2Y1T - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   BACILLUS SUBTILIS PROPHAGE DUTPASE IN COMPLEX WITH DUDP

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

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

Method :   X-RAY DIFFRACTION

Resolution :   1.89

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, Spb Prophage, 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

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	:	B834
	Expression System Taxid	:	562
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	DEOXYURIDINE TRIPHOSPHATE NUCLEOTIDOHYDROLASE, DUTPASE, DUTP PYROPHOSPHATASE

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	DUD	5	Ligand/Ion	DEOXYURIDINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	DUD	2	Ligand/Ion	DEOXYURIDINE-5'-DIPHOSPHATE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	DUD	3	Ligand/Ion	DEOXYURIDINE-5'-DIPHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:62 , HOH A:2051 , HOH A:2056 , ASN B:74 , GLY B:77 , ILE B:79 , TYR B:83 , TRP B:90 , PHE B:91 , PRO B:93 , HOH B:2061 , HOH B:2088 , HOH B:2089 , HOH B:2090 , HOH B:2091 , LYS E:101 , LYS E:103 , HOH E:2077	BINDING SITE FOR RESIDUE DUD B 143
2	AC2	SOFTWARE	SER B:62 , HOH B:2082 , ASN C:74 , GLY C:77 , VAL C:78 , ILE C:79 , TYR C:83 , TRP C:90 , PHE C:91 , PRO C:93 , HOH C:2056 , HOH C:2060 , HOH C:2078 , HOH C:2079 , HOH C:2080 , LYS F:101	BINDING SITE FOR RESIDUE DUD C 143
3	AC3	SOFTWARE	LYS B:101 , LYS B:103 , ASN D:74 , GLY D:77 , ILE D:79 , TYR D:83 , TRP D:90 , PHE D:91 , PRO D:93 , HOH D:2052 , HOH D:2071 , HOH D:2072 , HOH D:2073 , HOH D:2074 , HOH D:2075 , SER F:62 , HOH F:2049	BINDING SITE FOR RESIDUE DUD D 143
4	AC4	SOFTWARE	ARG E:61 , SER E:62 , SER E:63 , HOH E:2091 , HOH E:2092 , ASN F:74 , GLY F:77 , VAL F:78 , ILE F:79 , TYR F:83 , TRP F:90 , PHE F:91 , PRO F:93	BINDING SITE FOR RESIDUE DUD E 143
5	AC5	SOFTWARE	SER D:62 , HOH D:2039 , ASN E:74 , GLY E:77 , ILE E:79 , TYR E:83 , TRP E:90 , PHE E:91 , PRO E:93 , HOH E:2056 , HOH E:2093 , HOH E:2094 , HOH E:2095 , HOH E:2097	BINDING SITE FOR RESIDUE DUD E 144

(no "SS Bond" information available for 2Y1T)

(no "Cis Peptide Bond" information available for 2Y1T)

(no "SAP(SNP)/Variant" information available for 2Y1T)

(no "PROSITE Motif" information available for 2Y1T)

(no "Exon" information available for 2Y1T)

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 d2y1ta_ A: 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
                 2y1t 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 d2y1tb_ 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
                 2y1t B   1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:125
 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 d2y1tc_ C: 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
                 2y1t C   1 MQIKIKYLDETQTRIN---QGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10     |  20        30        40        50        60        70        80        90       100       110       120        
                                          16  20

Chain D 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 d2y1td_ D: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee................eeee....eee....eeeeeeeeeee....eeeeeee..hhhhhhheee....eee.........eeeeeeee...eee....eeeeeeeee.....eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y1t D   1 MQIKIKYLDETQTRINKMEQGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain E 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 d2y1te_ 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
                 2y1t E   1 MQIKIKYLDETQTRINKM-QGDWIDLRAAEDVAIKKDEFKLVPLGVAMELPEGYEAHVVPRSSTYKNFGVIQTNSMGVIDESYKGDNDFWFFPAYALRDTKIKKGDRICQFRIMKKMPAVDLIEVDRL 128
                                    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 d2y1tf_ F: automa ted matches                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------dUTPase -2y1tF01 F:11-128                                                                                              Pfam domains (1)
           Pfam domains (2) ----------dUTPase -2y1tF02 F:11-128                                                                                              Pfam domains (2)
           Pfam domains (3) ----------dUTPase -2y1tF03 F:11-128                                                                                              Pfam domains (3)
           Pfam domains (4) ----------dUTPase -2y1tF04 F:11-128                                                                                              Pfam domains (4)
           Pfam domains (5) ----------dUTPase -2y1tF05 F:11-128                                                                                              Pfam domains (5)
           Pfam domains (6) ----------dUTPase -2y1tF06 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
                 2y1t 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

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	d2y1ta_	A:
1b	d2y1tb_	B:
1c	d2y1tc_	C:
1d	d2y1td_	D:
1e	d2y1te_	E:
1f	d2y1tf_	F:

(no "CATH Domain" information available for 2Y1T)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: dUTPase (38)

Family: dUTPase (38)

Bacillus subtilis (3)

1a	dUTPase-2y1tF01	F:11-128
1b	dUTPase-2y1tF02	F:11-128
1c	dUTPase-2y1tF03	F:11-128
1d	dUTPase-2y1tF04	F:11-128
1e	dUTPase-2y1tF05	F:11-128
1f	dUTPase-2y1tF06	F:11-128

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2y1t)

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	2y1t
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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	YOSS_BACSU \| O34919
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	3.6.1.23
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	YOSS_BACSU \| O34919
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UniProtKB/Swiss-Prot
	YOSS_BACSU \| O34919	:	2baz 2xx6 2xy3 4ao5

2baz	STRUCTURE OF YOSS, A PUTATIVE DUTPASE FROM BACILLUS SUBTILIS
2xx6	STRUCTURE OF THE BACILLUS SUBTILIS PROPHAGE DUTPASE, YOSS
2xy3	STRUCTURE OF THE BACILLUS SUBTILIS PROPHAGE DUTPASE WITH DUPNHPP

Description

Compounds

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Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

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