Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  BIFUNCTIONAL DCTP DEAMINASE-DUTPASE MUTANT ENZYME VARIANT E145Q FROM METHANOCALDOCOCCUS JANNASCHII IN COMPLEX WITH PYROPHOSPHATE AND MAGNESIUM
 
Authors :  J. H. B. Siggaard, E. Johansson, T. Vognsen, S. S. Helt, P. Harris, M. Willemoes
Date :  26 Feb 09  (Deposition) - 10 Mar 09  (Release) - 10 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Dctp Deaminase-Dutpase, Bifunctional Hydrolase, Magnesium, Nucleotide Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. B. Siggaard, E. Johansson, T. Vognsen, S. S. Helt, P. Harris, S. Larsen, M. Willemoes
Pre-Steady State Kinetic And Structural Evidence For A Concerted Biofunctionality In Dctp Deaminase-Dutpase From Methanocaldococcus Jannaschii
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DCTP DEAMINASE, DUMP-FORMING
    Chains: A
    EC Number: 3.5.4.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2POP1Ligand/IonPYROPHOSPHATE 2-
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2POP3Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPOP A:277BINDING SITE FOR RESIDUE MG A 205
2AC2SOFTWAREGLU A:93 , GLY A:95 , ASP A:150BINDING SITE FOR RESIDUE MG A 206
3AC3SOFTWAREHIS A:128 , THR A:130BINDING SITE FOR RESIDUE MG A 207
4AC4SOFTWAREGLN A:115 , GLY A:116 , HIS A:128 , THR A:130 , ALA A:131 , HOH A:348BINDING SITE FOR RESIDUE MG A 276
5AC5SOFTWAREARG A:117 , SER A:118 , SER A:119 , TYR A:177 , SER A:183 , LYS A:184 , TYR A:185 , MG A:205 , HOH A:307BINDING SITE FOR RESIDUE POP A 277

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GF0)

(-) 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 3GF0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GF0)

(-) Exons   (0, 0)

(no "Exon" information available for 3GF0)

(-) 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 d3gf0a_ A: automated matches                                                                                                                                                                            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
                 3gf0 A   1 MILSDKDIIDYVTSKRIIIKPFNKDFVGPCSYDVTLGDEFIIYDDEVYDLSKELNYKRIKIKNSILVCPLNYNLTEEKINYFKEKYNVDYVVEGGVLGTTNEYIELPNDISAQYQGRSSLGRVFLTSHQTAGWIDAGFKGKITLQIVAFDKPVILYKNQRIGQLIFSKLLSPADVGYSERKTSKYAYQKSVMPSLIHLD 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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  (0, 0)

(no "CATH Domain" information available for 3GF0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GF0)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    POP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:20 - Pro A:21   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3gf0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DCD_METJA | Q57872
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.4.30
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DCD_METJA | Q57872
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1ogh SAME PROTEIN IN DIFFERENT SPACE GROUP WITH NOTHING BOUND
2hxb SAME PROTEIN AND SPACE GROUP, WILDTYPE WITH NOTHING BOUND
2hxd MUTANT ENZYME VARIANT E145A DCD-DUT IN COMPLEX WITH ALPHA,BETA- IMIDO DUTP AND MAGNESIUM