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(-) Description

Title :  CRYSTAL STRUCTURE OF RII ALPHA DIMERIZATION/DOCKING DOMAIN OF PKA BOUND TO THE D-AKAP2 PEPTIDE
 
Authors :  F. Kinderman, C. Kim
Date :  01 Aug 06  (Deposition) - 21 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Keywords :  Pka, Akap, Dimerization/Docking, D/D, Regulatory Subunit, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. S. Kinderman, C. Kim, S. Von Daake, Y. Ma, B. Q. Pham, G. Spraggon, N. H. Xuong, P. A. Jennings, S. S. Taylor
A Dynamic Mechanism For Akap Binding To Rii Isoforms Of Camp-Dependent Protein Kinase.
Mol. Cell V. 24 397 2006
PubMed-ID: 17081990  |  Reference-DOI: 10.1016/J.MOLCEL.2006.09.015

(-) Compounds

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE TYPE II-ALPHA REGULATORY SUBUNIT
    Chains: A, B, C, D
    EC Number: 2.7.11.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DIMERIZATION/DOCKING DOMAIN, RESIDUES 0-44
    Gene: PRKAR2A
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
 
Molecule 2 - A KINASE BINDING PEPTIDE
    Chains: E, F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:10 , GLU A:11 , GLN A:14 , GLN B:23 , PHE B:31 , ARG B:38 , HOH B:337 , HOH B:346 , LYS E:10 , HOH E:26BINDING SITE FOR RESIDUE GOL B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HWN)

(-) Sequences/Alignments

Asymmetric 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_RAT | P12368 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:39
                                    15        25        35         
             KAP2_RAT     6 IPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR  44
               SCOP domains d2hwna_ A: automated matches            SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 2hwn A   5 IPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR  43
                                    14        24        34         


Chain B from PDB  Type:PROTEIN  Length:45
 aligned with KAP2_RAT | P12368 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:45
                                    10        20        30        40     
             KAP2_RAT     1 MSHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR  45
               SCOP domains d2hwnb_ B: automated matches                  SCOP domains
               CATH domains 2hwnB00 B:0-44                                CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                 2hwn B   0 MSHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREARR  44
                                     9        19        29        39     


Chain C from PDB  Type:PROTEIN  Length:40
 aligned with KAP2_RAT | P12368 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:40
                                    14        24        34        44
             KAP2_RAT     5 QIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR  44
               SCOP domains d2hwnc_ C: automated matches             SCOP domains
               CATH domains 2hwnC00 C:4-43                           CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 2hwn C   4 QIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR  43
                                    13        23        33        43


Chain D from PDB  Type:PROTEIN  Length:43
 aligned with KAP2_RAT | P12368 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:43
                                    11        21        31        41   
             KAP2_RAT     2 SHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR  44
               SCOP domains d2hwnd_ D: automated matches                SCOP domains
               CATH domains 2hwnD00 D:1-43                              CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 2hwn D   1 SHIQIPPGLTELLQGYTVEVLRQQPPDLVDFAVEYFTRLREAR  43
                                    10        20        30        40   


Chain E from PDB  Type:PROTEIN  Length:19
 aligned with Q4R5S0_MACFA | Q4R5S0 from UniProtKB/TrEMBL  Length:636

    Alignment length:19
                                   615         
         Q4R5S0_MACFA   606 EELAWKIAKMIVSDVMQQA 624
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 2hwn E   2 EELAWKIAKMIVSDVMQQC  20
                                    11         


Chain F from PDB  Type:PROTEIN  Length:20
 aligned with Q4R5S0_MACFA | Q4R5S0 from UniProtKB/TrEMBL  Length:636

    Alignment length:20
                                   615       625
         Q4R5S0_MACFA   606 EELAWKIAKMIVSDVMQQAQ 625
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 2hwn F   2 EELAWKIAKMIVSDVMQQCK  21
                                    11        21
   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, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 E,F   (Q4R5S0_MACFA | Q4R5S0)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
biological process
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KAP2_RAT | P12368: 2drn 2h9r 2izy 3tmh

(-) Related Entries Specified in the PDB File

1r2a THE MOLECULAR BASIS FOR PROTEIN KINASE A ANCHORING REVEALED BY SOLUTION NMR