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(-) Description

Title :  BIFUNCTIONAL DCTP DEAMINASE-DUTPASE MUTANT ENZYME VARIANT E145A FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH ALPHA,BETA-IMIDO DUTP AND MAGNESIUM
 
Authors :  J. H. Bynck, E. Johansson
Date :  03 Aug 06  (Deposition) - 14 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  A  (6x)
Biol. Unit 3:  A  (24x)
Keywords :  Beta Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Bynck, M. Willemoes, S. Larsen, E. Johansson
Structural Evidence For A Concerted Bifunctionality In Dctp Deaminase-Dutpase From Methanocaldococcus Jannaschii
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DCTP DEAMINASE, DUMP-FORMING
    Chains: A
    EC Number: 3.5.4.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DCD
    Mutation: YES
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE, MJDCD-DUT, DCD/DUT

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A
Biological Unit 2 (6x): A
Biological Unit 3 (24x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1DUP1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1DUP3Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1DUP6Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 24)
No.NameCountTypeFull Name
1DUP24Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDUP A:206 , HOH A:260 , HOH A:306BINDING SITE FOR RESIDUE MG A 205
2AC2SOFTWAREARG A:117 , SER A:118 , SER A:119 , ARG A:122 , ALA A:131 , GLY A:132 , TRP A:133 , ASP A:135 , PHE A:138 , ILE A:142 , THR A:143 , GLN A:163 , TYR A:177 , LYS A:184 , TYR A:185 , GLN A:188 , MG A:205 , HOH A:218 , HOH A:219 , HOH A:239 , HOH A:265 , HOH A:274 , HOH A:292 , HOH A:306BINDING SITE FOR RESIDUE DUP A 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HXD)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HXD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HXD)

(-) Exons   (0, 0)

(no "Exon" information available for 2HXD)

(-) 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:199
 aligned with DCD_METJA | Q57872 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
            DCD_METJA     1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERKTSKYAYQKSVMPSLIHLD 199
               SCOP domains d2hxda_ A: Bifunctional dCTP deaminase/dUTPase                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eee..hhhhh....eeee...eeeee............eeeee...eeeee......hhhhhhhhhhhhh..eeee..eeeeeeeeee....eeeeeeehhhhhh..ee......ee....eeeeeeeeee....eeee...eeeeeeeee.......hhhhh..............hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hxd A   1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLAIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERKTSKYAYQKSVMPSLIHLD 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   Legend:   → Mismatch (orange background)
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  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 2HXD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HXD)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  2hxd
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  DCD_METJA | Q57872
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCD_METJA | Q57872: 1ogh 1pkh 1pkj 1pkk 2hxb 3gf0

(-) Related Entries Specified in the PDB File

2hxb SAME PROTEIN AND SPACE GROUP, WILDTYPE WITH NOTHING BOUND.
2hxe MUTANT ENZYME VARIANT E145Q DCD-DUT IN COMPLEX WITH PYROPHOSPHATE AND MAGNESIUM.