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Title :   FULL LENGTH STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND ALPHA,BETA-IMIDO-DUTP.

Authors :   O. Barabas, N. Nagy, E. Takacs, B. G. Vertessy

Date :   15 May 07 (Deposition) - 22 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.49

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Jelly-Roll, Enzyme-Ligand Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Varga, O. Barabas, E. Takacs, N. Nagy, P. Nagy, B. G. Vertessy
Active Site Of Mycobacterial Dutpase: Structural Characteristics And A Built-In Sensor.
Biochem. Biophys. Res. Commun. V. 373 8 2008
PubMed-ID: 18519027 | Reference-DOI: 10.1016/J.BBRC.2008.05.130

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
	Chains	:	A
	EC Number	:	3.6.1.23
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DUT
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	DUTPASE, DUTP PYROPHOSPHATASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	DUP	1	Ligand/Ion	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	DUP	3	Ligand/Ion	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TRS	3	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DUP A:777 , HOH A:902 , HOH A:907 , HOH A:909	BINDING SITE FOR RESIDUE MG A 200
2	AC2	SOFTWARE	ARG A:64 , SER A:65 , GLY A:66 , ASN A:77 , GLY A:80 , THR A:81 , ILE A:82 , ASP A:83 , TYR A:86 , GLU A:89 , ILE A:90 , LYS A:91 , GLN A:113 , ARG A:140 , GLY A:144 , HIS A:145 , GLY A:146 , SER A:147 , SER A:148 , MG A:200 , HOH A:780 , HOH A:787 , HOH A:792 , HOH A:813 , HOH A:902 , HOH A:907 , HOH A:909	BINDING SITE FOR RESIDUE DUP A 777
3	AC3	SOFTWARE	SER A:74 , ILE A:75 , VAL A:76 , HOH A:788	BINDING SITE FOR RESIDUE TRS A 201

(no "SS Bond" information available for 2PY4)

Asymmetric Unit

No.	Residues
1	Ser A:78	-	Pro A:79

(no "SAP(SNP)/Variant" information available for 2PY4)

(no "PROSITE Motif" information available for 2PY4)

(no "Exon" information available for 2PY4)

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
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Chain A from PDB  Type:PROTEIN  Length:153
 aligned with DUT_MYCTO | P9WNS4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
            DUT_MYCTO     2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGHGSSGGHASL 154
               SCOP domains d2py4a_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                                     SCOP domains
               CATH domains 2py4A00 A:2-154  [code=2.70.40.10, no name defined]                                                                                                       CATH domains
               Pfam domains ------------dUTPase-2py4A01 A:14-149                                                                                                                ----- Pfam domains
         Sec.struct. author ....eeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eee......eeeeeeee......eee....eeeeeeeee.................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py4 A   2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGHGSSGGHASL 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain A from PDB  Type:PROTEIN  Length:153
 aligned with DUT_MYCTU | P9WNS5 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151   
            DUT_MYCTU     2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGHGSSGGHASL 154
               SCOP domains d2py4a_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                                     SCOP domains
               CATH domains 2py4A00 A:2-154  [code=2.70.40.10, no name defined]                                                                                                       CATH domains
               Pfam domains ------------dUTPase-2py4A01 A:14-149                                                                                                                ----- Pfam domains
         Sec.struct. author ....eeee.................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eee......eeeeeeee......eee....eeeeeeeee.................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py4 A   2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLASTSRGDGGHGSSGGHASL 154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

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)

Mycobacterium tuberculosis, rv2697c [TaxId: 1773] (8)

d2py4a_

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)

Mycobacterium tuberculosis. Organism_taxid: 1773. (8)

2py4A00

A:2-154

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: dUTPase (38)

Family: dUTPase (38)

Mycobacterium tuberculosis (9)

dUTPase-2py4A01

A:14-149

Asymmetric Unit(hide GO term definitions)

Chain A (DUT_MYCTU | P9WNS5)

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:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	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:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A (DUT_MYCTO | P9WNS4)

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: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:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

Asymmetric Unit
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	Cis Peptide Bonds
		Ser A:78 - Pro A:79	[ RasMol ]

Biological Unit
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1mq7	USED AS MODEL IN MOLECULAR REPLACEMENT
1six	SAME PROTEIN-LIGAND COMPLEX WITH DISORDERED REGIONS IN THE PROTEIN SEQUENCE

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