn A    1 HMGHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR   46
                                    10        20        30        40

Chain B from PDB  Type:PROTEIN  Length:46
 aligned with KAP2_RAT | P12368 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:46
                             1                                            
                             |       9        19        29        39      
            KAP2_RAT      - -MSHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR   45
               SCOP domains d2drnb1 B:1-46                                 SCOP domains
               CATH domains 2drnB00 B:1-46                                 CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                2drn B    1 HMGHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR   46
                                    10        20        30        40

Chain C from PDB  Type:PROTEIN  Length:24
 aligned with AKP13_HUMAN | Q12802 from UniProtKB/Swiss-Prot  Length:2813

    Alignment length:24
                                  1255      1265    
         AKP13_HUMAN   1246 DLIEEAASRIVDAVIEQVKAAGAL 1269
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
               Transcript 1 Exon 1.8  PDB: C:1-24    Transcript 1
                2drn C    1 DLIEEAASRIVDAVIEQVKAAGAY   24
                                    10        20

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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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: cAMP-dependent Protein Kinase, Chain A (8)

Homologous Superfamily: cAMP-dependent Protein Kinase, Chain A (7)

Norway rat (Rattus norvegicus) (3)

1a	2drnA00	A:1-46
1b	2drnB00	B:1-46

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

NMR Structure(hide GO term definitions)

Chain A,B (KAP2_RAT | P12368)

molecular function
	GO:0030552	cAMP binding	Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
	GO:0008603	cAMP-dependent protein kinase regulator activity	Modulation of the activity of the enzyme cAMP-dependent protein kinase.
	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:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0034236	protein kinase A catalytic subunit binding	Interacting selectively and non-covalently with one or both of the catalytic subunits of protein kinase A.
	GO:0036094	small molecule binding	Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
biological process
	GO:0051291	protein heterooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers that are not all identical. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0045859	regulation of protein kinase activity	Any process that modulates the frequency, rate or extent of protein kinase activity.
	GO:0001932	regulation of protein phosphorylation	Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
	GO:0097338	response to clozapine	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 clozapine stimulus.
cellular component
	GO:0030315	T-tubule	Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane.
	GO:0005952	cAMP-dependent protein kinase complex	An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Chain C (AKP13_HUMAN | Q12802)

molecular function
	GO:0005078	MAP-kinase scaffold activity	The binding activity of a molecule that functions as a physical support for the assembly of a multiprotein mitogen-activated protein kinase (MAPK) complex. Binds multiple kinases of the MAPKKK cascade, and also upstream signaling proteins, permitting those molecules to function in a coordinated way. Bringing together multiple enzymes and their substrates enables the signal to be transduced quickly and efficiently.
	GO:0017048	Rho GTPase binding	Interacting selectively and non-covalently with Rho protein, any member of the Rho subfamily of the Ras superfamily of monomeric GTPases. Proteins in the Rho subfamily are involved in relaying signals from cell-surface receptors to the actin cytoskeleton.
	GO:0005089	Rho guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0004691	cAMP-dependent protein kinase activity	Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of cAMP.
	GO:0005085	guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0032947	protein complex scaffold activity	A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
	GO:0051018	protein kinase A binding	Interacting selectively and non-covalently with any subunit of protein kinase A.
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0071875	adrenergic receptor signaling pathway	A series of molecular signals generated as a consequence of an adrenergic receptor binding to one of its physiological ligands.
	GO:0086023	adrenergic receptor signaling pathway involved in heart process	A series of molecular signals beginning with a G-protein coupled adrenergic cell surface receptor combining with epinephrine or norepinephrine, which contributes to a circulatory system process carried out by the heart.
	GO:0060348	bone development	The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
	GO:0055007	cardiac muscle cell differentiation	The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	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:0051168	nuclear export	The directed movement of substances out of the nucleus.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	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:0035025	positive regulation of Rho protein signal transduction	Any process that activates or increases the frequency, rate or extent of Rho protein signal transduction.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0035023	regulation of Rho protein signal transduction	Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
	GO:0010611	regulation of cardiac muscle hypertrophy	Any process that modulates the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
	GO:1900169	regulation of glucocorticoid mediated signaling pathway	Any process that modulates the frequency, rate or extent of glucocorticoid mediated signaling pathway.
	GO:0045859	regulation of protein kinase activity	Any process that modulates the frequency, rate or extent of protein kinase activity.
	GO:0060297	regulation of sarcomere organization	Any process that modulates the rate, frequency or extent myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
	GO:0051056	regulation of small GTPase mediated signal transduction	Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
cellular component
	GO:0005938	cell cortex	The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
	GO:0030864	cortical actin cytoskeleton	The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

NMR Structure
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(no "Sites" information available for 2drn)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2drn)

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	2drn
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	AKP13_HUMAN \| Q12802
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	KAP2_RAT \| P12368
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	2.7.1.37
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	AKP13_HUMAN \| Q12802
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	KAP2_RAT \| P12368
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UniProtKB/Swiss-Prot
	AKP13_HUMAN \| Q12802	:	2lg1 4d0n 4d0o
	KAP2_RAT \| P12368	:	2h9r 2hwn 2izy 3tmh

1l6e	THE SAME PROTEIN OF CHAIN A AND B
1r2a	THE SAME PROTEIN OF CHAIN A AND B
2h9r	THE SAME PROTEIN COMPLEXED WITH A DIFFERENT FRAGMENT
2hwn	CRYSTAL STRUCTURE OF THE SAME PROTEIN (CHAIN A AND B)

Description

Compounds

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 (1, 1)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (50, 55)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File