Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF GAFB FROM THE HUMAN PHOSPHODIESTERASE 5
 
Authors :  C. Schlicker, M. Russwurm, C. Steegborn
Date :  30 Sep 10  (Deposition) - 18 May 11  (Release) - 18 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Russwurm, C. Schlicker, M. Weyand, D. Koesling, C. Steegborn
Crystal Structure Of The Gaf-B Domain From Human Phosphodiesterase 5.
Proteins V. 79 1682 2011
PubMed-ID: 21425347  |  Reference-DOI: 10.1002/PROT.22989

(-) Compounds

Molecule 1 - CGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE
    ChainsA, B
    EC Number3.1.4.35
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System VectorPPR-IBA2
    FragmentGAFB DOMAIN, RESIDUES 346-508
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE, CGB-PDE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2XSS)

(-) Sites  (0, 0)

(no "Site" information available for 2XSS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (7, 12)

Asymmetric Unit (7, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003549601aENSE00001851914chr4:120550146-120549675472PDE5A_HUMAN1-51510--
1.4ENST000003549604ENSE00001637089chr4:120528452-120527864589PDE5A_HUMAN51-2471970--
1.5bENST000003549605bENSE00000935544chr4:120517767-12051767890PDE5A_HUMAN248-277300--
1.6ENST000003549606ENSE00000970323chr4:120488299-12048822872PDE5A_HUMAN278-301241A:339-340
-
2
-
1.7ENST000003549607ENSE00000970324chr4:120486565-12048647690PDE5A_HUMAN302-331301A:341-341
-
1
-
1.8bENST000003549608bENSE00000970325chr4:120484125-120483988138PDE5A_HUMAN332-377462A:342-377
B:343-377
36
35
1.9ENST000003549609ENSE00000970326chr4:120481518-12048145168PDE5A_HUMAN378-400232A:378-400 (gaps)
B:378-400 (gaps)
23
23
1.10ENST0000035496010ENSE00000970327chr4:120474901-120474793109PDE5A_HUMAN400-436372A:400-434
B:400-434
35
35
1.11aENST0000035496011aENSE00000970328chr4:120473792-12047370588PDE5A_HUMAN437-466302A:446-466
B:448-466
21
19
1.13ENST0000035496013ENSE00000935541chr4:120463789-120463614176PDE5A_HUMAN466-524592A:466-508 (gaps)
B:466-509 (gaps)
43
44
1.15bENST0000035496015bENSE00000935545chr4:120460174-12046011560PDE5A_HUMAN525-544200--
1.18ENST0000035496018ENSE00001016848chr4:120446850-120446704147PDE5A_HUMAN545-593490--
1.19bENST0000035496019bENSE00001016844chr4:120442215-120442090126PDE5A_HUMAN594-635420--
1.20cENST0000035496020cENSE00001016846chr4:120440294-12044020095PDE5A_HUMAN636-667320--
1.22ENST0000035496022ENSE00001016843chr4:120432289-12043220288PDE5A_HUMAN667-696300--
1.23bENST0000035496023bENSE00001016840chr4:120428859-120428759101PDE5A_HUMAN697-730340--
1.24bENST0000035496024bENSE00001016847chr4:120427087-12042701078PDE5A_HUMAN730-756270--
1.25ENST0000035496025ENSE00001016842chr4:120425754-12042569164PDE5A_HUMAN756-777220--
1.26aENST0000035496026aENSE00001016841chr4:120423810-12042373675PDE5A_HUMAN778-802250--
1.27aENST0000035496027aENSE00001016845chr4:120422408-12042232584PDE5A_HUMAN803-830280--
1.28cENST0000035496028cENSE00001890486chr4:120419893-1204155504344PDE5A_HUMAN831-875450--

(-) 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:156
 aligned with PDE5A_HUMAN | O76074 from UniProtKB/Swiss-Prot  Length:875

    Alignment length:209
                                   309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499         
          PDE5A_HUMAN   300 EKDFAAYLAFCGIVLHNAQLYETSLLENKRNQVLLDLASLIFEEQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCSDSFSSVFHMECEELEKSSDTLTREHDANKINYMYAQYVKNTMEPLNIPDVSKDKRFPWTTENTGNVNQQCIRSLLCTPIKNGKKNKVIGVCQLVNKMEENTGKVKPFNRNDEQFLEAFVIFCGLGIQNTQM 508
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h---------------------------------------hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeee.........--hhhhhhhhhhhhhhhhhhhhh..eee..........-----------.....eeeeeee......eeeeeeee....-........hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.Exon 1.7  PDB: A:341-341      Exon 1.8b  PDB: A:342-377 UniProt: 332-377    ----------------------Exon 1.10  PDB: A:400-434            Exon 1.11a  PDB: A:446-466    ------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------Exon 1.9               -----------------------------------------------------------------Exon 1.13  PDB: A:466-508 (gaps)            Transcript 1 (2)
                 2xss A 339 EKG---------------------------------------AETASLEVILKKIAATIISFMQVQKCTIFIVDEDCSDSFSSVFHMECEELEKSSD--TREHDANKINYMYAQYVKNTMEPLNIPDVSKDKRFP-----------QCIRSLLCTPIKNGKKNKVIGVCQLVNKME-NTGKVKPFNRNDEQFLEAFVIFCGLGIQNTQM 508
                              |      -         -         -         -  |    349       359       369       379       389      |399       409       419       429    |    -      |449       459       469     | 479       489       499         
                              |                                     342                                                   396  |                                434         446                          475 |                               
                            341                                                                                              399                                                                           477                               

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with PDE5A_HUMAN | O76074 from UniProtKB/Swiss-Prot  Length:875

    Alignment length:167
                                   352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       
          PDE5A_HUMAN   343 EQQSLEVILKKIAATIISFMQVQKCTIFIVDEDCSDSFSSVFHMECEELEKSSDTLTREHDANKINYMYAQYVKNTMEPLNIPDVSKDKRFPWTTENTGNVNQQCIRSLLCTPIKNGKKNKVIGVCQLVNKMEENTGKVKPFNRNDEQFLEAFVIFCGLGIQNTQMY 509
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---GAF-2xssB01 B:346-503                                                                                                                                         ------ Pfam domains (1)
           Pfam domains (2) ---GAF-2xssB02 B:346-503                                                                                                                                         ------ Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeee.........--.hhhhhh...hhhhhhhhh....eee..........-------------...eeeeeee......eeeeeeee.ee..--..ee..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8b  PDB: B:343-377          ----------------------Exon 1.10  PDB: B:400-434            Exon 1.11a  PDB: B:448-466    ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.9               -----------------------------------------------------------------Exon 1.13  PDB: B:466-509 (gaps)             Transcript 1 (2)
                 2xss B 343 ETASLEVILKKIAATIISFMQVQKCTIFIVDEDCSDSFSSVFHMECEELEKSSD--TREHDANKINYMYAQYVKNTMEPLNIPDVSKDKRFP-------------IRSLLCTPIKNGKKNKVIGVCQLVNKMEE--GKVKPFNRNDEQFLEAFVIFCGLGIQNTQMY 509
                                   352       362       372       382       392   |  |402       412       422       432 |       -     | 452       462       472   |  |482       492       502       
                                                                               396  |                                434           448                         476  |                              
                                                                                  399                                                                             479                              

   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 2XSS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GAF (44)
(-)
Family: GAF (30)
1aGAF-2xssB01B:346-503
1bGAF-2xssB02B:346-503

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PDE5A_HUMAN | O76074)
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.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2xss)
 
  Sites
(no "Sites" information available for 2xss)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xss)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2xss
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PDE5A_HUMAN | O76074
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.4.35
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PDE5A_HUMAN | O76074
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PDE5A_HUMAN | O760741rkp 1t9r 1t9s 1tbf 1udt 1udu 1uho 1xoz 1xp0 2chm 2h40 2h42 2h44 3b2r 3bjc 3hc8 3hdz 3jwq 3jwr 3lfv 3mf0 3shy 3shz 3sie 3tge 3tgg 4g2w 4g2y 4i9z 4ia0 4md6 4oew 4oex 5jo3

(-) Related Entries Specified in the PDB File

1rkp CRYSTAL STRUCTURE OF PDE5A1-IBMX
1t9r CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A
1t9s CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEXWITH GMP
1tbf CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEXWITH SILDENAFIL
1udt CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 5 COMPLEXEDWITH SILDENAFIL(VIAGRA)
1udu CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 5 COMPLEXEDWITH TADALAFIL(CIALIS)
1uho CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 5 COMPLEXEDWITH VARDENAFIL(LEVITRA)
1xoz CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEX WITH TADALAFIL
1xp0 CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 5A IN COMPLEXWITH VARDENAFIL
2chm CRYSTAL STRUCTURE OF N2 SUBSTITUTED PYRAZOLO PYRIMIDINONES - A FLIPPED BINDING MODE IN PDE5
2h40 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF UNLIGANDED PDE5
2h42 CRYSTAL STRUCTURE OF PDE5 IN COMPLEX WITH SILDENAFIL
2h44 CRYSTAL STRUCTURE OF PDE5A1 IN COMPLEX WITH ICARISID II