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(-) Description

Title :  STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS DUTPASE D28N MUTANT
 
Authors :  I. Leveles, V. Harmat, G. Nagy, E. Takacs, A. Lopata, J. Toth, B. G. Verte
Date :  23 Apr 09  (Deposition) - 24 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  A  (1x)
Keywords :  Jelly-Roll, Hydrolase, Nucleotide Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Takacs, G. Nagy, I. Leveles, V. Harmat, A. Lopata, J. Toth, B. G. Vertessy
Direct Contacts Between Conserved Motifs Of Different Subunits Provide Major Contribution To Active Site Organization In Human And Mycobacterial Dutpases.
Febs Lett. V. 584 3047 2010
PubMed-ID: 20493855  |  Reference-DOI: 10.1016/J.FEBSLET.2010.05.018

(-) 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
Biological Unit 2 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1DUP1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1DUP3Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3TRS6Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1DUP1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDUP A:201BINDING SITE FOR RESIDUE MG A 200
2AC2SOFTWAREARG 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 , HOH A:188 , MG A:200 , HOH A:212 , HOH A:219 , HOH A:222 , HOH A:245BINDING SITE FOR RESIDUE DUP A 201
3AC3SOFTWARESER A:74 , ILE A:75 , VAL A:76 , LEU A:97 , HOH A:194BINDING SITE FOR RESIDUE TRS A 202
4AC4SOFTWAREARG A:9 , PRO A:12 , HOH A:208BINDING SITE FOR RESIDUE TRS A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H6D)

(-) 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 3H6D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H6D)

(-) Exons   (0, 0)

(no "Exon" information available for 3H6D)

(-) 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:145
 aligned with DUT_MYCTO | P9WNS4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:151
                                       1                                                                                                                                           
                                     - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139 
            DUT_MYCTO     - -----------MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSR 140
               SCOP domains d3h6da1 A:-10-133 automated matches                                                                                                             ------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.....eeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eeee.....eeeeeeee......eee....eeeeeeeee...............------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h6d A -10 HSSGLVPRGSHMSTTLAIVRLDPGLPLPSRAHDGDAGVNLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEA------R 140
                                    -1         9        19        29        39        49        59        69        79        89        99       109       119       129   |     -|
                                                                                                                                                                         133    140


Chain A from PDB  Type:PROTEIN  Length:145
 aligned with DUT_MYCTU | P9WNS5 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:151
                                       1                                                                                                                                           
                                     - |       9        19        29        39        49        59        69        79        89        99       109       119       129       139 
            DUT_MYCTU     - -----------MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSR 140
               SCOP domains d3h6da1 A:-10-133 automated matches                                                                                                             ------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.....eeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eeee.....eeeeeeee......eee....eeeeeeeee...............------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h6d A -10 HSSGLVPRGSHMSTTLAIVRLDPGLPLPSRAHDGDAGVNLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEA------R 140
                                    -1         9        19        29        39        49        59        69        79        89        99       109       119       129   |     -|
                                                                                                                                                                         133    140
   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 3H6D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H6D)

(-) 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 3hza 3i93 3loj 4gcy
        DUT_MYCTU | P9WNS5: 1mq7 1six 1sjn 1slh 1sm8 1smc 1snf 2py4 3hza 3i93 3loj 4gcy 5ect 5edd

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