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(-) Description

Title :  HUMAN DUTP PYROPHOSPHATASE
 
Authors :  C. D. Mol, J. M. Harris, E. M. Mcintosh, J. A. Tainer
Date :  11 Aug 03  (Deposition) - 19 Aug 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  X,Y,Z
Keywords :  Dna Repair, Enzyme-Dna Interactions, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. D. Mol, J. M. Harris, E. M. Mcintosh, J. A. Tainer
Human Dutp Pyrophosphatase: Uracil Recognition By A Beta Hairpin And Active Sites Formed By Three Separate Subunits
Structure V. 4 1077 1996
PubMed-ID: 8805593  |  Reference-DOI: 10.1016/S0969-2126(96)00114-1

(-) Compounds

Molecule 1 - DUTP PYROPHOSPHATASE
    ChainsX, Y, Z
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPEM409
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneHDUT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit XYZ

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1Q5U)

(-) Sites  (0, 0)

(no "Site" information available for 1Q5U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q5U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q5U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q5U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q5U)

(-) Exons   (7, 20)

Asymmetric/Biological Unit (7, 20)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003312001bENSE00001487133chr15:48623621-48623992372DUT_HUMAN1-94942X:-2-0
-
Z:-5--1
3
-
5
1.2bENST000003312002bENSE00001789447chr15:48624465-48624603139DUT_HUMAN94-140473X:1-29
Y:0-29
Z:0-29
29
30
30
1.3ENST000003312003ENSE00000686853chr15:48626614-4862670592DUT_HUMAN140-171323X:29-60
Y:29-60
Z:29-60
32
32
32
1.4ENST000003312004ENSE00000686856chr15:48628243-4862828745DUT_HUMAN171-186163X:60-75
Y:60-75
Z:60-75
16
16
16
1.5ENST000003312005ENSE00000686860chr15:48633486-4863356075DUT_HUMAN186-211263X:75-100
Y:75-100
Z:75-100
26
26
26
1.6ENST000003312006ENSE00000884477chr15:48633712-4863378271DUT_HUMAN211-234243X:100-123
Y:100-123
Z:100-123
24
24
24
1.7bENST000003312007bENSE00001030201chr15:48634219-486355701352DUT_HUMAN235-252183X:124-128
Y:124-126
Z:124-126
5
3
3

(-) 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 X from PDB  Type:PROTEIN  Length:131
 aligned with DUT_HUMAN | P33316 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:191
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238 
            DUT_HUMAN    49 AQHGIPRPLSSAGRLSQGCRGASTVGAAGWKGELPKAGGSPAPGPETPAISPSKRARPAEVGGMQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQALDDT 239
               SCOP domains d1q                                                            5ux_ X: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                               SCOP domains
               CATH domains 1q5                                                            uX00 X:-2-128  [code=2.70.40.10, no name defined]                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...------------------------------------------------------------.eeeeee.................eeee....eee...eeeeee..eeee....eeeeee.hhhhhhhhheeee..ee........eeeeee.....eee....eeeeeeeee.....eee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: X:-2-0 UniProt: 1-94          ---------------------------------------------Exon 1.3  PDB: X:29-60          --------------Exon 1.5  PDB: X:75-100   -----------------------1.7b  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.2b  PDB: X:1-29 UniProt: 94-140         ------------------------------Exon 1.4        ------------------------Exon 1.6  PDB: X:100-123----- Transcript 1 (2)
                 1q5u X  -2 HHH------------------------------------------------------------MQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQALDDT 128
                              |      -         -         -         -         -         -   |     7        17        27        37        47        57        67        77        87        97       107       117       127 
                              0                                                            1                                                                                                                               

Chain Y from PDB  Type:PROTEIN  Length:127
 aligned with DUT_HUMAN | P33316 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:127
                                   120       130       140       150       160       170       180       190       200       210       220       230       
            DUT_HUMAN   111 GMQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQALD 237
               SCOP domains d1q5uy_ Y: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                           SCOP domains
               CATH domains 1q5uY00 Y:0-126  [code=2.70.40.10, no name defined]                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee................eeeee....eee...eeeeee..eeee....eeeeee.hhhhhhhhheeee..ee........eeeeee.....eee....eeeeeeeee....eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -----------------------------Exon 1.3  PDB: Y:29-60          --------------Exon 1.5  PDB: Y:75-100   -----------------------1.7 Transcript 1 (1)
           Transcript 1 (2) Exon 1.2b  PDB: Y:0-29        ------------------------------Exon 1.4        ------------------------Exon 1.6  PDB: Y:100-123--- Transcript 1 (2)
                 1q5u Y   0 HMQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQALD 126
                                     9        19        29        39        49        59        69        79        89        99       109       119       

Chain Z from PDB  Type:PROTEIN  Length:132
 aligned with DUT_HUMAN | P33316 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:191
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236 
            DUT_HUMAN    47 RAAQHGIPRPLSSAGRLSQGCRGASTVGAAGWKGELPKAGGSPAPGPETPAISPSKRARPAEVGGMQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQALD 237
               SCOP domains d1q5u                                                           z_ Z: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                SCOP domains
               CATH domains 1q5uZ                                                           00 Z:-5-126  [code=2.70.40.10, no name defined]                                                                                 CATH domains
           Pfam domains (1) --------------------------------------------------------------------------dUTPase-1q5uZ01 Z:10-126                                                                                              Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------dUTPase-1q5uZ02 Z:10-126                                                                                              Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------dUTPase-1q5uZ03 Z:10-126                                                                                              Pfam domains (3)
         Sec.struct. author .....-----------------------------------------------------------...eeeee.................eeee....eee...eeeeee..eeee....eeeeee.hhhhhhhhheeee..ee........eeeeee.....eee....eeeeeeeee.....eee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: Z:-5--1 UniProt: 1-94           ---------------------------------------------Exon 1.3  PDB: Z:29-60          --------------Exon 1.5  PDB: Z:75-100   -----------------------1.7 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.2b  PDB: Z:0-29 UniProt: 94-140         ------------------------------Exon 1.4        ------------------------Exon 1.6  PDB: Z:100-123--- Transcript 1 (2)
                 1q5u Z  -5 HHHHH-----------------------------------------------------------HMQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPPMEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEKFEVKKGDRIAQLICERIFYPEIEEVQALD 126
                                |    -         -         -         -         -         -    |    5        15        25        35        45        55        65        75        85        95       105       115       125 
                               -1                                                           0                                                                                                                              

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: dUTPase (38)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X,Y,Z   (DUT_HUMAN | P33316)
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.
    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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    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:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0046134    pyrimidine nucleoside biosynthetic process    The chemical reactions and pathways resulting in the formation of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUT_HUMAN | P333161q5h 2hqu 3ara 3arn 3ehw 4mz5 4mz6

(-) Related Entries Specified in the PDB File

1q5h HUMAN DUTP PYROPHOSPHATASE COMPLEXED WITH DUDP