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(-) Description

Title :  STRUCTURE OF THE BACILLUS SUBTILIS PROPHAGE DUTPASE WITH DUPNHPP
 
Authors :  J. Garcia-Nafria, M. Harkiolaki, R. Persson, M. J. Fogg, K. S. Wilson
Date :  12 Nov 10  (Deposition) - 23 Feb 11  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Hydrolase, Phe-Lid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Garcia-Nafria, M. Harkiolaki, R. Persson, M. J. Fogg, K. S. Wilson
The Structure Of Bacillus Subtilis Sp Beta Prophage Dutpase And Its Complexes With Two Nucleotides
Acta Crystallogr. , Sect. D V. 67 167 2011
PubMed-ID: 21358047  |  Reference-DOI: 10.1107/S0907444911003234

(-) Compounds

Molecule 1 - SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
    Chains: A, B, C, D, E, F
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: B834
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: DUTPASE, DUTP PYROPHOSPHATASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1DUP6Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1DUP3Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1DUP3Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:61 , SER B:62 , SER B:63 , GLN B:110 , ASN C:74 , ILE C:79 , TYR C:83 , TRP C:90 , PHE C:91 , PRO C:93 , MG C:1130 , HOH C:2018 , HOH C:2020 , LYS F:101BINDING SITE FOR RESIDUE DUP C1129
2AC2SOFTWAREASN A:74 , GLY A:77 , ILE A:79 , TYR A:83 , TRP A:90 , PHE A:91 , PRO A:93 , HOH A:2017 , SER C:62 , HOH C:2006 , LYS D:101 , LYS D:103 , HOH D:2007BINDING SITE FOR RESIDUE DUP A1130
3AC3SOFTWAREASP B:31 , LYS B:103 , ASN D:74 , ILE D:79 , TYR D:83 , PHE D:91 , PRO D:93 , HOH D:2020 , HOH D:2021 , HOH D:2022 , SER F:62BINDING SITE FOR RESIDUE DUP D1130
4AC4SOFTWARELYS A:101 , ARG E:61 , SER E:62 , SER E:63 , GLN E:110 , ASN F:74 , GLY F:77 , VAL F:78 , ILE F:79 , TYR F:83 , TRP F:90 , PHE F:91 , PRO F:93 , MG F:1130 , HOH F:2014 , HOH F:2015 , HOH F:2016BINDING SITE FOR RESIDUE DUP F1129
5AC5SOFTWARESER A:62 , HOH A:2011 , ASN B:74 , ILE B:79 , TYR B:83 , TRP B:90 , PHE B:91 , PRO B:93 , LYS E:103BINDING SITE FOR RESIDUE DUP B1129
6AC6SOFTWARELYS C:101 , ARG D:61 , SER D:62 , SER D:63 , GLN D:110 , ASN E:74 , GLY E:77 , TYR E:83 , TRP E:90 , PHE E:91 , PRO E:93 , MG E:1131 , HOH E:2019 , HOH E:2020BINDING SITE FOR RESIDUE DUP E1130
7AC7SOFTWAREDUP C:1129BINDING SITE FOR RESIDUE MG C1130
8AC8SOFTWAREDUP E:1130BINDING SITE FOR RESIDUE MG E1131
9AC9SOFTWAREDUP F:1129BINDING SITE FOR RESIDUE MG F1130

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XY3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn D:16 -Lys D:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XY3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XY3)

(-) Exons   (0, 0)

(no "Exon" information available for 2XY3)

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

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           YOSS_BACSU     1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRLG 129
               SCOP domains d2xy3a_ A: autom ated matches                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........-......eeee....eee....eeeeeeeeeee....eeeeeee..hhhhhhheee....eeee........eeeeeeee...eee....eeeeeeeee.....eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xy3 A   1 MQIKIKYLDETQTRIN-MEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRLG 129
                                    10     | |20        30        40        50        60        70        80        90       100       110       120         
                                          16 |                                                                                                               
                                            18                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:127
 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 d2xy3b_ B: automat ed matches                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...........-....eeee....eee....eeeeeeeeeee....eeeeeee..hhhhhhheee....eeee........eeeeeeee...eee....eeeeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xy3 B   1 MQIKIKYLDETQTRINKM-QGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10       |20        30        40        50        60        70        80        90       100       110       120        
                                            18 |                                                                                                            
                                              20                                                                                                            


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 d2xy3c_ 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
                 2xy3 C   1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10        20        30        40        50        60        70        80        90       100       110       120        


Chain D from PDB  Type:PROTEIN  Length:129
 aligned with YOSS_BACSU | O34919 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           YOSS_BACSU     1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRLG 129
               SCOP domains d2xy3d_ D: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee................eeee....eee....eeeeeeeeeee....eeeeeee..hhhhhhheee....eeee........eeeeeeee...eee....eeeeeeeee.....eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xy3 D   1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRLG 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


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

    Alignment length:129
                                    10        20        30        40        50        60        70        80        90       100       110       120         
           YOSS_BACSU     1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRLG 129
               SCOP domains d2xy3e_ E: automat ed matches                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...........-....eeee....eee....eeeeeeeeeee....eeeeeee..hhhhhhheee....eeee........eeeeeeee...eee....eeeeeeeee.....eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xy3 E   1 MQIKIKYLDETQTRINKM-QGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRLG 129
                                    10       |20        30        40        50        60        70        80        90       100       110       120         
                                            18 |                                                                                                             
                                              20                                                                                                             


Chain F from PDB  Type:PROTEIN  Length:127
 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 d2xy3f_ F: automa ted matches                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------dUTPase -2xy3F01 F:11-128                                                                                              Pfam domains (1)
           Pfam domains (2) ----------dUTPase -2xy3F02 F:11-128                                                                                              Pfam domains (2)
           Pfam domains (3) ----------dUTPase -2xy3F03 F:11-128                                                                                              Pfam domains (3)
           Pfam domains (4) ----------dUTPase -2xy3F04 F:11-128                                                                                              Pfam domains (4)
           Pfam domains (5) ----------dUTPase -2xy3F05 F:11-128                                                                                              Pfam domains (5)
           Pfam domains (6) ----------dUTPase -2xy3F06 F:11-128                                                                                              Pfam domains (6)
         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
                 2xy3 F   1 MQIKIKYLDETQTRINK-EQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10      | 20        30        40        50        60        70        80        90       100       110       120        
                                           17 |                                                                                                             
                                             19
   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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XY3)

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: dUTPase (38)
(-)
Family: dUTPase (38)
(-)
Bacillus subtilis (3)
1adUTPase-2xy3F01F:11-128
1bdUTPase-2xy3F02F:11-128
1cdUTPase-2xy3F03F:11-128
1ddUTPase-2xy3F04F:11-128
1edUTPase-2xy3F05F:11-128
1fdUTPase-2xy3F06F:11-128

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (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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  2xy3
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  YOSS_BACSU | O34919
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 Related Entries

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

UniProtKB/Swiss-Prot
        YOSS_BACSU | O34919: 2baz 2xx6 2y1t 4ao5

(-) Related Entries Specified in the PDB File

2baz STRUCTURE OF YOSS, A PUTATIVE DUTPASE FROM BACILLUS SUBTILIS
2xx6 STRUCTURE OF THE BACILLUS SUBTILIS PROPHAGE DUTPASE, YOSS
2y1t BACILLUS SUBTILIS PROPHAGE DUTPASE IN COMPLEX WITH DUDP