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

(-) Description

Title :  CRYSTAL STRUCTURE OF DEOXYURIDINE 5-TRIPHOSPHATE NUCLEOTIDOHYDROLASE FROM BRUCELLA MELITENSIS, ORTHORHOMBIC CRYSTAL FORM
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  25 Mar 10  (Deposition) - 21 Apr 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Als Collaborative Crystallography, Deoxyuridine 5-Triphosphate Nucleotidohydrolase, Hydrolase, Metal-Binding, Nucleotide Metabolism, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Abendroth, T. Sankaran, A. Gardberg, B. Staker
Crystal Structure Of Deoxyuridine 5-Triphosphate Nucleotidohydrolase From Brucella Melitensis, Orthorhombic Crystal Form
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
    Chains: A, B, C
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DUT, BAB1_1687
    Organism Scientific: BRUCELLA MELITENSIS
    Organism Taxid: 359391
    Strain: 2308
    Synonym: DUTPASE, DUTP PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:54 , GLY B:110 , ASP B:111 , ASP B:112 , HOH B:158BINDING SITE FOR RESIDUE SO4 B 201
02AC2SOFTWAREARG A:38 , ARG A:121 , HOH A:158BINDING SITE FOR RESIDUE SO4 A 203
03AC3SOFTWAREARG B:54 , HOH B:243 , LYS C:82 , GLY C:110 , ASP C:111 , ASP C:112 , HOH C:225BINDING SITE FOR RESIDUE SO4 C 201
04AC4SOFTWARELYS A:82 , GLY A:110 , ASP A:111 , ASP A:112 , ARG C:54BINDING SITE FOR RESIDUE SO4 A 201
05AC5SOFTWAREARG C:38 , ARG C:121BINDING SITE FOR RESIDUE SO4 C 203
06AC6SOFTWAREARG C:138 , ALA C:139 , LYS C:140BINDING SITE FOR RESIDUE SO4 C 206
07AC7SOFTWAREASP A:23 , ASP A:36 , LEU A:37 , ARG A:38 , HOH A:207BINDING SITE FOR RESIDUE EDO A 200
08AC8SOFTWAREARG A:76 , SER A:77 , GLY A:78 , ARG A:121BINDING SITE FOR RESIDUE EDO A 202
09AC9SOFTWAREILE A:73 , CYS A:87 , ASN A:89 , LYS A:103 , VAL A:104 , LEU A:105 , PHE C:151BINDING SITE FOR RESIDUE EDO A 205
10BC1SOFTWAREASP B:23 , ASP B:36 , LEU B:37 , ARG B:38 , HOH B:173BINDING SITE FOR RESIDUE EDO B 200
11BC2SOFTWAREARG B:76 , SER B:77 , GLY B:78 , GLN B:124 , HOH B:326 , HOH B:329BINDING SITE FOR RESIDUE EDO B 202
12BC3SOFTWAREILE B:73 , CYS B:87 , ASN B:89 , LYS B:103 , VAL B:104 , LEU B:105 , HOH B:246BINDING SITE FOR RESIDUE EDO B 205
13BC4SOFTWAREILE C:73 , CYS C:87 , ASN C:89 , LYS C:103 , VAL C:104 , LEU C:105BINDING SITE FOR RESIDUE EDO C 205
14BC5SOFTWARELEU A:16 , GLU A:17 , HIS A:18BINDING SITE FOR RESIDUE GOL A 204
15BC6SOFTWAREARG C:76 , SER C:77 , GLY C:78 , GLN C:124 , HOH C:217 , HOH C:318 , HOH C:319BINDING SITE FOR RESIDUE GOL C 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr A:90 -Pro A:91
2Thr B:90 -Pro B:91
3Thr C:90 -Pro C:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MBQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MBQ)

(-) Sequences/Alignments

Asymmetric/Biological 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:135
 aligned with DUT_BRUA2 | Q2YRG4 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:135
                                    17        27        37        47        57        67        77        87        97       107       117       127       137     
            DUT_BRUA2     8 APTLGIIRLEHAKGLDLPAYETAGSAGMDLRAAVAEDRQIVLLPGRRTLVPTGLILEIPQGYEVQIRPRSGLAFKNGITCLNTPGTIDSDYRGEVKVLLINLGDDDFRIERGMRIAQAVFAPVIQPKIEERAKIS 142
               SCOP domains d3mbqa_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhh..............eeee........eee....eeeeeeeeeee....eeeeeeehhhhhhhhheee....eee......eeeeeeee.....eee....eeeeeeeee....eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mbq A   8 APTLGIIRLEHAKGLDLPAYETAGSAGMDLRAAVAEDRQIVLLPGRRTLVPTGLILEIPQGYEVQIRPRSGLAFKNGITCLNTPGTIDSDYRGEVKVLLINLGDDDFRIERGMRIAQAVFAPVIQPKIEERAKIS 142
                                    17        27        37        47        57        67        77        87        97       107       117       127       137     


Chain B from PDB  Type:PROTEIN  Length:132
 aligned with DUT_BRUA2 | Q2YRG4 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:132
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  
            DUT_BRUA2     8 APTLGIIRLEHAKGLDLPAYETAGSAGMDLRAAVAEDRQIVLLPGRRTLVPTGLILEIPQGYEVQIRPRSGLAFKNGITCLNTPGTIDSDYRGEVKVLLINLGDDDFRIERGMRIAQAVFAPVIQPKIEERA 139
               SCOP domains d3mbqb_ B: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.hhhh..............eeee........eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eeee.....eeeeeeee.....eee....eeeeeeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mbq B   8 APTLGIIRLEHAKGLDLPAYETAGSAGMDLRAAVAEDRQIVLLPGRRTLVPTGLILEIPQGYEVQIRPRSGLAFKNGITCLNTPGTIDSDYRGEVKVLLINLGDDDFRIERGMRIAQAVFAPVIQPKIEERA 139
                                    17        27        37        47        57        67        77        87        97       107       117       127       137  


Chain C from PDB  Type:PROTEIN  Length:139
 aligned with DUT_BRUA2 | Q2YRG4 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:144
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147    
            DUT_BRUA2     8 APTLGIIRLEHAKGLDLPAYETAGSAGMDLRAAVAEDRQIVLLPGRRTLVPTGLILEIPQGYEVQIRPRSGLAFKNGITCLNTPGTIDSDYRGEVKVLLINLGDDDFRIERGMRIAQAVFAPVIQPKIEERAKISETARGAGGF 151
               SCOP domains d3mbqc_ C: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------dUTPase-3mbqC01 C:20-151                                                                                                             Pfam domains (1)
           Pfam domains (2) ------------dUTPase-3mbqC02 C:20-151                                                                                                             Pfam domains (2)
           Pfam domains (3) ------------dUTPase-3mbqC03 C:20-151                                                                                                             Pfam domains (3)
         Sec.struct. author ..eeeeee.hhhh..............eeee........eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eee......eeeeeeee.....eee....eeeeeeeee....eeee....-----..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mbq C   8 APTLGIIRLEHAKGLDLPAYETAGSAGMDLRAAVAEDRQIVLLPGRRTLVPTGLILEIPQGYEVQIRPRSGLAFKNGITCLNTPGTIDSDYRGEVKVLLINLGDDDFRIERGMRIAQAVFAPVIQPKIEERAKI-----GAGGF 151
                                    17        27        37        47        57        67        77        87        97       107       117       127       137   |   147    
                                                                                                                                                               141   147
   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, 3)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: dUTPase (38)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (DUT_BRUA2 | Q2YRG4)
molecular function
    GO:0004170    dUTP diphosphatase activity    Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
    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.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:0046080    dUTP metabolic process    The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
    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:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:90 - Pro A:91   [ RasMol ]  
    Thr B:90 - Pro B:91   [ RasMol ]  
    Thr C:90 - Pro C:91   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  3mbq
    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
  DUT_BRUA2 | Q2YRG4
    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)
  3.6.1.23
    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
  DUT_BRUA2 | Q2YRG4
    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
        DUT_BRUA2 | Q2YRG4: 3mdx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3MBQ)