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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICAL MODEL OF BOVINE PHOSPHODIESTERASE 5 1ST GAF DOMAIN
 
Authors :  Y. -S. J. Ho, L. M. Burden, J. H. Hurley
Date :  11 Aug 00  (Deposition) - 25 Oct 00  (Release) - 01 Apr 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Phosphodiesterase, Gaf Domain, Homology Model, Cgmp Binding Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. S. Ho, L. M. Burden, J. H. Hurley
Structure Of The Gaf Domain, A Ubiquitous Signaling Motif And A New Class Of Cyclic Gmp Receptor.
Embo J. V. 19 5288 2000
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CGMP-SPECIFIC 3'-5'-CYCLIC PHOSPHODIESTERASE
    ChainsA
    EC Number3.1.4.17
    Organism CommonBOVINE
    Organism ScientificBOS TAURUS
    SynonymCGB-PDE, CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1FL4)

(-) Sites  (0, 0)

(no "Site" information available for 1FL4)

(-) SS Bonds  (1, 1)

Theoretical Model
No.Residues
1A:159 -A:300

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1FL4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1FL4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1FL4)

(-) Exons   (4, 4)

Theoretical Model (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENSBTAT000000144791aENSBTAE00000117781chr6:6158563-6158782220PDE5A_BOVIN1-41410--
1.2ENSBTAT000000144792ENSBTAE00000117782chr6:6181347-6181935589PDE5A_BOVIN41-2371971A:118-237120
1.3ENSBTAT000000144793ENSBTAE00000371931chr6:6194696-619478590PDE5A_BOVIN238-267301A:238-26730
1.4ENSBTAT000000144794ENSBTAE00000401006chr6:6222745-622281672PDE5A_BOVIN268-291241A:268-29124
1.5ENSBTAT000000144795ENSBTAE00000427993chr6:6224503-622459290PDE5A_BOVIN292-321301A:292-30918
1.6ENSBTAT000000144796ENSBTAE00000416381chr6:6227342-6227479138PDE5A_BOVIN322-367460--
1.7ENSBTAT000000144797ENSBTAE00000387810chr6:6229635-622970268PDE5A_BOVIN368-390230--
1.8ENSBTAT000000144798ENSBTAE00000117791chr6:6268137-6268245109PDE5A_BOVIN390-426370--
1.9ENSBTAT000000144799ENSBTAE00000117792chr6:6269284-626937188PDE5A_BOVIN427-456300--
1.10ENSBTAT0000001447910ENSBTAE00000272915chr6:6280948-6281123176PDE5A_BOVIN456-514590--
1.11ENSBTAT0000001447911ENSBTAE00000117795chr6:6284212-628427160PDE5A_BOVIN515-534200--
1.12ENSBTAT0000001447912ENSBTAE00000400099chr6:6298732-6298878147PDE5A_BOVIN535-583490--
1.13ENSBTAT0000001447913ENSBTAE00000388523chr6:6303220-6303345126PDE5A_BOVIN584-625420--
1.14ENSBTAT0000001447914ENSBTAE00000383599chr6:6305099-630519395PDE5A_BOVIN626-657320--
1.15ENSBTAT0000001447915ENSBTAE00000412455chr6:6313874-631396188PDE5A_BOVIN657-686300--
1.16ENSBTAT0000001447916ENSBTAE00000419489chr6:6317584-6317684101PDE5A_BOVIN687-720340--
1.17ENSBTAT0000001447917ENSBTAE00000396551chr6:6319397-631947478PDE5A_BOVIN720-746270--
1.18ENSBTAT0000001447918ENSBTAE00000385385chr6:6323293-632335664PDE5A_BOVIN746-767220--
1.19ENSBTAT0000001447919ENSBTAE00000382443chr6:6328112-632818675PDE5A_BOVIN768-792250--
1.20ENSBTAT0000001447920ENSBTAE00000377146chr6:6329921-633000484PDE5A_BOVIN793-820280--
1.21bENSBTAT0000001447921bENSBTAE00000371919chr6:6332007-6332360354PDE5A_BOVIN821-865450--

(-) Sequences/Alignments

Theoretical Model
   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:192
 aligned with PDE5A_BOVIN | Q28156 from UniProtKB/Swiss-Prot  Length:865

    Alignment length:192
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307  
          PDE5A_BOVIN   118 SDKKEQMPLTSPRFDNDEGDQCSRLLELVKDISSHLDVTALCHKIFLHIHGLISADRYSLFLVCEDSSNDKFLISRLFDVAEGSTLEEASNNCIRLEWNKGIVGHVAAFGEPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNGGTFTEKDEKDFAAYLAFCGIVLHNAQL 309
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeeee.........eee.......ee..........eee..hhhhhhhhhhh..eee.......................eeeeeee.....eeeeeeee.hhhhh....hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.2  PDB: A:118-237 UniProt: 41-237 [INCOMPLETE]                                                                   Exon 1.3  PDB: A:238-267      Exon 1.4  PDB: A:268-291Exon 1.5           Transcript 1
                 1fl4 A 118 SDKKEQMPLTSPRFDNDEGDQCSRLLELVKDISSHLDVTALCHKIFLHIHGLISADRYSLFLVCEDSSNDKFLISRLFDVAEGSTLEEASNNCIRLEWNKGIVGHVAAFGEPLNIKDAYEDPRFNAEVDQITGYKTQSILCMPIKNHREEVVGVAQAINKKSGNGGTFTEKDEKDFAAYLAFCGIVLHNAQL 309
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307  

   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  (0, 0)

(no "SCOP Domain" information available for 1FL4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1FL4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1FL4)

(-) Gene Ontology  (20, 20)

Theoretical Model(hide GO term definitions)
Chain A   (PDE5A_BOVIN | Q28156)
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE5A_BOVIN | Q281563jab 3jbq

(-) Related Entries Specified in the PDB File

1f5m 1F5M IS STRUCTURE OF THE GAF DOMAIN