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Title :   HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE

Authors :   N. Schormann, D. Chattopadhyay

Date :   16 Jan 07 (Deposition) - 01 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Fold, Jelly-Roll, Superfamily, Dutpase-Like, Forms Tight Trimer Through An Additional Beta-Sheet In Each Subunit, Subunit Beta- Sheets Are Orthogonally Packed Around The Three-Fold Axis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Samal, N. Schormann, W. J. Cook, L. J. Delucas, D. Chattopadhyay
Structures Of Vaccinia Virus Dutpase And Its Nucleotide Complexes.
Acta Crystallogr. , Sect. D V. 63 571 2007
PubMed-ID: 17452782 | Reference-DOI: 10.1107/S0907444907007871

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	:	PET15B
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DUT
	Organism Scientific	:	VACCINIA VIRUS
	Organism Taxid	:	10245
	Synonym	:	DUTPASE, DUTP PYROPHOSPHATASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 18)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	9	Ligand/Ion	1,2-ETHANEDIOL
3	SO4	9	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:69 , SER A:70 , GLY A:71 , ARG A:111 , EDO A:1302 , HOH A:1415	BINDING SITE FOR RESIDUE SO4 A 1201
2	AC2	SOFTWARE	ARG B:69 , SER B:70 , GLY B:71 , ARG B:111 , HOH B:1413	BINDING SITE FOR RESIDUE SO4 B 1202
3	AC3	SOFTWARE	CYS A:102 , THR A:103 , ARG C:69 , SER C:70 , GLY C:71 , ARG C:111 , HOH C:1210 , HOH C:1274	BINDING SITE FOR RESIDUE SO4 C 1203
4	AC4	SOFTWARE	ARG B:65 , ARG C:65	BINDING SITE FOR RESIDUE CL B 1401
5	AC5	SOFTWARE	ARG A:111 , HOH A:1488	BINDING SITE FOR RESIDUE CL A 1402
6	AC6	SOFTWARE	SER A:70 , ILE B:66 , GLY B:81 , GLY B:82 , GLY B:93 , HOH B:1404	BINDING SITE FOR RESIDUE EDO B 1301
7	AC7	SOFTWARE	ASP A:33 , ARG A:69 , ARG A:111 , ALA A:113 , GLN A:114 , SO4 A:1201 , HOH A:1415 , HOH A:1438	BINDING SITE FOR RESIDUE EDO A 1302
8	AC8	SOFTWARE	ASN A:99 , GLY B:45 , GLU B:46 , ARG B:47 , ILE B:97 , ASN B:98 , ASN B:99	BINDING SITE FOR RESIDUE EDO B 1303

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

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

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

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

(no "Exon" information available for 2OKB)

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:113
 aligned with A4GD96_9POXV | A4GD96 from UniProtKB/TrEMBL  Length:147

    Alignment length:113
                                    20        30        40        50        60        70        80        90       100       110       120   
         A4GD96_9POXV    11 RFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYP 123
               SCOP domains d2okba_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                             SCOP domains
               CATH domains 2okbA00 A:11-123  [code=2.70.40.10, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.................eeee....eee...eeeeeeeeeeee....eeeeee.hhhhhh..eeee..ee....eeeeeeeeee.....eee....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2okb A  11 MFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYP 123
                                    20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with A4GD96_9POXV | A4GD96 from UniProtKB/TrEMBL  Length:147

    Alignment length:113
                                    20        30        40        50        60        70        80        90       100       110       120   
         A4GD96_9POXV    11 RFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYP 123
               SCOP domains d2okbb_ B: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                             SCOP domains
               CATH domains 2okbB00 B:11-123  [code=2.70.40.10, no name defined]                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhh..eeee..ee....eeeeeeeeee.....eee....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2okb B  11 MFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYP 123
                                    20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:113
 aligned with A4GD96_9POXV | A4GD96 from UniProtKB/TrEMBL  Length:147

    Alignment length:113
                                    20        30        40        50        60        70        80        90       100       110       120   
         A4GD96_9POXV    11 RFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYP 123
               SCOP domains d2okbc_ C: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                             SCOP domains
               CATH domains 2okbC00 C:11-123  [code=2.70.40.10, no name defined]                                                              CATH domains
           Pfam domains (1) ------dUTPase-2okbC01 C:17-123                                                                                    Pfam domains (1)
           Pfam domains (2) ------dUTPase-2okbC02 C:17-123                                                                                    Pfam domains (2)
           Pfam domains (3) ------dUTPase-2okbC03 C:17-123                                                                                    Pfam domains (3)
         Sec.struct. author .eee.................eeee....eee...eeeeeeeeeeee....eeeeee.hhhhhh..eeee..ee....eeeeeeeeee.....eee....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2okb C  11 MFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYP 123
                                    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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-clip (280)

Superfamily: dUTPase-like (122)

Family: dUTPase-like (71)

Protein domain: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) (36)

Vaccinia virus [TaxId: 10245] (5)

1a	d2okba_	A:
1b	d2okbb_	B:
1c	d2okbc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A (52)

Homologous Superfamily: [code=2.70.40.10, no name defined] (51)

Vaccinia virus. Organism_taxid: 10245. (5)

1a	2okbA00	A:11-123
1b	2okbB00	B:11-123
1c	2okbC00	C:11-123

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: dUTPase (38)

Family: dUTPase (38)

Vaccinia virus (5)

1a	dUTPase-2okbC01	C:17-123
1b	dUTPase-2okbC02	C:17-123
1c	dUTPase-2okbC03	C:17-123

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (A4GD96_9POXV | A4GD96)

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.
biological process
	GO:0046080	dUTP metabolic process	The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.

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Biological Units
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	A4GD96_9POXV \| A4GD96	:	2okd 2oke 2ol0 2ol1

1q5u	HUMAN DUTPASE
2okd	HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE
2oke	HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE
2ol0	HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE
2ol1	HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE

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