3Q93 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN 8-OXO-DGTPASE (MTH1)

Authors :   L. Tresaugues, M. I. Siponen, C. H. Arrowsmith, H. Berglund, C. Bountra R. Collins, A. M. Edwards, T. Ekblad, S. Flodin, A. Flores, S. Graslund M. Hammarstrom, I. Johansson, T. Karlberg, S. Kol, T. Kotenyova, E. Kouznetsova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, A. G. Thorsell, S. Van Der Berg, E. Wahlberg, J. Weigelt, M. Welin, P. Structural Genomics Consortium (Sgc)

Date :   07 Jan 11 (Deposition) - 02 Mar 11 (Release) - 02 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Structural Genomics, Structural Genomics Consortium, Sgc, Nudix, Mutt-Like, Hydrolase, Magnesium Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Tresaugues, M. I. Siponen, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, T. Ekblad, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Johansson, T. Karlberg, S. Kol, T. Kotenyova, E. Kouznetsova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, A. G. Thorsell, S. Van Der Berg, E. Wahlberg, J. Weigelt, M. Welin, P. Nordlund
Crystal Structure Of Human 8-Oxo-Dgtpase (Mth1)
To Be Published
PubMed: search

Molecule 1 - 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 (DE3) R3 PRARE
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MTH1, NUDT1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	8-OXO-DGTPASE, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 1, NUDIX MOTIF 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	IMD	1	Ligand/Ion	IMIDAZOLE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	IMD	1	Ligand/Ion	IMIDAZOLE
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	IMD	-1	Ligand/Ion	IMIDAZOLE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:63 , HIS A:65 , THR A:88 , ASP A:89 , SER A:90 , HOH A:233 , HOH A:301	BINDING SITE FOR RESIDUE SO4 A 157
2	AC2	SOFTWARE	HIS A:65 , LYS A:66 , HOH A:238	BINDING SITE FOR RESIDUE SO4 A 158
3	AC3	SOFTWARE	ARG A:17 , TRP A:105 , HOH A:276 , LYS B:132	BINDING SITE FOR RESIDUE SO4 A 159
4	AC4	SOFTWARE	ASN A:33 , PHE A:72 , TRP A:117 , ASP A:119 , HOH A:191 , HOH A:277	BINDING SITE FOR RESIDUE IMD A 160
5	AC5	SOFTWARE	LYS A:23 , LYS A:24 , GLY A:30 , HOH A:181 , HOH A:240 , HOH A:245 , HOH A:288 , HOH A:298	BINDING SITE FOR RESIDUE GOL A 161
6	AC6	SOFTWARE	LYS A:24 , GLU A:97 , TYR A:136 , LYS A:138 , ASP A:147 , TYR B:122 , TYR B:148	BINDING SITE FOR RESIDUE GOL A 162
7	AC7	SOFTWARE	HOH A:225 , HIS B:134 , ARG B:151 , HOH B:214	BINDING SITE FOR RESIDUE SO4 B 157
8	AC8	SOFTWARE	HOH A:302 , ARG B:151 , VAL B:153 , ASP B:154 , THR B:155 , HOH B:166	BINDING SITE FOR RESIDUE SO4 B 158

(no "SS Bond" information available for 3Q93)

(no "Cis Peptide Bond" information available for 3Q93)

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068715	G	77	W	8ODP_HUMAN	Polymorphism	11547459	A/B	G	36	W
2	UniProt	VAR_013757	V	124	M	8ODP_HUMAN	Polymorphism	4866	A/B	V	83	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068715	G	77	W	8ODP_HUMAN	Polymorphism	11547459	A	G	36	W
2	UniProt	VAR_013757	V	124	M	8ODP_HUMAN	Polymorphism	4866	A	V	83	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_068715	G	77	W	8ODP_HUMAN	Polymorphism	11547459	B	G	36	W
2	UniProt	VAR_013757	V	124	M	8ODP_HUMAN	Polymorphism	4866	B	V	83	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	8ODP_HUMAN	44-173	2	A:3-132 B:3-132
2	NUDIX_BOX	PS00893	Nudix box signature.	8ODP_HUMAN	78-99	2	A:37-58 B:37-58

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	8ODP_HUMAN	44-173	1	A:3-132 -
2	NUDIX_BOX	PS00893	Nudix box signature.	8ODP_HUMAN	78-99	1	A:37-58 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	8ODP_HUMAN	44-173	1	- B:3-132
2	NUDIX_BOX	PS00893	Nudix box signature.	8ODP_HUMAN	78-99	1	- B:37-58

(no "Exon" information available for 3Q93)

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:154
 aligned with 8ODP_HUMAN | P36639 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:154
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    
           8ODP_HUMAN    44 ASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV 197
               SCOP domains d3q93a_ A: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................................hhhhhhhhhhhhhhh.....................................................hhhhhhhhhhhhhhhhhh........................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------W----------------------------------------------M------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NUDIX  PDB: A:3-132 UniProt: 44-173                                                                                               ------------------------ PROSITE (1)
                PROSITE (2) ----------------------------------NUDIX_BOX  PDB: A:37-5-------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q93 A   3 ASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV 156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with 8ODP_HUMAN | P36639 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:154
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    
           8ODP_HUMAN    44 ASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV 197
               SCOP domains d3q93b_ B: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -NUDIX-3q93B01 B:4-130                                                                                                          -------------------------- Pfam domains (1)
           Pfam domains (2) -NUDIX-3q93B02 B:4-130                                                                                                          -------------------------- Pfam domains (2)
         Sec.struct. author .........................................hhhhhhhhhhhhhhh..................................................hhhhhhhhhhhhhhhhhhhhh........................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------W----------------------------------------------M------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) NUDIX  PDB: B:3-132 UniProt: 44-173                                                                                               ------------------------ PROSITE (1)
                PROSITE (2) ----------------------------------NUDIX_BOX  PDB: B:37-5-------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q93 B   3 ASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV 156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Nudix (141)

Superfamily: Nudix (141)

Family: MutT-like (82)

Protein domain: automated matches (16)

Human (Homo sapiens) [TaxId: 9606] (9)

1a	d3q93a_	A:
1b	d3q93b_	B:

(no "CATH Domain" information available for 3Q93)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Homo sapiens (Human) (12)

1a	NUDIX-3q93B01	B:4-130
1b	NUDIX-3q93B02	B:4-130

Asymmetric Unit(hide GO term definitions)

Chain A,B (8ODP_HUMAN | P36639)

molecular function
	GO:0044714	2-hydroxy-(deoxy)adenosine-triphosphate pyrophosphatase activity	Catalysis of the reaction: 2-hydroxy-(deoxy)adenosine-triphosphate + H2O = 2-hydroxy-(deoxy)adenosine phosphate + diphosphate.
	GO:0044713	2-hydroxy-adenosine triphosphate pyrophosphatase activity	Catalysis of the reaction: 2-hydroxy-adenosine-triphosphate + H2O = 2-hydroxy-adenosine phosphate + diphosphate.
	GO:0035539	8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity	Catalysis of the reaction: 8-oxo-7,8-dihydrodeoxyguanosine-triphosphate + H2O = 8-oxo-7,8-dihydrodeoxyguanosine phosphate + diphosphate. 8-oxo-7,8-dihydrodeoxyguanosine-triphosphate, or 8-oxo-dGTP, is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for DNA synthesis causing transversion mutations. 8-oxo-dGTPase hydrolyses 8-oxo-dGTP to its monophosphate form to prevent the misincorporation of 8-oxo-dGTP into cellular DNA.
	GO:0008413	8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity	Catalysis of the reaction: 8-oxo-7,8-dihydroguanosine triphosphate = 8-oxo-7,8-dihydroguanosine phosphate + diphosphate. 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for transcription.
	GO:0047693	ATP diphosphatase activity	Catalysis of the reaction: ATP + H2O = AMP + diphosphate.
	GO:0036219	GTP diphosphatase activity	Catalysis of the reaction: GTP + H2O = GMP + diphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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:0050072	m7G(5')pppN diphosphatase activity	Catalysis of the reaction: 7-methylguanosine 5'-triphospho-5'-polynucleotide + H2O = 7-methylguanosine 5'-phosphate + polynucleotide.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0030515	snoRNA binding	Interacting selectively and non-covalently with small nucleolar RNA.
biological process
	GO:0042262	DNA protection	Any process in which DNA is protected from damage by, for example, oxidative stress.
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0046061	dATP catabolic process	The chemical reactions and pathways resulting in the breakdown of dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate).
	GO:0006203	dGTP catabolic process	The chemical reactions and pathways resulting in the breakdown of dGTP, guanosine triphosphate.
	GO:0034656	nucleobase-containing small molecule catabolic process	The chemical reactions and pathways resulting in the breakdown of a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
	GO:0006195	purine nucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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	3q93
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(no "Related Entries Specified in the PDB File" available for 3Q93)

Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

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