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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 :   2.40

Chains :   Asym./Biol. Unit : A,B,C

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/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:63 , ARG A:65 , GLN A:118 , ARG B:65 , GLN B:118 , GLN C:118	BINDING SITE FOR RESIDUE CL A 200
2	AC2	SOFTWARE	ASP A:78 , HOH A:212 , ILE B:79 , ILE B:97	BINDING SITE FOR RESIDUE EDO A 201
3	AC3	SOFTWARE	GLY A:82 , GLY A:93 , ILE A:95 , HOH A:210 , SER C:70	BINDING SITE FOR RESIDUE EDO A 202
4	AC4	SOFTWARE	SER A:70 , GLY B:82 , GLY B:93 , ILE B:95 , HOH B:218	BINDING SITE FOR RESIDUE EDO B 203
5	AC5	SOFTWARE	TYR A:63 , GLN A:118 , ARG A:119 , ILE A:120 , GLN B:118 , ARG B:119 , GLN C:118 , ARG C:119	BINDING SITE FOR RESIDUE EDO A 204

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

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

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

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

(no "Exon" information available for 2OKD)

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:124
 aligned with A4GD96_9POXV | A4GD96 from UniProtKB/TrEMBL  Length:147

    Alignment length:124
                                    18        28        38        48        58        68        78        88        98       108       118       128    
         A4GD96_9POXV     9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSLD 132
               SCOP domains d2okda_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                        SCOP domains
               CATH domains 2okdA00 A:9-132  [code=2.70.40.10, no name defined]                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.................eeee....eee...eeeeee..eee.....eeeeee.hhhhhh..eeee..ee........eeeeee.....eee....eeeeeeeeeee...eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okd A   9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSLD 132
                                    18        28        38        48        58        68        78        88        98       108       118       128

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with A4GD96_9POXV | A4GD96 from UniProtKB/TrEMBL  Length:147

    Alignment length:123
                                    18        28        38        48        58        68        78        88        98       108       118       128   
         A4GD96_9POXV     9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
               SCOP domains d2okdb_ B: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                       SCOP domains
               CATH domains 2okdB00 B:9-131  [code=2.70.40.10, no name defined]                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.................eeee....eee...eeeeee..eee.....eeeeee.hhhhhh..eeee..ee........eeeeee.....eee....eeeeeeeeeee...eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okd B   9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
                                    18        28        38        48        58        68        78        88        98       108       118       128

Chain C from PDB  Type:PROTEIN  Length:125
 aligned with A4GD96_9POXV | A4GD96 from UniProtKB/TrEMBL  Length:147

    Alignment length:125
                                    16        26        36        46        56        66        76        86        96       106       116       126     
         A4GD96_9POXV     7 NSPVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
               SCOP domains d2okdc_ C: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                         SCOP domains
               CATH domains 2okdC00 C:7-131  [code=2.70.40.10, no name defined]                                                                           CATH domains
           Pfam domains (1) ----------dUTPase-2okdC01 C:17-131                                                                                            Pfam domains (1)
           Pfam domains (2) ----------dUTPase-2okdC02 C:17-131                                                                                            Pfam domains (2)
           Pfam domains (3) ----------dUTPase-2okdC03 C:17-131                                                                                            Pfam domains (3)
         Sec.struct. author ...eeeee.................eeee....eee....eeeee..eee.....eeeeee.hhhhhhh.eeee..ee........eeeeee.....eee....eeeeeeeeeee...eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2okd C   7 NSPVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
                                    16        26        36        46        56        66        76        86        96       106       116       126

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/Biological 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	d2okda_	A:
1b	d2okdb_	B:
1c	d2okdc_	C:

Asymmetric/Biological 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	2okdC00	C:7-131
1b	2okdA00	A:9-132
1c	2okdB00	B:9-131

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: dUTPase (38)

Family: dUTPase (38)

Vaccinia virus (5)

1a	dUTPase-2okdC01	C:17-131
1b	dUTPase-2okdC02	C:17-131
1c	dUTPase-2okdC03	C:17-131

Asymmetric/Biological 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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2okd)

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	A4GD96_9POXV \| A4GD96	:	2okb 2oke 2ol0 2ol1

1q5u	HUMAN DUTPASE
2okb	N-TERMINALLY TRUNCATED VERSION 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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