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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) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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
(for further references see the PDB file header)

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 (4, 6)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	DUP	3	Ligand/Ion	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:25 , DUP C:202	BINDING SITE FOR RESIDUE MG B 300
2	AC2	SOFTWARE	TYR A:63 , GLN A:118 , GLN B:118 , ARG C:65 , GLN C:118	BINDING SITE FOR RESIDUE CL A 301
3	AC3	SOFTWARE	GLY A:80 , GLY A:82 , VAL A:83 , ILE A:84 , ASP A:85 , TYR A:88 , ASN A:91 , GLY A:93 , HOH A:309 , HOH A:330 , GLU B:46 , ARG C:69 , SER C:70 , ARG C:111 , HOH C:441 , HOH C:444	BINDING SITE FOR RESIDUE DUP A 200
4	AC4	SOFTWARE	ARG A:69 , SER A:70 , GLY A:71 , GLN A:114 , GLY B:82 , VAL B:83 , ILE B:84 , ASP B:85 , TYR B:88 , ASN B:91 , GLY B:93 , HOH B:302 , HOH B:319 , HOH B:345	BINDING SITE FOR RESIDUE DUP B 201
5	AC5	SOFTWARE	GLN B:25 , ASP B:33 , ARG B:69 , SER B:70 , ARG B:111 , GLN B:114 , MG B:300 , GLY C:82 , VAL C:83 , ILE C:84 , ASP C:85 , TYR C:88 , GLY C:93 , ILE C:95 , HOH C:405 , HOH C:443	BINDING SITE FOR RESIDUE DUP C 202
6	AC6	SOFTWARE	ASN B:99 , ARG C:47 , ILE C:97 , ASN C:99 , HOH C:424	BINDING SITE FOR RESIDUE EDO C 401

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

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

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

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

(no "Exon" information available for 2OKE)

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: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 d2okea_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                       SCOP domains
               CATH domains 2okeA00 A:9-131  [code=2.70.40.10, no name defined]                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.................eeee....eee....eeeee..eee.....eeeeee.hhhhhhh.eeee..ee........eeeeee.....eee....eeeeeeeee.....eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oke A   9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
                                    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 d2okeb_ B: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                       SCOP domains
               CATH domains 2okeB00 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.hhhhhhh.eeee..ee........eeeeee.....eee....eeeeeeeeeee...eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oke B   9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
                                    18        28        38        48        58        68        78        88        98       108       118       128

Chain C 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 d2okec_ C: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                       SCOP domains
               CATH domains 2okeC00 C:9-131  [code=2.70.40.10, no name defined]                                                                         CATH domains
           Pfam domains (1) --------dUTPase-2okeC01 C:17-131                                                                                            Pfam domains (1)
           Pfam domains (2) --------dUTPase-2okeC02 C:17-131                                                                                            Pfam domains (2)
           Pfam domains (3) --------dUTPase-2okeC03 C:17-131                                                                                            Pfam domains (3)
         Sec.struct. author .eeeee.................eeee....eee...eeeeee..eeee....eeeeee.hhhhhhh.eeee..ee........eeeeee.....eee....eeeeeeeee.....eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oke C   9 PVRFVKETNRAKSPTRQSPGAAGYDLYSAYDYTIPPGERQLIKTDISMSMPKFCYGRIAPRSGLSLKGIDIGGGVIDEDYRGNIGVILINNGKCTFNVNTGDRIAQLIYQRIYYPELEEVQSL 131
                                    18        28        38        48        58        68        78        88        98       108       118       128

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	d2okea_	A:
1b	d2okeb_	B:
1c	d2okec_	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	2okeA00	A:9-131
1b	2okeB00	B:9-131
1c	2okeC00	C:9-131

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: dUTPase (38)

Family: dUTPase (38)

Vaccinia virus (5)

1a	dUTPase-2okeC01	C:17-131
1b	dUTPase-2okeC02	C:17-131
1c	dUTPase-2okeC03	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 2oke)

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UniProtKB/TrEMBL
	A4GD96_9POXV \| A4GD96	:	2okb 2okd 2ol0 2ol1

2okb	N-TERMINALLY TRUNCATED VERSION OF VACCINIA VIRUS DUTPASE
2okd	APO-ENZYME OF VACCINIA VIRUS DUTPASE
2ol0	HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE
2ol1	HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE

Description

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