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(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND ALPHA, BETA-IMIDO-DUTP
 
Authors :  M. R. Sawaya, S. Chan, B. Segelke, T. Lekin, H. Krupka, U. -S. Cho, M. Kim, Y. Kim, C. M. Naranjo, Y. C. Rogers, M. S. Park, G. S. Waldo, I. Pashkov, D T. O. Yeates, J. L. Perry, T. C. Terwilliger, D. Eisenberg, Tb Structu Genomics Consortium (Tbsgc)
Date :  01 Mar 04  (Deposition) - 09 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Jelly-Roll, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chan, B. Segelke, T. Lekin, H. Krupka, U. S. Cho, M. -Y. Kim, M. So, C. -Y. Kim, C. M. Naranjo, Y. C. Rogers, M. S. Park, G. S. Waldo, I. Pashkov, D. Cascio, J. L. Perry, M. R. Sawaya
Crystal Structure Of The Mycobacterium Tuberculosis Dutpase Insights Into The Catalytic Mechanism.
J. Mol. Biol. V. 341 503 2004
PubMed-ID: 15276840  |  Reference-DOI: 10.1016/J.JMB.2004.06.028

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
    Chains: A
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET28B
    Expression System Strain: BL21PRO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DUT, RV2697C, MT2771, MTCY05A6.18C, MB2716C
    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  (3, 3)

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

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDUP A:170 , HOH A:301 , HOH A:302 , HOH A:303BINDING SITE FOR RESIDUE MG A 171
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 , GLY A:144 , MG A:171 , HOH A:301 , HOH A:302 , HOH A:303 , HOH A:304 , HOH A:310 , HOH A:321 , HOH A:336 , HOH A:349 , HOH A:379 , HOH A:380 , HOH A:390BINDING SITE FOR RESIDUE DUP A 170
3AC3SOFTWARESER A:74 , ILE A:75 , VAL A:76 , HOH A:307BINDING SITE FOR RESIDUE TRS A 172

(-) SS Bonds  (0, 0)

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

(-) 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 1SIX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1SIX)

(-) 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:153
 aligned with DUT_MYCTO | P9WNS4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                     1                                                                                                                                               
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141   
            DUT_MYCTO     - ---------MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGG 144
               SCOP domains d1sixa_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                                     SCOP domains
               CATH domains 1sixA00 A:-8-144  [code=2.70.40.10, no name defined]                                                                                                      CATH domains
               Pfam domains ----------------------dUTPase-1sixA01 A:14-144                                                                                                            Pfam domains
         Sec.struct. author ..............eeee.................eeee....eee....eeeee..eeee....eeeeee.hhhhhhhhheee....eeee.......eeeeee......eee....eeeeeeeee..........hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1six A  -8 SGLVPRGSHMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGG 144
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141   


Chain A from PDB  Type:PROTEIN  Length:153
 aligned with DUT_MYCTU | P9WNS5 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                     1                                                                                                                                               
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141   
            DUT_MYCTU     - ---------MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGG 144
               SCOP domains d1sixa_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                                     SCOP domains
               CATH domains 1sixA00 A:-8-144  [code=2.70.40.10, no name defined]                                                                                                      CATH domains
               Pfam domains ----------------------dUTPase-1sixA01 A:14-144                                                                                                            Pfam domains
         Sec.struct. author ..............eeee.................eeee....eee....eeeee..eeee....eeeeee.hhhhhhhhheee....eeee.......eeeeee......eee....eeeeeeeee..........hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1six A  -8 SGLVPRGSHMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGG 144
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141
   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  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: dUTPase (38)

(-) Gene Ontology  (11, 19)

Asymmetric Unit(hide GO term definitions)
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.

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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1mq7 1MQ7 IS THE SAME PROTEIN BUT UNLIGANDED RELATED ID: RV2697C RELATED DB: TARGETDB