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(-) Description

Title :  STRUCTURAL BASIS FOR RECOGNITION AND CATALYSIS BY THE BIFUNCTIONAL DCTP DEAMINASE AND DUTPASE FROM METHANOCOCCUS JANNASCHII
 
Authors :  J. L. Huffman, H. Li, R. H. White, J. A. Tainer
Date :  05 Jun 03  (Deposition) - 23 Sep 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (3x),B (3x)
Biol. Unit 2:  A  (3x)
Keywords :  Dctp Deaminase, Dutpase, Dcd-Dut, Mj0430, Dctp, Dutp, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Huffman, H. Li, R. H. White, J. A. Tainer
Structural Basis For Recognition And Catalysis By The Bifunctional Dctp Deaminase And Dutpase From Methanococcus Jannaschii
J. Mol. Biol. V. 331 885 2003
PubMed-ID: 12909016  |  Reference-DOI: 10.1016/S0022-2836(03)00789-7

(-) Compounds

Molecule 1 - BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE
    Chains: A, B
    EC Number: 3.5.4.13, 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: BL21 (DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MJ0430
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: MJDCD-DUT, DCD/DUT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A (3x)B (3x)
Biological Unit 2 (3x): A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2EDO7Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 15)
No.NameCountTypeFull Name
1DCP3Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2EDO12Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1DCP-1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2EDO9Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:117 , SER B:118 , SER B:119 , ARG B:122 , HIS B:128 , PHE B:138 , THR B:143 , GLU B:145 , HOH B:455 , HOH B:557BINDING SITE FOR RESIDUE DCP B 293
2AC2SOFTWAREASP A:25 , VAL A:27 , GLY A:28 , ASP A:33 , ARG A:160 , ASN B:87 , HOH B:571BINDING SITE FOR RESIDUE EDO A 294
3AC3SOFTWAREGLU B:39 , LEU B:97 , GLY B:98 , THR B:99 , HOH B:344 , HOH B:442BINDING SITE FOR RESIDUE EDO B 295
4AC4SOFTWAREASP A:174 , TYR A:177 , SER A:178 , HOH A:508 , LYS B:60 , ILE B:61 , LYS B:62BINDING SITE FOR RESIDUE EDO A 296
5AC5SOFTWAREARG B:16 , GLU B:105 , LEU B:106 , HOH B:376 , HOH B:524BINDING SITE FOR RESIDUE EDO B 297
6AC6SOFTWAREASN A:23 , HOH A:471BINDING SITE FOR RESIDUE EDO A 298
7AC7SOFTWAREASP B:38 , ASN B:101 , ASN B:158BINDING SITE FOR RESIDUE EDO B 299
8AC8SOFTWARETHR B:35 , HOH B:515BINDING SITE FOR RESIDUE EDO B 300

(-) SS Bonds  (0, 0)

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

(-) 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 1PKK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PKK)

(-) 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:182
 aligned with DCD_METJA | Q57872 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
            DCD_METJA     1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERKT 182
               SCOP domains d1pkka_ A: Bifunctional dCTP deaminase/dUTPase                                                                                                                                         SCOP domains
               CATH domains 1pkkA00 A:1-182  [code=2.70.40.10, no name defined]                                                                                                                                    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........eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pkk A   1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERKT 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with DCD_METJA | Q57872 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       
            DCD_METJA     1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADVGY 177
               SCOP domains d1pkkb_ B: Bifunctional dCTP deaminase/dUTPase                                                                                                                                    SCOP domains
               CATH domains 1pkkB00 B:1-177  [code=2.70.40.10, no name defined]                                                                                                                               CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------dUTPase-1pkkB01 B:85-177                                                                      Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------dUTPase-1pkkB02 B:85-177                                                                      Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhh...eee..hhh.ee..eeeee...eeeee............eeeeee..eeeee......hhhhhhhhhhhhh..eeee..eeeeeeeeee....eeeeeeehhhhhh..ee......ee....eeeeeeeeee....eeee...eeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pkk B   1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLEIVAFDKPVILYKNQRIGQLIFSKLLSPADVGY 177
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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

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

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

(-) Related Entries Specified in the PDB File

1pkh CRYSTAL STRUCTURE OF BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE
1pkj CRYSTAL STRUCTURE OF BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE COMPLEXED WITH DEOXYURIDINE-5'-TRIPHOSPHATE