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(-) Description

Title :  STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DUTPASE H145A MUTANT
 
Authors :  I. Leveles, V. Harmat, I. Pecsi, A. Lopata, B. G. Vertessy, J. Toth
Date :  04 Feb 10  (Deposition) - 11 Aug 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Hydrolase, Jelly Roll, Domain Swapping, Nucleotide Metabolism, Magnesium, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Pecsi, I. Leveles, V. Harmat, B. G. Vertessy, J. Toth
Aromatic Stacking Between Nucleobase And Enzyme Promotes Phosphate Ester Hydrolysis In Dutpase
Nucleic Acids Res. V. 38 7179 2010
PubMed-ID: 20601405  |  Reference-DOI: 10.1093/NAR/GKQ584

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
    Chains: A
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DUT, MT2771, MTCY05A6.18C, RV2697C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: DUTPASE, DUTP PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1DUP1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4MN1Ligand/IonMANGANESE (II) ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1DUP3Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2GOL6Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4MN-1Ligand/IonMANGANESE (II) ION
5TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:64 , SER A:65 , GLY A:66 , ASN A:77 , GLY A:80 , THR A:81 , ILE A:82 , ASP A:83 , TYR A:86 , GLU A:89 , ILE A:90 , LYS A:91 , GLN A:113 , ARG A:140 , GLY A:144 , ALA A:145 , GLY A:146 , SER A:147 , SER A:148 , MG A:155 , MN A:156 , HOH A:207 , HOH A:212 , HOH A:220 , HOH A:227 , HOH A:238 , HOH A:239 , HOH A:245BINDING SITE FOR RESIDUE DUP A 201
2AC2SOFTWARESER A:129 , PHE A:130 , ASP A:131 , HOH A:290BINDING SITE FOR RESIDUE GOL A 202
3AC3SOFTWARETYR A:30 , ARG A:110 , HOH A:183 , HOH A:232 , HOH A:288BINDING SITE FOR RESIDUE GOL A 203
4AC4SOFTWARESER A:74 , ILE A:75 , VAL A:76 , HOH A:215BINDING SITE FOR RESIDUE TRS A 204
5AC5SOFTWAREDUP A:201 , HOH A:212 , HOH A:239 , HOH A:245BINDING SITE FOR RESIDUE MG A 155
6AC6SOFTWAREDUP A:201 , HOH A:212 , HOH A:239 , HOH A:245BINDING SITE FOR RESIDUE MN A 156

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LOJ)

(-) 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:160
 aligned with DUT_MYCTO | P9WNS4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:160
                                  1                                                                                                                                                         
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154
            DUT_MYCTO     - ------MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGHGSSGGHASL 154
               SCOP domains d3loja_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------dUTPase-3lojA01 A:14-149                                                                                                                ----- Pfam domains
         Sec.struct. author ...........eeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eeee.....eeeeeeee......eee....eeeeeeeee.................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3loj A  -7 GLVPSHMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGAGSSGGHASL 154
                               ||    4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154
                              -4|                                                                                                                                                           
                               -1                                                                                                                                                           


Chain A from PDB  Type:PROTEIN  Length:160
 aligned with DUT_MYCTU | P9WNS5 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:160
                                  1                                                                                                                                                         
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154
            DUT_MYCTU     - ------MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGHGSSGGHASL 154
               SCOP domains d3loja_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------dUTPase-3lojA01 A:14-149                                                                                                                ----- Pfam domains
         Sec.struct. author ...........eeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eeee.....eeeeeeee......eee....eeeeeeeee.................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3loj A  -7 GLVPSHMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGAGSSGGHASL 154
                               ||    4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154
                              -4|                                                                                                                                                           
                               -1
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LOJ)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: dUTPase (38)

(-) Gene Ontology  (11, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (DUT_MYCTO | P9WNS4)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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).
    GO:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

Chain A   (DUT_MYCTU | P9WNS5)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    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:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DUT_MYCTO | P9WNS4: 1mq7 1six 1sjn 1slh 1sm8 1smc 1snf 2py4 3h6d 3hza 3i93 4gcy
        DUT_MYCTU | P9WNS5: 1mq7 1six 1sjn 1slh 1sm8 1smc 1snf 2py4 3h6d 3hza 3i93 4gcy 5ect 5edd

(-) Related Entries Specified in the PDB File

3hza MUTATION AT THE SAME AMINOACID POSITION