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(-) Description

Title :  SOLUTION STRUCTURE OF CGMP-BINDING GAF DOMAIN OF PHOSPHODIESTERASE 5
 
Authors :  C. C. Heikaus, J. R. Stout, M. R. Sekharan, C. M. Eakin, P. Rajagopal, P. S. Brzovic, J. A. Beavo, R. E. Klevit
Date :  16 Apr 08  (Deposition) - 03 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cyclic Nucleotide Phosphodiesterase, Pde5, Gaf Domain, Cgmp, Nmr, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. C. Heikaus, J. R. Stout, M. R. Sekharan, C. M. Eakin, P. Rajagopal, P. S. Brzovic, J. A. Beavo, R. E. Klevit
Solution Structure Of The Cgmp Binding Gaf Domain From Phosphodiesterase 5: Insights Into Nucleotide Selectivity, Dimerization, And Cgmp-Dependent Conformational Change.
J. Biol. Chem. V. 283 22749 2008
PubMed-ID: 18534985  |  Reference-DOI: 10.1074/JBC.M801577200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHODIESTERASE 5A, CGMP-SPECIFIC
    ChainsA
    EC Number3.1.4.35
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)STAR
    Expression System VectorPRUNH
    FragmentCGMP-BINDING GAF DOMAIN (UNP RESIDUES 154-320)
    GenePDE5A
    MutationYES
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
135G1Ligand/IonGUANOSINE-3',5'-MONOPHOSPHATE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:174 , TYR A:175 , SER A:176 , PHE A:178 , PHE A:195 , LEU A:213 , ILE A:219 , ALA A:235 , TYR A:236BINDING SITE FOR RESIDUE 35G A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K31)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K31)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K31)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2K31)

(-) Exons   (0, 0)

(no "Exon" information available for 2K31)

(-) Sequences/Alignments

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
(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:149
 aligned with PDE5A_MOUSE | Q8CG03 from UniProtKB/Swiss-Prot  Length:865

    Alignment length:149
                                   163       173       183       193       203       213       223       233       243       253       263       273       283       293         
          PDE5A_MOUSE   154 DVTALCHKIFLHIHGLISADRYSLFLVCEDSSKDKFLISRLFDVAEGSTLEEASNNCIRLEWNKGIVGHVAAFGEPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNGGTFTEKDEKDFAAYLAFCGI 302
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains GAF-2k31A01 A:154-302                                                                                                                                 Pfam domains
         Sec.struct. author ...hhhhhhhhhhh......eeeeeeeeee...eeeeeeee.........hhhh....eee...hhhhhhhhhh..eee...........hhhhhhh.....eeeeeeee...eeeeeeeee..........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2k31 A 154 DVTALCHKIFLHIHGLISADRYSLFLVCEDSSKDKFLISRLFDVAEGSTLEEASNNCIRLEWNKGIVGHVAAFGEPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNGGTFTEKDEKDFAEYLAFCGE 302
                                   163       173       183       193       203       213       223       233       243       253       263       273       283       293         

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    → 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  (0, 0)

(no "SCOP Domain" information available for 2K31)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2K31)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: GAF (44)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (PDE5A_MOUSE | Q8CG03)
molecular function
    GO:0047555    3',5'-cyclic-GMP phosphodiesterase activity    Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate.
    GO:0004114    3',5'-cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
    GO:0030553    cGMP binding    Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004112    cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: a nucleoside cyclic phosphate + H2O = a nucleoside phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
biological process
    GO:0046069    cGMP catabolic process    The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate.
    GO:0046068    cGMP metabolic process    The chemical reactions and pathways involving cyclic GMP, guanosine 3',5'-phosphate.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0055118    negative regulation of cardiac muscle contraction    Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction.
    GO:0045745    positive regulation of G-protein coupled receptor protein signaling pathway    Any process that activates or increases the frequency, rate or extent of G-protein coupled receptor protein signaling pathway activity.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0010613    positive regulation of cardiac muscle hypertrophy    Any process that increases 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:0060282    positive regulation of oocyte development    Any process that increases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
    GO:0030823    regulation of cGMP metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving cGMP.
    GO:0055119    relaxation of cardiac muscle    The process in which the extent of cardiac muscle contraction is reduced.
    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.

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