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Title :   CRYSTAL STRUCTURE OF CAMP-DEPENDENT PROTEIN KINASE A REGULATORY SUBUNIT I ALPHA IN COMPLEX WITH DUAL-SPECIFIC A-KINASE ANCHORING PROTEIN 2

Authors :   G. N. Sarma, F. S. Kinderman, C. Kim, S. Von Daake, S. S. Taylor

Date :   09 Aug 09 (Deposition) - 02 Feb 10 (Release) - 02 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.29

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

Keywords :   Four-Helix Bundle, Acetylation, Camp, Camp-Binding, Disulfide Bond, Nucleotide-Binding, Phosphoprotein, Cytoplasm, Membrane, Mitochondrion, Polymorphism, Transit Peptide, Structural Protein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. N. Sarma, F. S. Kinderman, C. Kim, S. Von Daake, L. Chen, B. C. Wang, S. S. Taylor
Structure Of D-Akap2:Pka Ri Complex: Insights Into Akap Specificity And Selectivity
Structure V. 18 155 2010
PubMed-ID: 20159461 | Reference-DOI: 10.1016/J.STR.2009.12.012

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE TYPE I-ALPHA REGULATORY SUBUNIT
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET C
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PRKAR1A
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913

Molecule 2 - DUAL SPECIFICITY A KINASE-ANCHORING PROTEIN 2
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX 4T-1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PKA-RII SUBUNIT BINDING: UNP RESIDUES 623-662
	Gene	:	AKAP10
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	KINASE ANCHOR PROTEIN 10, PROTEIN KINASE A- ANCHORING PROTEIN 10, PRKA10, D-AKAP-2

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	ZN	5	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:23 , GLU A:42 , GLU C:633	BINDING SITE FOR RESIDUE ZN A 701
2	AC2	SOFTWARE	GLU A:15 , ARG A:49 , GLU A:50 , HOH A:127 , GLU B:56	BINDING SITE FOR RESIDUE ZN A 702
3	AC3	SOFTWARE	HIS A:23 , GLU A:42 , HOH A:103 , HOH C:111	BINDING SITE FOR RESIDUE ZN A 705
4	AC4	SOFTWARE	HIS B:23 , GLU B:42 , HOH B:101 , GLU C:629	BINDING SITE FOR RESIDUE ZN B 703
5	AC5	SOFTWARE	GLU A:56 , GLU B:15 , ARG B:49	BINDING SITE FOR RESIDUE ZN B 704

Asymmetric/Biological Unit

No.	Residues
1	A:16	-	B:37
2	A:37	-	B:16

(no "Cis Peptide Bond" information available for 3IM4)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024608	I	646	V	AKA10_HUMAN	Polymorphism	203462	C	V	646	V

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

(no "PROSITE Motif" information available for 3IM4)

Asymmetric/Biological Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000011371	1	ENSBTAE00000313083	chr19:63667746-63667642	105	KAP0_BOVIN	-	0	0	-	-
1.2	ENSBTAT00000011371	2	ENSBTAE00000092376	chr19:63665339-63665143	197	KAP0_BOVIN	1-59	59	2	A:12-58 B:12-58	47 47
1.3	ENSBTAT00000011371	3	ENSBTAE00000092377	chr19:63660511-63660341	171	KAP0_BOVIN	60-116	57	2	A:59-61 B:59-60	3 2
1.4	ENSBTAT00000011371	4	ENSBTAE00000092378	chr19:63659532-63659441	92	KAP0_BOVIN	117-147	31	0	-	-
1.5	ENSBTAT00000011371	5	ENSBTAE00000092380	chr19:63659241-63659180	62	KAP0_BOVIN	147-168	22	0	-	-
1.6	ENSBTAT00000011371	6	ENSBTAE00000092381	chr19:63658431-63658385	47	KAP0_BOVIN	168-183	16	0	-	-
1.7	ENSBTAT00000011371	7	ENSBTAE00000092382	chr19:63657530-63657372	159	KAP0_BOVIN	184-236	53	0	-	-
1.8	ENSBTAT00000011371	8	ENSBTAE00000092383	chr19:63656713-63656653	61	KAP0_BOVIN	237-257	21	0	-	-
1.9	ENSBTAT00000011371	9	ENSBTAE00000092384	chr19:63655618-63655497	122	KAP0_BOVIN	257-297	41	0	-	-
1.10	ENSBTAT00000011371	10	ENSBTAE00000092385	chr19:63654637-63654556	82	KAP0_BOVIN	298-325	28	0	-	-
1.11	ENSBTAT00000011371	11	ENSBTAE00000092386	chr19:63654278-63653922	357	KAP0_BOVIN	325-381	57	0	-	-

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
	(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:50
 aligned with KAP0_BOVIN | P00514 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:50
                                    22        32        42        52        62
           KAP0_BOVIN    13 SLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFEKLEKEEAK  62
               SCOP domains d3im4a_ A:                                         SCOP domains
               CATH domains -------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: A:12-58 UniProt: 1-59           1.3 Transcript 1
                 3im4 A  12 SLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFEKLEKEEAK  61
                                    21        31        41        51        61

Chain B from PDB  Type:PROTEIN  Length:49
 aligned with KAP0_BOVIN | P00514 from UniProtKB/Swiss-Prot  Length:380

    Alignment length:49
                                    22        32        42        52         
           KAP0_BOVIN    13 SLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFEKLEKEEA  61
               SCOP domains d3im4b_ B:                                        SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
               Transcript 1 Exon 1.2  PDB: B:12-58 UniProt: 1-59           1. Transcript 1
                 3im4 B  12 SLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFEKLEKEEA  60
                                    21        31        41        51

Chain C from PDB  Type:PROTEIN  Length:27
 aligned with AKA10_HUMAN | O43572 from UniProtKB/Swiss-Prot  Length:662

    Alignment length:27
                                   637       647       
          AKA10_HUMAN   628 DEAQEELAWKIAKMIVSDIMQQAQYDQ 654
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------V-------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                 3im4 C 628 DEAQEELAWKIAKMIVSDVMQQAQYDQ 654
                                   637       647

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 '\|'

(no "CATH Domain" information available for 3IM4)

(no "Pfam Domain" information available for 3IM4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (KAP0_BOVIN | P00514)

molecular function
	GO:0030552	cAMP binding	Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
	GO:0004862	cAMP-dependent protein kinase inhibitor activity	Stops, prevents or reduces the activity of a cAMP-dependent protein kinase.
	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: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:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0060038	cardiac muscle cell proliferation	The expansion of a cardiac muscle cell population by cell division.
	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:0001707	mesoderm formation	The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
	GO:0046007	negative regulation of activated T cell proliferation	Any process that stops, prevents or reduces the rate or extent of activated T cell proliferation.
	GO:2000480	negative regulation of cAMP-dependent protein kinase activity	Any process that stops, prevents or reduces the frequency, rate or extent of cAMP-dependent protein kinase activity.
	GO:0006469	negative regulation of protein kinase activity	Any process that stops, prevents, or reduces 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:0045214	sarcomere organization	The myofibril assembly process that results in the 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.
cellular component
	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:0001772	immunological synapse	An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031594	neuromuscular junction	The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
	GO:0031588	nucleotide-activated protein kinase complex	A protein complex that possesses nucleotide-dependent protein kinase activity. The nucleotide can be AMP (in S. pombe and human) or ADP (in S. cerevisiae).
	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:0044853	plasma membrane raft	A membrane raft that is part of the plasma membrane.
	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 (AKA10_HUMAN | O43572)

biological process
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0008104	protein localization	Any process in which a protein is transported to, or maintained in, a specific location.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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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3im3	CRYSTAL STRUCTURE OF PKA RI ALPHA DIMERIZATION/DOCKING DOMAIN (SAME PROTEIN WITHOUT D-AKAP2 PEPTIDE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

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Exons (2, 4)

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