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(-) Description

Title :  CRYSTAL STRUCTURE OF A H121A ESCHERICHIA COLI DCTP DEAMINASE MUTANT ENZYME
 
Authors :  E. Johansson, M. Thymark, J. H. Bynck, M. Fanoe, S. Larsen, M. Willemoes
Date :  31 Aug 06  (Deposition) - 07 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Dctp Deaminase, Hydrolase, Nucleotide Metabolism, Trimer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Johansson, M. Thymark, J. H. Bynck, M. Fanoe, S. Larsen, M. Willemoes
Regulation Of Dctp Deaminase From Escherichia Coli By Nonallosteric Dttp Binding To An Inactive Form Of The Enzyme
Febs J. V. 274 4188 2007
PubMed-ID: 17651436  |  Reference-DOI: 10.1111/J.1742-4658.2007.05945.X

(-) Compounds

Molecule 1 - DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
    Chains: A, B
    EC Number: 3.5.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DCTP DEAMINASE

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2YYY2Ligand/IonDEOXYCYTIDINE DIPHOSPHATE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2YYY3Ligand/IonDEOXYCYTIDINE DIPHOSPHATE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2YYY3Ligand/IonDEOXYCYTIDINE DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:109 , ARG A:110 , SER A:111 , SER A:112 , ARG A:115 , ALA A:121 , ALA A:124 , ARG A:126 , ASP A:128 , TRP A:131 , ILE A:135 , VAL A:136 , GLU A:138 , MG A:1176BINDING SITE FOR RESIDUE YYY A1175
2AC2SOFTWAREYYY A:1175BINDING SITE FOR RESIDUE MG A1176
3AC3SOFTWAREGLY B:109 , ARG B:110 , SER B:111 , SER B:112 , ARG B:115 , ALA B:121 , ALA B:124 , ARG B:126 , ASP B:128 , TRP B:131 , ILE B:135 , VAL B:136 , GLU B:138 , MG B:1174BINDING SITE FOR RESIDUE YYY B1173
4AC4SOFTWAREYYY B:1173BINDING SITE FOR RESIDUE MG B1174
5AC5SOFTWAREALA A:121 , VAL A:122 , HIS A:125BINDING SITE FOR RESIDUE MG A1177
6AC6SOFTWARELEU B:107 , ALA B:121 , VAL B:122 , HIS B:125BINDING SITE FOR RESIDUE MG B1175

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J4H)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:20 -Pro A:21
2Ala A:121 -Val A:122
3Asn B:20 -Pro B:21
4Ala B:121 -Val B:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J4H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J4H)

(-) Exons   (0, 0)

(no "Exon" information available for 2J4H)

(-) 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:174
 aligned with DCD_ECOLI | P28248 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
            DCD_ECOLI     1 MRLCDRDIEAWLDEGRLSINPRPPVERINGATVDVRLGNKFRTFRGHTAAFIDLSGPKDEVSAALDRVMSDEIVLDEGEAFYLHPGELALAVTLESVTLPADLVGWLDGRSSLARLGLMVHVTAHRIDPGWSGCIVLEFYNSGKLPLALRPGMLIGALSFEPLSGPAVRPYNRR 174
               SCOP domains d2j4ha_ A: Deoxycytidine triphosphate deaminase (dCTP deaminase)                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eee...hhh.ee..eeeee...ee...hhhhh.......hhhhhhhhhhhhh...ee......eee....eeeeeeeeeee....eeeeeeehhhhhh..eee.....ee....eeeeeeeeee.....eee....eeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2j4h A   1 MRLCDRDIEAWLDEGRLSINPRPPVERINGATVDVRLGNKFRTFRGHTAAFIDLSGPKDEVSAALDRVMSDEIVLDEGEAFYLHPGELALAVTLESVTLPADLVGWLDGRSSLARLGLMVAVTAHRIDPGWSGCIVLEFYNSGKLPLALRPGMLIGALSFEPLSGPAVRPYNRR 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain B from PDB  Type:PROTEIN  Length:172
 aligned with DCD_ECOLI | P28248 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
            DCD_ECOLI     1 MRLCDRDIEAWLDEGRLSINPRPPVERINGATVDVRLGNKFRTFRGHTAAFIDLSGPKDEVSAALDRVMSDEIVLDEGEAFYLHPGELALAVTLESVTLPADLVGWLDGRSSLARLGLMVHVTAHRIDPGWSGCIVLEFYNSGKLPLALRPGMLIGALSFEPLSGPAVRPYN 172
               SCOP domains d2j4hb_ B: Deoxycytidine triphosphate deaminase (dCTP deaminase)                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eee...hhh.ee..eeeee...ee...hhhhh.......hhhhhhhhhhhhh...ee......eee....eeeeeeeeeee....eeeeeeehhhhhh..eee.....ee....eeeeeeeeee.....eee....eeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4h B   1 MRLCDRDIEAWLDEGRLSINPRPPVERINGATVDVRLGNKFRTFRGHTAAFIDLSGPKDEVSAALDRVMSDEIVLDEGEAFYLHPGELALAVTLESVTLPADLVGWLDGRSSLARLGLMVAVTAHRIDPGWSGCIVLEFYNSGKLPLALRPGMLIGALSFEPLSGPAVRPYN 172
                                    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  (0, 0)

(no "CATH Domain" information available for 2J4H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J4H)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DCD_ECOLI | P28248)
molecular function
    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:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCD_ECOLI | P28248: 1xs1 1xs4 1xs6 2j4q 2v9x

(-) Related Entries Specified in the PDB File

1xs1 DCTP DEAMINASE FROM ESCHERICHIA COLI IN COMPLEX WITH DUTP
1xs4 DCTP DEAMINASE FROM ESCHERICHIA COLI- E138A MUTANT ENZYMEIN COMPLEX WITH DCTP
1xs6 DCTP DEAMINASE FROM ESCHERICHIA COLI. E138A MUTANT ENZYMEIN COMPLEX WITH DUTP
2j4q CRYSTAL STRUCTURE OF A E138A ESCHERICHIA COLI DCTP DEAMINASE MUTANT ENZYME IN COMPLEX WITH DTTP