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(-) Description

Title :  NATIVE CRYSTAL STRUCTURE ANALYSIS ON ARABIDOPSIS DUTPASE
 
Authors :  H. Moriyama, M. Bajaj
Date :  29 Mar 07  (Deposition) - 12 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dutpase, Arabidopsis, Magnesium, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bajaj, H. Moriyama
Purification, Crystallization And Preliminary Crystallographic Analysis Of Deoxyuridine Triphosphate Nucleotidohydrolase From Arabidopsis Thaliana.
Acta Crystallogr. , Sect. F V. 63 409 2007
PubMed-ID: 17565183  |  Reference-DOI: 10.1107/S1744309107016004

(-) Compounds

Molecule 1 - DUTP PYROPHOSPHATASE-LIKE PROTEIN
    Chains: A, B, C
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: T6H20.30
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:138 , GLU B:138 , GLU C:138BINDING SITE FOR RESIDUE MG A 167

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PC5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro B:25 -Ser B:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PC5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PC5)

(-) Exons   (0, 0)

(no "Exon" information available for 2PC5)

(-) 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:127
 aligned with DUT_ARATH | Q9STG6 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:127
                                    35        45        55        65        75        85        95       105       115       125       135       145       
            DUT_ARATH    26 SPFFKVKKLSEKAVIPTRGSPLSAGYDLSSAVDSKVPARGKALIPTDLSIAVPEGTYARIAPRSGLAWKHSIDVGAGVIDADYRGPVGVILFNHSDADFEVKFGDRIAQLIIEKIVTPDVVEVDDLD 152
               SCOP domains d2pc5a_ A: automated matches                                                                                                    SCOP domains
               CATH domains 2pc5A00 A:26-152  [code=2.70.40.10, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.................eeee....eee....eeee...eeee....eeeeee.hhhhhhhhheeee..eee........eeeee.....eee....eeeeeeeeeee...eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pc5 A  26 SPFFKVKKLSEKAVIPTRGSPLSAGYDLSSAVDSKVPARGKALIPTDLSIAVPEGTYARIAPRSGLAWKHSIDVGAGVIDADYRGPVGVILFNHSDADFEVKFGDRIAQLIIEKIVTPDVVEVDDLD 152
                                    35        45        55        65        75        85        95       105       115       125       135       145       


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with DUT_ARATH | Q9STG6 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:126
                                    34        44        54        64        74        84        94       104       114       124       134       144      
            DUT_ARATH    25 PSPFFKVKKLSEKAVIPTRGSPLSAGYDLSSAVDSKVPARGKALIPTDLSIAVPEGTYARIAPRSGLAWKHSIDVGAGVIDADYRGPVGVILFNHSDADFEVKFGDRIAQLIIEKIVTPDVVEVDD 150
               SCOP domains d2pc5b_ B: automated matches                                                                                                   SCOP domains
               CATH domains 2pc5B00 B:25-150  [code=2.70.40.10, no name defined]                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee................eeeee....eee....eeeee..eeee....eeeeee.hhhhhhhhheee...eee.......eeeeee.....eee....eeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pc5 B  25 PSPFFKVKKLSEKAVIPTRGSPLSAGYDLSSAVDSKVPARGKALIPTDLSIAVPEGTYARIAPRSGLAWKHSIDVGAGVIDADYRGPVGVILFNHSDADFEVKFGDRIAQLIIEKIVTPDVVEVDD 150
                                    34        44        54        64        74        84        94       104       114       124       134       144      


Chain C from PDB  Type:PROTEIN  Length:127
 aligned with DUT_ARATH | Q9STG6 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:127
                                    35        45        55        65        75        85        95       105       115       125       135       145       
            DUT_ARATH    26 SPFFKVKKLSEKAVIPTRGSPLSAGYDLSSAVDSKVPARGKALIPTDLSIAVPEGTYARIAPRSGLAWKHSIDVGAGVIDADYRGPVGVILFNHSDADFEVKFGDRIAQLIIEKIVTPDVVEVDDLD 152
               SCOP domains d2pc5c_ C: automated matches                                                                                                    SCOP domains
               CATH domains 2pc5C00 C:26-152  [code=2.70.40.10, no name defined]                                                                            CATH domains
           Pfam domains (1) ----------dUTPase-2pc5C01 C:36-152                                                                                              Pfam domains (1)
           Pfam domains (2) ----------dUTPase-2pc5C02 C:36-152                                                                                              Pfam domains (2)
           Pfam domains (3) ----------dUTPase-2pc5C03 C:36-152                                                                                              Pfam domains (3)
         Sec.struct. author ....eeee........ee.......eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheeee..ee......eeeeeeee.....eee....eeeeeeeeeee...eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pc5 C  26 SPFFKVKKLSEKAVIPTRGSPLSAGYDLSSAVDSKVPARGKALIPTDLSIAVPEGTYARIAPRSGLAWKHSIDVGAGVIDADYRGPVGVILFNHSDADFEVKFGDRIAQLIIEKIVTPDVVEVDDLD 152
                                    35        45        55        65        75        85        95       105       115       125       135       145
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (DUT_ARATH | Q9STG6)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    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: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).
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUT_ARATH | Q9STG6: 4oop 4ooq

(-) Related Entries Specified in the PDB File

2p9o