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(-) Description

Title :  MOLECULAR BASIS OF AKAP SPECIFICITY FOR PKA REGULATORY SUBUNITS
 
Authors :  M. G. Gold, B. Lygren, P. Dokurno, N. Hoshi, G. Mcconnachie, K. Tasken, C. R. Carlson, J. D. Scott, D. Barford
Date :  27 Jul 06  (Deposition) - 08 Nov 06  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Camp-Binding, Phosphorylation, Nucleotide-Binding, Pka, Camp, Akap, Anchor, Kinase, Acetylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. G. Gold, B. Lygren, P. Dokurno, N. Hoshi, G. Mcconnachie, K. Tasken, C. R. Carlson, J. D. Scott, D. Barford
Molecular Basis Of Akap Specificity For Pka Regulatory Subunits.
Mol. Cell V. 24 383 2006
PubMed-ID: 17081989  |  Reference-DOI: 10.1016/J.MOLCEL.2006.09.006

(-) Compounds

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY SUBUNIT
    ChainsA, B
    EC Number2.7.11.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P1
    Expression System StrainBL21
    Expression System Taxid511693
    Fragment3-43
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCAMP-DEPENDENT PROTEIN KINASE REGULATORY SUBUNIT II
 
Molecule 2 - AKAP-IS
    ChainsC
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1DTD2Ligand/IonDITHIANE DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:23 , PHE A:31 , GLU A:34 , TYR A:35 , ARG A:38 , DTD A:1045 , HOH A:2037 , GLN B:23BINDING SITE FOR RESIDUE DTD A1044
2AC2SOFTWAREARG A:38 , LEU A:39 , DTD A:1044 , HOH A:2038 , HOH A:2039 , GLN B:23 , ARG B:38BINDING SITE FOR RESIDUE DTD A1045

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002655631aENSE00001926435chr3:48885279-48884768512KAP2_HUMAN1-88882A:5-43
B:3-43
39
41
1.2ENST000002655632ENSE00001335223chr3:48845117-4884508236KAP2_HUMAN88-100130--
1.3aENST000002655633aENSE00001321402chr3:48831482-4883143053KAP2_HUMAN100-117180--
1.4bENST000002655634bENSE00001318834chr3:48828060-4882797784KAP2_HUMAN118-145280--
1.5ENST000002655635ENSE00001296318chr3:48820525-48820419107KAP2_HUMAN146-181360--
1.6ENST000002655636ENSE00001315035chr3:48810541-48810388154KAP2_HUMAN181-232520--
1.7bENST000002655637bENSE00001169115chr3:48802782-48802681102KAP2_HUMAN233-266340--
1.8ENST000002655638ENSE00000768107chr3:48802511-4880243775KAP2_HUMAN267-291250--
1.9ENST000002655639ENSE00000768105chr3:48793877-4879381266KAP2_HUMAN292-313220--
1.10bENST0000026556310bENSE00000768103chr3:48789750-48789609142KAP2_HUMAN314-361480--
1.11dENST0000026556311dENSE00001841831chr3:48789151-487840125140KAP2_HUMAN361-404440--

(-) Sequences/Alignments

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:39
 aligned with KAP2_HUMAN | P13861 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:39
                                    15        25        35         
            KAP2_HUMAN    6 IPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREAR 44
               SCOP domains d2izxa_ A: automated matches            SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: A:5-43 UniProt: 1-88    Transcript 1
                  2izx A  5 IPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREAR 43
                                    14        24        34         

Chain B from PDB  Type:PROTEIN  Length:41
 aligned with KAP2_HUMAN | P13861 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:41
                                    13        23        33        43 
            KAP2_HUMAN    4 IQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREAR 44
               SCOP domains d2izxb_ B: automated matches              SCOP domains
               CATH domains 2izxB00 B:3-43                            CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: B:3-43 UniProt: 1-88      Transcript 1
                  2izx B  3 IQIPPGLTELLQGYTVEVLRQQPPDLVEFAVEYFTRLREAR 43
                                    12        22        32        42 

Chain C from PDB  Type:PROTEIN  Length:18
                                                 
               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 ------------------ Transcript
                  2izx C  4 QIEYLAKQIVDNAIQQAK 21
                                    13        

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KAP2_HUMAN | P13861)
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: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: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:0034199    activation of protein kinase A activity    Any process that initiates the activity of the inactive enzyme protein kinase A.
    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:0071377    cellular response to glucagon 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 glucagon stimulus.
    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: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: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:0003091    renal water homeostasis    Renal process involved in the maintenance of an internal steady state of water in the body.
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: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:0097546    ciliary base    Area of the cilium (also called flagellum) where the basal body and the axoneme are anchored to the plasma membrane. The ciliary base encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium, and many ciliary proteins localize specifically to this area.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        KAP2_HUMAN | P138612kyg 4zp3 5h77 5h78 5xby

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