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

(-) Description

Title :  CRYSTAL STRUCTURAL ANALYSIS OF DROSOPHILA MELANOGASTER DUTPASE
 
Authors :  E. Takacs, O. Barabas, B. G. Vertessy
Date :  02 Sep 08  (Deposition) - 07 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Jelly-Roll, Dimeric Assembly, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Takacs, O. Barabas, M. V. Petoukhov, D. I. Svergun, B. G. Vertessy
Molecular Shape And Prominent Role Of Beta-Strand Swapping In Organization Of Dutpase Oligomers.
Febs Lett. V. 583 865 2009
PubMed-ID: 19302784  |  Reference-DOI: 10.1016/J.FEBSLET.2009.02.011

(-) Compounds

Molecule 1 - CG4584-PA, ISOFORM A (BCDNA.LD08534)
    Chains: A, B
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DUTPASE, BCDNA.LD08534, CG4584, DMEL_CG4584
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3ECY)

(-) Sites  (0, 0)

(no "Site" information available for 3ECY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ECY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:93 -Ala A:94
2Gly B:93 -Ala B:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ECY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ECY)

(-) Exons   (0, 0)

(no "Exon" information available for 3ECY)

(-) 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:119
 aligned with Q9V3I1_DROME | Q9V3I1 from UniProtKB/TrEMBL  Length:188

    Alignment length:126
                                    28        38        48        58        68        78        88        98       108       118       128       138      
         Q9V3I1_DROME    19 TCVLRFAKLTENALEPVRGSAKAAGVDLRSAYDVVVPARGKAIVKTDLQVQVPEGSYGRVAPRSGLAVKNFIDVGAGVVDEDYRGNLGVVLFNHSDVDFEVKHGDRIAQFICERIFYPQLVMVDKL 144
               SCOP domains d3ecya_ A: automated matches                                                                                                   SCOP domains
               CATH domains 3ecyA00 A:19-144  [code=2.70.40.10, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.................eeee....eee....eeeee..eeee.....eeeee..-------.eeee.eee........eeeeee.....eee....eeeeeeeeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ecy A  19 TCVLRFAKLTENALEPVRGSAKAAGVDLRSAYDVVVPARGKAIVKTDLQVQVPEGSYGRVAPR-------FIDVGAGVVDEDYRGNLGVVLFNHSDVDFEVKHGDRIAQFICERIFYPQLVMVDKL 144
                                    28        38        48        58        68        78  |      -|       98       108       118       128       138      
                                                                                         81      89                                                       


Chain B from PDB  Type:PROTEIN  Length:119
 aligned with Q9V3I1_DROME | Q9V3I1 from UniProtKB/TrEMBL  Length:188

    Alignment length:126
                                    28        38        48        58        68        78        88        98       108       118       128       138      
         Q9V3I1_DROME    19 TCVLRFAKLTENALEPVRGSAKAAGVDLRSAYDVVVPARGKAIVKTDLQVQVPEGSYGRVAPRSGLAVKNFIDVGAGVVDEDYRGNLGVVLFNHSDVDFEVKHGDRIAQFICERIFYPQLVMVDKL 144
               SCOP domains d3ecyb_ B: automated matches                                                                                                   SCOP domains
               CATH domains 3ecyB00 B:19-144  [code=2.70.40.10, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.................eeee....eee....eeeee..eeee.....eeeee..-------.eeee.eeee.......eeeeee.....eee....eeeeeeeeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ecy B  19 TCVLRFAKLTENALEPVRGSAKAAGVDLRSAYDVVVPARGKAIVKTDLQVQVPEGSYGRVAPR-------FIDVGAGVVDEDYRGNLGVVLFNHSDVDFEVKHGDRIAQFICERIFYPQLVMVDKL 144
                                    28        38        48        58        68        78  |      -|       98       108       118       128       138      
                                                                                         81      89
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ECY)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9V3I1_DROME | Q9V3I1)
molecular function
    GO:0004170    dUTP diphosphatase activity    Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
biological process
    GO:0006226    dUMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
    GO:0046081    dUTP catabolic process    The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate.
    GO:0046080    dUTP metabolic process    The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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
(no "Ligands, Modified Residues, Ions" information available for 3ecy)
 
  Sites
(no "Sites" information available for 3ecy)
 
  Cis Peptide Bonds
    Gly A:93 - Ala A:94   [ RasMol ]  
    Gly B:93 - Ala B:94   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3ecy
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9V3I1_DROME | Q9V3I1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.6.1.23
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9V3I1_DROME | Q9V3I1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3ECY)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3ECY)