2XX6 - JenaLib

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Title :   STRUCTURE OF THE BACILLUS SUBTILIS PROPHAGE DUTPASE, YOSS

Authors :   J. Garcia-Nafria, M. Harkiolaki, R. Persson, M. J. Fogg, K. S. Wilson

Date :   08 Nov 10 (Deposition) - 23 Feb 11 (Release) - 23 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D  (3x)

Keywords :   Hydrolase (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

Molecule 1 - SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
	Chains	:	A, B, C, D
	EC Number	:	3.6.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	B834
	Expression System Taxid	:	562
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	DUTPASE, DUTP PYROPHOSPHATASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (3x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2XX6)

(no "Site" information available for 2XX6)

(no "SS Bond" information available for 2XX6)

(no "Cis Peptide Bond" information available for 2XX6)

(no "SAP(SNP)/Variant" information available for 2XX6)

(no "PROSITE Motif" information available for 2XX6)

(no "Exon" information available for 2XX6)

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:128
                                    10        20        30        40        50        60        70        80        90       100       110       120        
           YOSS_BACSU     1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
               SCOP domains d2xx6a_ A: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeee...eeee....eee....eeeee..eeee....eeeeeee..hhhhhhheee....eeee..........eeeeee...eee....eeeeeeeee.....eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xx6 A   1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:124
 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 d2xx6b_ B: 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....eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xx6 B   1 MQIKIKYLDETQTRIN----GDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10     |   -|       30        40        50        60        70        80        90       100       110       120        
                                          16   21

Chain C from PDB  Type:PROTEIN  Length:126
 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 d2xx6c_ C: auto  mated 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
                 2xx6 C   1 MQIKIKYLDETQTRI--MEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10    |  |20        30        40        50        60        70        80        90       100       110       120        
                                         15 18

Chain D from PDB  Type:PROTEIN  Length:123
 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 d2xx6d_ D: auto     mated matches                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------dUTPa     se-2xx6D01 D:11-128                                                                                          Pfam domains (1)
           Pfam domains (2) ----------dUTPa     se-2xx6D02 D:11-128                                                                                          Pfam domains (2)
           Pfam domains (3) ----------dUTPa     se-2xx6D03 D:11-128                                                                                          Pfam domains (3)
           Pfam domains (4) ----------dUTPa     se-2xx6D04 D:11-128                                                                                          Pfam domains (4)
         Sec.struct. author ...eeee........-----...eeee....eee....eeeeeeeeeee....eeeeeee..hhhhhhheee....eeee........eeeeeeee...eee....eeeeeeeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xx6 D   1 MQIKIKYLDETQTRI-----GDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10    |    -|       30        40        50        60        70        80        90       100       110       120        
                                         15    21

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-clip (280)

Superfamily: dUTPase-like (122)

Family: automated matches (51)

Protein domain: automated matches (51)

Bacillus subtilis [TaxId: 1423] (11)

1a	d2xx6a_	A:
1b	d2xx6b_	B:
1c	d2xx6c_	C:
1d	d2xx6d_	D:

(no "CATH Domain" information available for 2XX6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: dUTPase (38)

Family: dUTPase (38)

Bacillus subtilis (3)

1a	dUTPase-2xx6D01	D:11-128
1b	dUTPase-2xx6D02	D:11-128
1c	dUTPase-2xx6D03	D:11-128
1d	dUTPase-2xx6D04	D:11-128

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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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Biological Units
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	2xx6
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	YOSS_BACSU \| O34919
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	3.6.1.23
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	YOSS_BACSU \| O34919	:	2baz 2xy3 2y1t 4ao5

2baz	STRUCTURE OF YOSS, A PUTATIVE DUTPASE FROM BACILLUS SUBTILIS

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Ligands, Modified Residues, Ions (0, 0)

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