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(-) Description

Title :  EVOLUTION OF CHLORELLA VIRUS DUTPASE
 
Authors :  M. Yamanishi, K. Homma, Y. Zhang, L. V. J. Etten, H. Moriyama
Date :  19 Feb 08  (Deposition) - 03 Mar 09  (Release) - 17 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Dutpase Chlorella Virus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Homma, H. Moriyama
Crystallization And Crystal-Packing Studies Of Chlorella Virus Deoxyuridine Triphosphatase.
Acta Crystallogr. , Sect. F V. 65 1030 2009
PubMed-ID: 19851015  |  Reference-DOI: 10.1107/S1744309109034459
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEOXYURIDINE TRIPHOSPHATASE
    Chains: A, B
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-23A
    Expression System Strain: BL21-DE3-PLYS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: PBCV-IL3A
    Organism Scientific: PARAMECIUM BURSARIA CHLORELLA VIRUS IL3A
    Organism Taxid: 46019

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1DUD2Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1DUD3Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1DUD3Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:73BINDING SITE FOR RESIDUE MG A 998
2AC2SOFTWAREARG A:63 , SER A:64 , GLY A:65 , ALA A:76 , GLY A:77 , ILE A:79 , ASP A:80 , TYR A:83 , GLU A:86 , LYS A:88BINDING SITE FOR RESIDUE DUD A 777
3AC3SOFTWAREARG B:63 , SER B:64 , GLY B:65 , ALA B:76 , GLY B:77 , ILE B:79 , ASP B:80 , TYR B:83 , LYS B:88BINDING SITE FOR RESIDUE DUD B 778

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CA9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CA9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CA9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CA9)

(-) Exons   (0, 0)

(no "Exon" information available for 3CA9)

(-) Sequences/Alignments

Asymmetric 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:128
 aligned with Q5I3E5_PBCVI | Q5I3E5 from UniProtKB/TrEMBL  Length:141

    Alignment length:128
                               1                                                                                                                            
                               |     7        17        27        37        47        57        67        77        87        97       107       117        
         Q5I3E5_PBCVI     - ---MSSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDEDYTGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLD 125
               SCOP domains d3ca9a_ A: automated matches                                                                                                     SCOP domains
               CATH domains 3ca9A00 A:-2-125  [code=2.70.40.10, no name defined]                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.................eeee....eee....eeeee..eeee....eeeeee.hhhhhhhhheee...ee........eeeeee.....eee....eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ca9 A  -2 SEFMSSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDEDYTGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLD 125
                                     7        17        27        37        47        57        67        77        87        97       107       117        


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with Q5I3E5_PBCVI | Q5I3E5 from UniProtKB/TrEMBL  Length:141

    Alignment length:126
                             1                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119      
         Q5I3E5_PBCVI     - -MSSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDEDYTGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLD 125
               SCOP domains d3ca9b_ B: automated matches                                                                                                   SCOP domains
               CATH domains 3ca9B00 B:0-125  [code=2.70.40.10, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.................eeee....eee....eeeee..eeee....eeeeee.hhhhhhhhheee...ee........eeeeee.....eee....eeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ca9 B   0 FMSSLLVKKLVESATTPMRGSEGAAGYDISSVEDVVVPAMGRIAVSTGISIRVPDGTYGRIAPRSGLAYKYGIDVLAGVIDEDYTGEVKVILYNTTERDYIIKKGDRIAQLILEQIVTPGVAVVLD 125
                                     9        19        29        39        49        59        69        79        89        99       109       119
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CA9)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5I3E5_PBCVI | Q5I3E5)
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.
biological process
    GO:0046080    dUTP metabolic process    The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.

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  3.6.1.23
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 Related Entries

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

UniProtKB/TrEMBL
        Q5I3E5_PBCVI | Q5I3E5: 3c2t 3c3i

(-) Related Entries Specified in the PDB File

3c2t WILD TYPE WITHOUT TAG
3c3i MU-22 MUTANT WITHOUT TAG