1SM8 - JenaLib

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Asym./Biol. Unit - sites (Jmol Viewer)

Title :   M. TUBERCULOSIS DUTPASE COMPLEXED WITH CHROMIUM AND DUTP

Authors :   M. R. Sawaya, S. Chan, B. Segelke, T. Lekin, H. Krupka, U. S. Cho, M. - Y. Kim, M. So, C. -Y. Kim, C. M. Naranjo, Y. C. Rogers, M. S. Park, G. S. Waldo, I. Pashkov, D. Cascio, T. O. Yeates, J. L. Perry, T. C. Terwilliger, D. Eisenberg, Tb Structural Genomics Consortium (Tbsgc)

Date :   08 Mar 04 (Deposition) - 16 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Jelly-Roll, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chan, B. Segelke, T. Lekin, H. Krupka, U. S. Cho, M. -Y. Kim, M. So, C. -Y. Kim, C. M. Naranjo, Y. C. Rogers, M. S. Park, G. S. Waldo, I. Pashkov, D. Cascio, J. L. Perry, M. R. Sawaya
Crystal Structure Of The Mycobacterium Tuberculosis Dutpase: Insights Into The Catalytic Mechanism.
J. Mol. Biol. V. 341 503 2004
PubMed-ID: 15276840 | Reference-DOI: 10.1016/J.JMB.2004.06.028
(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	:	MODIFIED PET28B
	Expression System Strain	:	BL21PRO
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DUT, RV2697C, MT2771, MTCY05A6.18C, MB2716C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	DUTPASE, DUTP PYROPHOSPHATASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	CR	3	Ligand/Ion	CHROMIUM ION
2	DUT	3	Ligand/Ion	DEOXYURIDINE-5'-TRIPHOSPHATE
3	NO3	1	Ligand/Ion	NITRATE ION
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DUT C:1170	BINDING SITE FOR RESIDUE CR C 1171
2	AC2	SOFTWARE	DUT B:2170	BINDING SITE FOR RESIDUE CR A 2171
3	AC3	SOFTWARE	DUT C:3170	BINDING SITE FOR RESIDUE CR B 3171
4	AC4	SOFTWARE	PHE A:130 , ASP A:131 , THR B:4 , LEU B:5 , ALA B:6 , ARG C:87	BINDING SITE FOR RESIDUE NO3 A 2172
5	AC5	SOFTWARE	ASN A:77 , THR A:81 , ILE A:82 , ASP A:83 , TYR A:86 , GLU A:89 , ILE A:90 , LYS A:91 , ARG C:64 , SER C:65 , GLY C:66 , GLN C:113 , CR C:1171	BINDING SITE FOR RESIDUE DUT C 1170
6	AC6	SOFTWARE	ARG A:64 , SER A:65 , GLY A:66 , GLN A:113 , CR A:2171 , ASN B:77 , GLY B:80 , THR B:81 , ILE B:82 , ASP B:83 , TYR B:86 , GLU B:89 , ILE B:90 , LYS B:91	BINDING SITE FOR RESIDUE DUT B 2170
7	AC7	SOFTWARE	ARG B:64 , SER B:65 , GLY B:66 , GLN B:113 , SER B:128 , GLU B:132 , CR B:3171 , ASN C:77 , GLY C:80 , THR C:81 , ASP C:83 , TYR C:86 , LYS C:91 , HOH C:3176	BINDING SITE FOR RESIDUE DUT C 3170
8	AC8	SOFTWARE	SER A:74 , ILE A:75 , SER B:74 , ILE B:75 , VAL B:76 , SER C:74 , ILE C:75 , VAL C:76	BINDING SITE FOR RESIDUE TRS B 3172

(no "SS Bond" information available for 1SM8)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:78	-	Pro A:79
2	Ser B:78	-	Pro B:79
3	Ser C:78	-	Pro C:79

(no "SAP(SNP)/Variant" information available for 1SM8)

(no "PROSITE Motif" information available for 1SM8)

(no "Exon" information available for 1SM8)

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:131
 aligned with DUT_MYCTO | P9WNS4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:131
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 
            DUT_MYCTO     2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDE 132
               SCOP domains d1sm8a_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                               SCOP domains
               CATH domains 1sm8A00 A:2-132  [code=2.70.40.10, no name defined]                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.................eeeee....eee....eeeee...ee.....eeeeee.hhhhhhhhheee....eee........eeeeee......eee....eeeeeeeee....eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sm8 A   2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDE 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain A from PDB  Type:PROTEIN  Length:131
 aligned with DUT_MYCTU | P9WNS5 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:131
                                    11        21        31        41        51        61        71        81        91       101       111       121       131 
            DUT_MYCTU     2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDE 132
               SCOP domains d1sm8a_ A: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                               SCOP domains
               CATH domains 1sm8A00 A:2-132  [code=2.70.40.10, no name defined]                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.................eeeee....eee....eeeee...ee.....eeeeee.hhhhhhhhheee....eee........eeeeee......eee....eeeeeeeee....eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sm8 A   2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDE 132
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with DUT_MYCTO | P9WNS4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:137
                             1                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       
            DUT_MYCTO     - -MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLA 136
               SCOP domains d1sm8b_ B: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                     SCOP domains
               CATH domains 1sm8B00 B:0-136  [code=2.70.40.10, no name defined]                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eee......eeeeeeee......eee....eeeeeeeee....eeee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sm8 B   0 HMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLA 136
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with DUT_MYCTU | P9WNS5 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:137
                             1                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       
            DUT_MYCTU     - -MSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLA 136
               SCOP domains d1sm8b_ B: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                                     SCOP domains
               CATH domains 1sm8B00 B:0-136  [code=2.70.40.10, no name defined]                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..................eeee....eee....eeeeeeeeeee....eeeeee.hhhhhhhhheee....eee......eeeeeeee......eee....eeeeeeeee....eeee..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sm8 B   0 HMSTTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSFDEAGLA 136
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with DUT_MYCTO | P9WNS4 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
            DUT_MYCTO     2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSF 130
               SCOP domains d1sm8c_ C: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                             SCOP domains
               CATH domains 1sm8C00 C:2-130  [code=2.70.40.10, no name defined]                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..................eeee....eee....eeeee...ee.....eeeeee.hhhhhhhh.eee....eee........eeeeee......eee....eeeeeeeee....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sm8 C   2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSF 130
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain C from PDB  Type:PROTEIN  Length:129
 aligned with DUT_MYCTU | P9WNS5 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
            DUT_MYCTU     2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSF 130
               SCOP domains d1sm8c_ C: Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase)                                                             SCOP domains
               CATH domains 1sm8C00 C:2-130  [code=2.70.40.10, no name defined]                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..................eeee....eee....eeeee...ee.....eeeeee.hhhhhhhh.eee....eee........eeeeee......eee....eeeeeeeee....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sm8 C   2 STTLAIVRLDPGLPLPSRAHDGDAGVDLYSAEDVELAPGRRALVRTGVAVAVPFGMVGLVHPRSGLATRVGLSIVNSPGTIDAGYRGEIKVALINLDPAAPIVVHRGDRIAQLLVQRVELVELVEVSSF 130
                                    11        21        31        41        51        61        71        81        91       101       111       121

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)

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

1a	d1sm8a_	A:
1b	d1sm8b_	B:
1c	d1sm8c_	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)

Mycobacterium tuberculosis. Organism_taxid: 1773. (8)

1a	1sm8A00	A:2-132
1b	1sm8C00	C:2-130
1c	1sm8B00	B:0-136

(no "Pfam Domain" information available for 1SM8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (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,B,C (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/Biological Unit
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		Ser C:78 - Pro C:79	[ RasMol ]

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	1sm8
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1mq7	M. TUBERCULOSIS DUTPASE UNLIGANDED
1six	M. TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND ALPHA, BETA-IMIDO-DUTP
1sjn	M. TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND ALPHA, BETA-IMIDO-DUTP
1slh	M. TUBERCULOSIS DUTPASE COMPLEXED WITH MAGNESIUM AND DUDP
1smc	M. TUBERCULOSIS DUTPASE COMPLEXED WITH DUTP IN THE ABSENCE OF METAL IONS RELATED ID: RV2697C RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (0, 0)

Gene Ontology (11, 19)

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