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(-) Description

Title :  STRUCTURE OF THE BIFUNCTIONAL DCTP DEAMINASE-DUTPASE FROM METHANOCALDOCOCCUS JANNASCHII
 
Authors :  E. Johansson, O. Bjornberg, P. O. Nyman, S. Larsen
Date :  02 May 03  (Deposition) - 05 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Bifunctional Enzyme, Nucleotide Metabolism, Dctp Deaminase, Dutpase, Homotrimer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Johansson, O. Bjornberg, P. O. Nyman, S. Larsen
Structure Of The Bifunctional Dctp Deaminase-Dutpase From Methanocaldococcus Jannaschii And Its Relation To Other Homotrimeric Dutpases
J. Biol. Chem. V. 278 27916 2003
PubMed-ID: 12756253  |  Reference-DOI: 10.1074/JBC.M304361200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE
    Atcc: 43067
    Chains: A, B
    EC Number: 3.5.4.13, 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A/MJ0430
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: MJDCD-DUT, DCD/DUT, (INCLUDES: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE, (DCTP DEAMINASE), DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE, (DUTPASE, DUTP PYROPHOSPHATASE))

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1OGH)

(-) Sites  (0, 0)

(no "Site" information available for 1OGH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:20 -Pro A:21
2Lys B:20 -Pro B:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OGH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OGH)

(-) 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:175
 aligned with DCD_METJA | Q57872 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
            DCD_METJA     1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADV 175
               SCOP domains d1ogha_ A: Bifunctional dCTP deaminase/dUTPase                                                                                                                                  SCOP domains
               CATH domains 1oghA00 A:1-175  [code=2.70.40.10, no name defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eee..hhhh.....eeee...eeeee............eeeee...eeeee......hhhhhhhhhhhhh..eeee..eeeeeeeeee....eeeeeeehhhhhh..ee......ee....eeeeeeeeee....eeee...eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogh A   1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADV 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     


Chain B from PDB  Type:PROTEIN  Length:181
 aligned with DCD_METJA | Q57872 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
            DCD_METJA     1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERK 181
               SCOP domains d1oghb_ B: Bifunctional dCTP deaminase/dUTPase                                                                                                                                        SCOP domains
               CATH domains 1oghB00 B:1-181  [code=2.70.40.10, no name defined]                                                                                                                                   CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------dUTPase-1oghB01 B:85-181                                                                          Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------dUTPase-1oghB02 B:85-181                                                                          Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhh...eee..hhhh.....eeee...eeeee............eeeee...eeeee......hhhhhhhhhhhhh..eeee..eeeeeeeeee....eeeeeeehhhhhh..ee......ee....eeeeeeeeee....eeee...eeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogh B   1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERK 181
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: dUTPase (38)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DCD_METJA | Q57872)
molecular function
    GO:0033973    dCTP deaminase (dUMP-forming) activity    Catalysis of the reaction: dCTP + 2 H(2)O = diphosphate + dUMP + H(+) + NH(4)(+).
    GO:0008829    dCTP deaminase activity    Catalysis of the reaction: dCTP + H2O = dUTP + NH3.
    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:0006226    dUMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
    GO:0006229    dUTP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUTP, deoxyuridine (5'-)triphosphate.
    GO:0046080    dUTP metabolic process    The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    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:0009220    pyrimidine ribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a 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

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        DCD_METJA | Q57872: 1pkh 1pkj 1pkk 2hxb 2hxd 3gf0

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