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(-) Description

Title :  STRUCTURE OF YOSS, A PUTATIVE DUTPASE FROM BACILLUS SUBTILIS
 
Authors :  Y. -H. Liang, J. Wang, X. -D. Su
Date :  16 Oct 05  (Deposition) - 17 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Homotrimer, Beta Barrel, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wang, Y. -H. Liang, X. -D. Su
Structure Of Yoss, A Putative Dutpase From Bacillus Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN BSU20020
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21A
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: YOSS

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2BAZ)

(-) Sites  (0, 0)

(no "Site" information available for 2BAZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BAZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BAZ)

(-) 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:128
 aligned with YOSS_BACSU | O34919 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
           YOSS_BACSU     1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
               SCOP domains d2baza_ A: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee................eeee....eee....eeeee..eeee....eeeeeee..hhhhhhheee....eeee..........eeeeee...eee....eeeeeeeee.....eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2baz A   1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10        20        30        40        50        60        70        80        90       100       110       120        


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with YOSS_BACSU | O34919 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
           YOSS_BACSU     1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
               SCOP domains d2bazb_ B: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee................eeee....eee....eeeee..eeee....eeeeeee..hhhhhhheee....eeee..........eeeeee...eee....eeeeeeeee.....eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2baz B   1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10        20        30        40        50        60        70        80        90       100       110       120        


Chain C from PDB  Type:PROTEIN  Length:128
 aligned with YOSS_BACSU | O34919 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
           YOSS_BACSU     1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
               SCOP domains d2bazc_ C: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee................eeee....eee....eeeee..eeee....eeeeeee..hhhhhhheee....eeee..........eeeeee...eee....eeeeeeeee.....eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2baz C   1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 2BAZ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (YOSS_BACSU | O34919)
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:0046081    dUTP catabolic process    The chemical reactions and pathways resulting in the breakdown of dUTP, deoxyuridine (5'-)triphosphate.
    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:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
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
        YOSS_BACSU | O34919: 2xx6 2xy3 2y1t 4ao5

(-) Related Entries Specified in the PDB File

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