2QXX - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   BIFUNCTIONAL DCTP DEAMINASE: DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH DTTP

Authors :   S. Christophersen, P. Harris, M. Willemoes

Date :   13 Aug 07 (Deposition) - 19 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Distorted Beta Barrel, Hydrolase, Nucleotide Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. S. Helt, M. Thymark, P. Harris, C. Aagaard, J. Dietrich, S. Larsen, M. Willemoes
Mechanism Of Dttp Inhibition Of The Bifunctional Dctp Deaminase:Dutpase Encoded By Mycobacterium Tuberculosis.
J. Mol. Biol. V. 376 554 2008
PubMed-ID: 18164314 | Reference-DOI: 10.1016/J.JMB.2007.11.099

Molecule 1 - DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
	Chains	:	A, B
	EC Number	:	3.5.4.13
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PTBDCD7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET11A
	Gene	:	DCD
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	DCTP DEAMINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	1PE	3	Ligand/Ion	PENTAETHYLENE GLYCOL
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	TTP	2	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	1PE	3	Ligand/Ion	PENTAETHYLENE GLYCOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TTP	3	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	1PE	6	Ligand/Ion	PENTAETHYLENE GLYCOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TTP	3	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TTP A:201 , HOH A:237 , HOH A:239 , HOH A:265	BINDING SITE FOR RESIDUE MG A 202
2	AC2	SOFTWARE	TTP B:201 , HOH B:229 , HOH B:247 , HOH B:268	BINDING SITE FOR RESIDUE MG B 202
3	AC3	SOFTWARE	LYS A:101 , SER A:102 , SER A:103 , ARG A:106 , ALA A:115 , GLY A:116 , PHE A:117 , ILE A:118 , ASP A:119 , ILE A:126 , THR A:127 , GLN A:148 , TYR A:162 , SER A:169 , LYS A:170 , TYR A:171 , GLN A:174 , MG A:202 , HOH A:233 , HOH A:237 , HOH A:239 , HOH A:240 , HOH A:243 , HOH A:265 , HOH A:288	BINDING SITE FOR RESIDUE TTP A 201
4	AC4	SOFTWARE	ARG A:47 , TYR A:48 , THR A:49 , GLN A:57	BINDING SITE FOR RESIDUE 1PE A 203
5	AC5	SOFTWARE	LYS B:101 , SER B:102 , SER B:103 , ARG B:106 , ALA B:115 , GLY B:116 , PHE B:117 , ASP B:119 , ILE B:126 , THR B:127 , GLN B:148 , TYR B:162 , SER B:169 , LYS B:170 , TYR B:171 , GLN B:174 , MG B:202 , HOH B:228 , HOH B:229 , HOH B:234 , HOH B:235 , HOH B:237 , HOH B:247 , HOH B:268 , HOH B:279	BINDING SITE FOR RESIDUE TTP B 201
6	AC6	SOFTWARE	GLY B:15 , ARG B:16 , THR B:89	BINDING SITE FOR RESIDUE 1PE B 203
7	AC7	SOFTWARE	ARG B:47 , TYR B:48 , THR B:49 , GLN B:57 , SER B:165	BINDING SITE FOR RESIDUE 1PE B 204

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

Asymmetric Unit

No.	Residues
1	Asp A:20	-	Pro A:21
2	Asp B:20	-	Pro B:21

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

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

(no "Exon" information available for 2QXX)

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:189
 aligned with DCD_MYCTO | P9WP16 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
            DCD_MYCTO     1 MLLSDRDLRAEISSGRLGIDPFDDTLVQPSSIDVRLDCLFRVFNNTRYTHIDPAKQQDELTSLVQPVDGEPFVLHPGEFVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTHSTAGFIDPGFSGHITLELSNVANLPITLWPGMKIGQLCMLRLTSPSEHPYGSSRAGSKYQGQRGPTPSRSYQNFIRS 189
               SCOP domains d2qxxa_ A: Deoxycytidine triphosphate deaminase (dCTP deaminase)                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eee..hhh.ee..eeeee....eee..............hhhhheee.......eee....eeeee...eee....eeeeee.hhhhhh..eee.....ee....ee..eeeeee.....eee....eeeeeeeee.................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qxx A   1 MLLSDRDLRAEISSGRLGIDPFDDTLVQPSSIDVRLDCLFRVFNNTRYTHIDPAKQQDELTSLVQPVDGEPFVLHPGEFVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTHSTAGFIDPGFSGHITLELSNVANLPITLWPGMKIGQLCMLRLTSPSEHPYGSSRAGSKYQGQRGPTPSRSYQNFIRS 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain A from PDB  Type:PROTEIN  Length:189
 aligned with DCD_MYCTU | P9WP17 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
            DCD_MYCTU     1 MLLSDRDLRAEISSGRLGIDPFDDTLVQPSSIDVRLDCLFRVFNNTRYTHIDPAKQQDELTSLVQPVDGEPFVLHPGEFVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTHSTAGFIDPGFSGHITLELSNVANLPITLWPGMKIGQLCMLRLTSPSEHPYGSSRAGSKYQGQRGPTPSRSYQNFIRS 189
               SCOP domains d2qxxa_ A: Deoxycytidine triphosphate deaminase (dCTP deaminase)                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eee..hhh.ee..eeeee....eee..............hhhhheee.......eee....eeeee...eee....eeeeee.hhhhhh..eee.....ee....ee..eeeeee.....eee....eeeeeeeee.................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qxx A   1 MLLSDRDLRAEISSGRLGIDPFDDTLVQPSSIDVRLDCLFRVFNNTRYTHIDPAKQQDELTSLVQPVDGEPFVLHPGEFVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTHSTAGFIDPGFSGHITLELSNVANLPITLWPGMKIGQLCMLRLTSPSEHPYGSSRAGSKYQGQRGPTPSRSYQNFIRS 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:189
 aligned with DCD_MYCTO | P9WP16 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
            DCD_MYCTO     1 MLLSDRDLRAEISSGRLGIDPFDDTLVQPSSIDVRLDCLFRVFNNTRYTHIDPAKQQDELTSLVQPVDGEPFVLHPGEFVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTHSTAGFIDPGFSGHITLELSNVANLPITLWPGMKIGQLCMLRLTSPSEHPYGSSRAGSKYQGQRGPTPSRSYQNFIRS 189
               SCOP domains d2qxxb_ B: Deoxycytidine triphosphate deaminase (dCTP deaminase)                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------dUTPase-2qxxB01 B:52-181                                                                                                          -------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------dUTPase-2qxxB02 B:52-181                                                                                                          -------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhh...eee..hhh.ee..eeeee....eee..............hhhhheee.......eee....eeeee...eee....eeeeee.hhhhhh..eee.....ee....ee..eeeeee.....eee....eeeeeeeee.................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qxx B   1 MLLSDRDLRAEISSGRLGIDPFDDTLVQPSSIDVRLDCLFRVFNNTRYTHIDPAKQQDELTSLVQPVDGEPFVLHPGEFVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTHSTAGFIDPGFSGHITLELSNVANLPITLWPGMKIGQLCMLRLTSPSEHPYGSSRAGSKYQGQRGPTPSRSYQNFIRS 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:189
 aligned with DCD_MYCTU | P9WP17 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
            DCD_MYCTU     1 MLLSDRDLRAEISSGRLGIDPFDDTLVQPSSIDVRLDCLFRVFNNTRYTHIDPAKQQDELTSLVQPVDGEPFVLHPGEFVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTHSTAGFIDPGFSGHITLELSNVANLPITLWPGMKIGQLCMLRLTSPSEHPYGSSRAGSKYQGQRGPTPSRSYQNFIRS 189
               SCOP domains d2qxxb_ B: Deoxycytidine triphosphate deaminase (dCTP deaminase)                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------dUTPase-2qxxB01 B:52-181                                                                                                          -------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------dUTPase-2qxxB02 B:52-181                                                                                                          -------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhh...eee..hhh.ee..eeeee....eee..............hhhhheee.......eee....eeeee...eee....eeeeee.hhhhhh..eee.....ee....ee..eeeeee.....eee....eeeeeeeee.................................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qxx B   1 MLLSDRDLRAEISSGRLGIDPFDDTLVQPSSIDVRLDCLFRVFNNTRYTHIDPAKQQDELTSLVQPVDGEPFVLHPGEFVLGSTLELFTLPDNLAGRLEGKSSLGRLGLLTHSTAGFIDPGFSGHITLELSNVANLPITLWPGMKIGQLCMLRLTSPSEHPYGSSRAGSKYQGQRGPTPSRSYQNFIRS 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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: Deoxycytidine triphosphate deaminase (dCTP deaminase) (9)

Mycobacterium tuberculosis [TaxId: 83332] (3)

1a	d2qxxa_	A:
1b	d2qxxb_	B:

(no "CATH Domain" information available for 2QXX)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: dUTPase (38)

Family: dUTPase (38)

Mycobacterium tuberculosis (9)

1a	dUTPase-2qxxB01	B:52-181
1b	dUTPase-2qxxB02	B:52-181

Asymmetric Unit(hide GO term definitions)

Chain A,B (DCD_MYCTO | P9WP16)

molecular function
	GO:0008829	dCTP deaminase activity	Catalysis of the reaction: dCTP + H2O = dUTP + NH3.
	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:0006226	dUMP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
	GO:0006229	dUTP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUTP, deoxyuridine (5'-)triphosphate.
	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:0009220	pyrimidine ribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

Chain A,B (DCD_MYCTU | P9WP17)

molecular function
	GO:0033973	dCTP deaminase (dUMP-forming) activity	Catalysis of the reaction: dCTP + 2 H(2)O = diphosphate + dUMP + H(+) + NH(4)(+).
	GO:0008829	dCTP deaminase activity	Catalysis of the reaction: dCTP + H2O = dUTP + NH3.
	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:0006226	dUMP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
	GO:0006229	dUTP biosynthetic process	The chemical reactions and pathways resulting in the formation of dUTP, deoxyuridine (5'-)triphosphate.
	GO:0046080	dUTP metabolic process	The chemical reactions and pathways involving dUTP, deoxyuridine (5'-)triphosphate.
	GO:0015949	nucleobase-containing small molecule interconversion	The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
	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:0009220	pyrimidine ribonucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a 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.

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	Cis Peptide Bonds
		Asp A:20 - Pro A:21	[ RasMol ]
		Asp B:20 - Pro B:21	[ RasMol ]

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	DCD_MYCTO \| P9WP16	:	2qlp 4a6a
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2qlp	BIFUNCTIONAL DCTP DEAMINASE:DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS, APO FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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SCOP Domains (1, 2)

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