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(-) Description

Title :  CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 1B
 
Authors :  K. Y. J. Zhang, G. L. Card, Y. Suzuki, D. R. Artis, D. Fong, S. Gillette, D. J. Neiman, B. L. West, C. Zhang, M. V. Milburn, S. -H. Kim, J. Schlessing G. Bollag
Date :  19 May 04  (Deposition) - 03 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A
Keywords :  Pde1B, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Y. J. Zhang, G. L. Card, Y. Suzuki, D. R. Artis, D. Fong, S. Gillette, D. Hsieh, J. Neiman, B. L. West, C. Zhang, M. V. Milburn, S. -H. Kim, J. Schlessinger, G. Bollag
A Glutamine Switch Mechanism For Nucleotide Selectivity By Phosphodiesterases
Mol. Cell V. 15 279 2004
PubMed-ID: 15260978  |  Reference-DOI: 10.1016/J.MOLCEL.2004.07.005

(-) Compounds

Molecule 1 - CALCIUM/CALMODULIN-DEPENDENT 3',5'-CYCLIC NUCLEOTIDE PHOSPHODIESTERASE 1B
    ChainsA
    EC Number3.1.4.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)CODON PLUS(RIL)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN
    GenePDE1B, PDE1B1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCAM-PDE 1B, 63 KDA CAM-PDE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
2MG1Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:227 , HIS A:263 , ASP A:264 , ASP A:370 , HOH A:1007 , HOH A:1008BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREASP A:264 , HOH A:1003 , HOH A:1004 , HOH A:1005 , HOH A:1006 , HOH A:1007BINDING SITE FOR RESIDUE MG A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TAZ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE1B_HUMAN263-274  1A:263-274

(-) Exons   (10, 10)

Asymmetric/Biological Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002430521ENSE00001183864chr12:54943404-54943556153PDE1B_HUMAN-00--
1.2ENST000002430522ENSE00001147374chr12:54943644-54943769126PDE1B_HUMAN1-38380--
1.4ENST000002430524ENSE00000838447chr12:54960758-54960871114PDE1B_HUMAN38-76390--
1.5ENST000002430525ENSE00000920047chr12:54962968-54963150183PDE1B_HUMAN76-137620--
1.6ENST000002430526ENSE00000920048chr12:54963330-5496339667PDE1B_HUMAN137-159231A:146-15914
1.7ENST000002430527ENSE00000920049chr12:54964025-54964141117PDE1B_HUMAN160-198391A:160-19839
1.8ENST000002430528ENSE00000920050chr12:54966385-54966525141PDE1B_HUMAN199-245471A:199-24547
1.9ENST000002430529ENSE00000920051chr12:54966932-54967032101PDE1B_HUMAN246-279341A:246-27934
1.10ENST0000024305210ENSE00000920052chr12:54967139-54967264126PDE1B_HUMAN279-321431A:279-32143
1.11ENST0000024305211ENSE00000920053chr12:54967392-54967493102PDE1B_HUMAN321-355351A:321-355 (gaps)35
1.12ENST0000024305212ENSE00000920054chr12:54968882-54969002121PDE1B_HUMAN355-395411A:355-39541
1.13ENST0000024305213ENSE00000920055chr12:54969335-5496941682PDE1B_HUMAN396-423281A:396-423 (gaps)28
1.14ENST0000024305214ENSE00000920056chr12:54969776-54969884109PDE1B_HUMAN423-459371A:423-44523
1.15ENST0000024305215ENSE00000920057chr12:54970355-54970485131PDE1B_HUMAN459-503451A:473-50230
1.16ENST0000024305216ENSE00000920058chr12:54971009-54971129121PDE1B_HUMAN503-536340--
1.17ENST0000024305217ENSE00001147267chr12:54971644-549730231380PDE1B_HUMAN-00--

(-) 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:322
 aligned with PDE1B_HUMAN | Q01064 from UniProtKB/Swiss-Prot  Length:536

    Alignment length:357
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       
          PDE1B_HUMAN   146 VGPTYSTAVLNCLKNLDLWCFDVFSLNQAADDHALRTIVFELLTRHNLISRFKIPTVFLMSFLDALETGYGKYKNPYHNQIHAADVTQTVHCFLLRTGMVHCLSEIELLAIIFAAAIHDYEHTGTTNSFHIQTKSECAIVYNDRSVLENHHISSVFRLMQDDEMNIFINLTKDEFVELRALVIEMVLATDMSCHFQQVKTMKTALQQLERIDKPKALSLLLHAADISHPTKQWLVHSRWTKALMEEFFRQGDKEAELGLPFSPLCDRTSTLVAQSQIGFIDFIVEPTFSVLTDVAEKSVQPLADEDSKSKNQPSFQWRQPSLDVEVGDPNPDVVSFRSTWVKRIQENKQKWKERAAS 502
               SCOP domains d1taza_ A: Catalytic domain of cyclic nucleotide phosphodiesterase 1b, PDE1B                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1tazA00 A:146-502 Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------PDEase_I-1tazA01 A:222-445                                                                                                                                                                                                                                 ------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhh.......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------PDEASE_I    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6      Exon 1.7  PDB: A:160-198               Exon 1.8  PDB: A:199-245 UniProt: 199-245      ---------------------------------Exon 1.10  PDB: A:279-321 UniProt: 279-321 ---------------------------------Exon 1.12  PDB: A:355-395                Exon 1.13 UniProt: 396-423  -----------------------------------Exon 1.15  PDB: A:473-502 UniProt: 459-503   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:246-279          -----------------------------------------Exon 1.11  PDB: A:321-355 (gaps)   -------------------------------------------------------------------Exon 1.14  PDB: A:423-445            ------------------------------------------- Transcript 1 (2)
                 1taz A 146 VGPTYSTAVLNCLKNLDLWCFDVFSLNQAADDHALRTIVFELLTRHNLISRFKIPTVFLMSFLDALETGYGKYKNPYHNQIHAADVTQTVHcFLLRTGMVHCLSEIELLAIIFAAAIHDYEHTGTTNSFHIQTKSECAIVYNDRSVLENHHISSVFRLMQDDEMNIFINLTKDEFVELRALVIEMVLATDMSCHFQQVKTMKTALQQ--RIDKPKALSLLLHAADISHPTKQWLVHSRWTKALMEEFFRQGDKEAELGLP------RTSTLVAQSQIGFIDFIVEPTFSVLTDVAEKSVQ---------------------------DPNPDVVSFRSTWVKRIQENKQKWKERAAS 502
                                   155       165       175       185       195       205       215       225       235 |     245       255       265       275       285       295       305       315       325       335       345      |355       365       375       385       395       405      |415       425       435       445         -         -       475       485       495       
                                                                                                                     237-CME                                                                                                            352  |                                               405    412                              445                         473                             
                                                                                                                                                                                                                                           355                                                                                                                                                   

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PDE1B_HUMAN | Q01064)
molecular function
    GO:0004115    3',5'-cyclic-AMP phosphodiesterase activity    Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
    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:0048101    calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity    Catalysis of the reaction: guanosine 3',5'-cyclic phosphate + H2O = guanosine 5'-phosphate. The reaction is calmodulin and calcium-sensitive.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0004117    calmodulin-dependent cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is regulated by calmodulin.
    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:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
    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).
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006198    cAMP catabolic process    The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0046069    cGMP catabolic process    The chemical reactions and pathways resulting in the breakdown of cyclic GMP, guanosine 3',5'-phosphate.
    GO:0097011    cellular response to granulocyte macrophage colony-stimulating factor 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 granulocyte macrophage colony-stimulating factor stimulus.
    GO:0036006    cellular response to macrophage colony-stimulating factor 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 macrophage colony-stimulating factor stimulus.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:0030224    monocyte differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte.
    GO:0042053    regulation of dopamine metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving dopamine.
    GO:0001505    regulation of neurotransmitter levels    Any process that modulates levels of neurotransmitter.
    GO:0001975    response to amphetamine    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 an amphetamine stimulus. Amphetamines consist of a group of compounds related to alpha-methylphenethylamine.
    GO:0042428    serotonin metabolic process    The chemical reactions and pathways involving serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties.
    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.
    GO:0008542    visual learning    Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
    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:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE1B_HUMAN | Q010641lxr 4npv 4npw 5b25 5uoy 5up0

(-) Related Entries Specified in the PDB File

1t9r 1t9s 1tb5 1tb7 1tbb 1tbf