Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL GAF DOMAIN OF HUMAN PHOSPHODIESTERASE 10A
 
Authors :  N. Handa, S. Kishishita, E. Mizohata, K. Omori, J. Kotera, T. Terada, M. S. Yokoyama, Riken Structural Genomics/Proteomics Initiative
Date :  17 Apr 08  (Deposition) - 29 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gaf Domain, Phosphodiesterase, Camp, Cgmp, Cgmp-Binding, Hydrolase, Nucleotide-Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Handa, E. Mizohata, S. Kishishita, M. Toyama, S. Morita, T. Uchikubo-Kamo, R. Akasaka, K. Omori, J. Kotera, T. Terada, M. Shirouzu, S. Yokoyama
Crystal Structure Of The Gaf-B Domain From Human Phosphodiesterase 10A Complexed With Its Ligand, Camp
J. Biol. Chem. V. 283 19657 2008
PubMed-ID: 18477562  |  Reference-DOI: 10.1074/JBC.M800595200

(-) Compounds

Molecule 1 - CAMP AND CAMP-INHIBITED CGMP 3',5'-CYCLIC PHOSPHODIESTERASE 10A
    ChainsA, B
    EC Number3.1.4.17
    EngineeredYES
    Expression SystemCELL FREE (ESCHERICHIA COLI)
    Expression System PlasmidPX060608-01
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL GAF DOMAIN
    GenePDE10A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1CMP2Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:286 , CYS A:287 , ALA A:288 , PHE A:304 , ASP A:305 , PHE A:324 , GLY A:329 , ILE A:330 , ALA A:331 , PHE A:352 , ASN A:353 , ASP A:357 , THR A:364 , ILE A:367 , GLN A:383 , HOH A:2003 , HOH A:2004BINDING SITE FOR RESIDUE CMP A 2001
2AC2SOFTWAREARG B:286 , CYS B:287 , ALA B:288 , PHE B:304 , ASP B:305 , GLY B:329 , ILE B:330 , ALA B:331 , PHE B:352 , ASN B:353 , ASP B:357 , TYR B:362 , THR B:364 , ILE B:367 , GLN B:383 , HOH B:2002 , HOH B:2003BINDING SITE FOR RESIDUE CMP B 2001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076800F290LPDE10_HUMANDisease (ADSD2)875989841A/BF290L
2UniProtVAR_008797L303PPDE10_HUMANPolymorphism  ---A/BL303P
3UniProtVAR_076801F324LPDE10_HUMANDisease (ADSD2)875989840A/BF324L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003668821aENSE00001442893chr6:166075588-166075435154PDE10_HUMAN-00--
1.2aENST000003668822aENSE00001442892chr6:165989937-16598990038PDE10_HUMAN1-13130--
1.4bENST000003668824bENSE00001152350chr6:165957056-165956928129PDE10_HUMAN13-56440--
1.5ENST000003668825ENSE00001010817chr6:165895831-16589580329PDE10_HUMAN56-65100--
1.6ENST000003668826ENSE00000828843chr6:165863850-165863730121PDE10_HUMAN66-106410--
1.7ENST000003668827ENSE00000766019chr6:165862465-16586241650PDE10_HUMAN106-122170--
1.8ENST000003668828ENSE00000766017chr6:165848865-165848725141PDE10_HUMAN123-169470--
1.9ENST000003668829ENSE00000766015chr6:165846617-165846462156PDE10_HUMAN170-221520--
1.10ENST0000036688210ENSE00000766013chr6:165844960-16584491051PDE10_HUMAN222-238170--
1.11ENST0000036688211ENSE00000766011chr6:165843833-16584377559PDE10_HUMAN239-258202A:246-258
B:248-258
13
11
1.12ENST0000036688212ENSE00000766009chr6:165842197-16584214652PDE10_HUMAN258-275182A:258-275
B:258-275
18
18
1.13ENST0000036688213ENSE00000766008chr6:165832265-165832123143PDE10_HUMAN276-323482A:276-323
B:276-323
48
48
1.14ENST0000036688214ENSE00000766007chr6:165829769-16582967793PDE10_HUMAN323-354322A:323-354
B:323-354
32
32
1.15ENST0000036688215ENSE00000766006chr6:165827175-165826989187PDE10_HUMAN354-416632A:354-416
B:354-416
63
63
1.16ENST0000036688216ENSE00000766005chr6:165809948-165809806143PDE10_HUMAN417-464482A:417-422
B:417-419
6
3
1.17ENST0000036688217ENSE00000766004chr6:165808753-16580867084PDE10_HUMAN464-492290--
1.18ENST0000036688218ENSE00000766003chr6:165806285-165806135151PDE10_HUMAN492-542510--
1.19ENST0000036688219ENSE00000766002chr6:165801942-165801787156PDE10_HUMAN543-594520--
1.20ENST0000036688220ENSE00000766001chr6:165792855-165792683173PDE10_HUMAN595-652580--
1.21ENST0000036688221ENSE00000765999chr6:165756991-165756880112PDE10_HUMAN652-689380--
1.22ENST0000036688222ENSE00000765998chr6:165752847-16575276781PDE10_HUMAN690-716270--
1.23ENST0000036688223ENSE00000765997chr6:165749700-16574961289PDE10_HUMAN717-746300--
1.24bENST0000036688224bENSE00001442887chr6:165746616-1657407765841PDE10_HUMAN746-779340--

(-) 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:177
 aligned with PDE10_HUMAN | Q9Y233 from UniProtKB/Swiss-Prot  Length:779

    Alignment length:177
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       
          PDE10_HUMAN   246 QTELNDFLLDVSKTYFDNIVAIDSLLEHIMIYAKNLVNADRCALFQVDHKNKELYSDLFDIGEEKEGKPVFKKTKEIRFSIEKGIAGQVARTGEVLNIPDAYADPRFNREVDLYTGYTTRNILCMPIVSRGSVIGVVQMVNKISGSAFSKTDENNFKMFAVFCALALHCANMYHRIR 422
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zmfA00 A:246-422  [code=3.30.450.40, no name defined]                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhheeeeeeeeee....eeeeeee....ee..ee..ee....eee..hhhhhhhhhhh..eee.hhhhh....hhhhhhhh.....eeeeeeee..eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------L------------P--------------------L-------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11    -----------------Exon 1.13  PDB: A:276-323 UniProt: 276-323      ------------------------------Exon 1.15  PDB: A:354-416 UniProt: 354-416                     1.16   Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.12         -----------------------------------------------Exon 1.14  PDB: A:323-354       -------------------------------------------------------------------- Transcript 1 (2)
                 2zmf A 246 QTELNDFLLDVSKTYFDNIVAIDSLLEHImIYAKNLVNADRCALFQVDHKNKELYSDLFDIGEEKEGKPVFKKTKEIRFSIEKGIAGQVARTGEVLNIPDAYADPRFNREVDLYTGYTTRNILCmPIVSRGSVIGVVQmVNKISGSAFSKTDENNFKmFAVFCALALHCANmYHRIR 422
                                   255       265       275       285       295       305       315       325       335       345       355       365    |  375       385       395       405       415 |     
                                                       275-MSE                                                                                        370-MSE       384-MSE            403-MSE       417-MSE 

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with PDE10_HUMAN | Q9Y233 from UniProtKB/Swiss-Prot  Length:779

    Alignment length:172
                                   257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417  
          PDE10_HUMAN   248 ELNDFLLDVSKTYFDNIVAIDSLLEHIMIYAKNLVNADRCALFQVDHKNKELYSDLFDIGEEKEGKPVFKKTKEIRFSIEKGIAGQVARTGEVLNIPDAYADPRFNREVDLYTGYTTRNILCMPIVSRGSVIGVVQMVNKISGSAFSKTDENNFKMFAVFCALALHCANMYH 419
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zmfB00 B:248-419  [code=3.30.450.40, no name defined]                                                                                                                       CATH domains
           Pfam domains (1) ------------------GAF-2zmfB01 B:266-412                                                                                                                              ------- Pfam domains (1)
           Pfam domains (2) ------------------GAF-2zmfB02 B:266-412                                                                                                                              ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee....eeeeeeeeeeee....eeeee....eee..hhhhhhhhhhh..eee.hhhhh....hhhhhhhh.....eeeeeeee..eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------L------------P--------------------L----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11  -----------------Exon 1.13  PDB: B:276-323 UniProt: 276-323      ------------------------------Exon 1.15  PDB: B:354-416 UniProt: 354-416                     1.1 Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.12         -----------------------------------------------Exon 1.14  PDB: B:323-354       ----------------------------------------------------------------- Transcript 1 (2)
                 2zmf B 248 ELNDFLLDVSKTYFDNIVAIDSLLEHImIYAKNLVNADRCALFQVDHKNKELYSDLFDIGEEKEGKPVFKKTKEIRFSIEKGIAGQVARTGEVLNIPDAYADPRFNREVDLYTGYTTRNILCmPIVSRGSVIGVVQmVNKISGSAFSKTDENNFKmFAVFCALALHCANmYH 419
                                   257       267       277       287       297       307       317       327       337       347       357       367  |    377      |387       397     | 407       417  
                                                     275-MSE                                                                                        370-MSE       384-MSE            403-MSE       417-MSE

   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 2ZMF)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GAF (44)
(-)
Family: GAF (30)
1aGAF-2zmfB01B:266-412
1bGAF-2zmfB02B:266-412

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PDE10_HUMAN | Q9Y233)
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:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0030553    cGMP binding    Interacting selectively and non-covalently with cGMP, the nucleotide cyclic GMP (guanosine 3',5'-cyclophosphate).
    GO:0004118    cGMP-stimulated cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate; catalytic activity is increased in the presence of cGMP.
    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:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    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: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: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:0043949    regulation of cAMP-mediated signaling    Any process which modulates the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
    GO:0010738    regulation of protein kinase A signaling    Any process that modulates the rate, frequency, or extent of protein kinase A signaling. PKA signaling is the series of reactions, mediated by the intracellular serine/threonine kinase protein kinase A, which occurs as a result of a single trigger reaction or compound.
    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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2zmf)
 

(-) 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
  2zmf
    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
  PDE10_HUMAN | Q9Y233
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.4.17
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  616922
    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
  PDE10_HUMAN | Q9Y233
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PDE10_HUMAN | Q9Y2331lrb 2oun 2oup 2ouq 2our 2ous 2ouu 2ouv 2ouy 2wey 2y0j 3sn7 3sni 3snl 3ui7 3uuo 3wi2 3ws8 3ws9 3wyk 3wyl 3wym 4ael 4ajd 4ajf 4ajg 4ajm 4bbx 4ddl 4dff 4fcb 4fcd 4heu 4hf4 4lkq 4llj 4llk 4llp 4llx 4lm0 4lm1 4lm2 4lm3 4lm4 4mrw 4mrz 4ms0 4msa 4msc 4mse 4msh 4msn 4muw 4mvh 4p0n 4p1r 4phw 4tpm 4tpp 4wn1 4xy2 4yqh 4ys7 4zo5 5axp 5axq 5b4k 5b4l 5c1w 5c28 5c29 5c2a 5c2e 5c2h 5dh4 5dh5 5ede 5edg 5edh 5edi 5i2r 5k9r 5uwf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2ZMF)