2W35 - JenaLib

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Title :   STRUCTURES OF ENDONUCLEASE V WITH DNA REVEAL INITIATION OF DEAMINATED ADENINE REPAIR

Authors :   B. Dalhus, A. S. Arvai, I. Rosnes, O. E. Olsen, P. H. Backe, I. Alseth, H. Gao, W. Cao, J. A. Tainer, M. Bjoras

Date :   06 Nov 08 (Deposition) - 20 Jan 09 (Release) - 21 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

Chains :   Asym. Unit : A,B,C,D,F,G
Biol. Unit 1: A,C,D  (2x)
Biol. Unit 2: B,F,G  (2x)
Biol. Unit 3: A  (1x)
Biol. Unit 4: B  (1x)
Biol. Unit 5: C  (1x)
Biol. Unit 6: D  (1x)
Biol. Unit 7: F  (1x)
Biol. Unit 8: G  (1x)

Keywords :   Hypoxanthine, Endonuclease, Endonucleasev, Hydrolase, Inosine, Dna Damage, Dna Repair (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Dalhus, A. S. Arvai, I. Rosnes, O. E. Olsen, P. H. Backe, I. Alseth, H. Gao, W. Cao, J. A. Tainer, M. Bjoras
Structures Of Endonuclease V With Dna Reveal Initiation Of Deaminated Adenine Repair.
Nat. Struct. Mol. Biol. V. 16 138 2009
PubMed-ID: 19136958 | Reference-DOI: 10.1038/NSMB.1538

Molecule 1 - ENDONUCLEASE V
	Chains	:	A, B
	EC Number	:	3.1.21.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)RIL
	Expression System Taxid	:	469008
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	DEOXYINOSINE 3'ENDONUCLEASE, DEOXYRIBONUCLEASE V, DNASE V

*Molecule 2 - 5'-D(APTPGPCPGPAPCPIPGP)-3'**
	Chains	:	C, F
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - 5'-D(APGPCPCPGPTP)-3'*
	Chains	:	D, G
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	F	G
Biological Unit 1 (2x)	:	A		C	D
Biological Unit 2 (2x)	:		B			F	G
Biological Unit 3 (1x)	:	A
Biological Unit 4 (1x)	:		B
Biological Unit 5 (1x)	:			C
Biological Unit 6 (1x)	:				D
Biological Unit 7 (1x)	:					F
Biological Unit 8 (1x)	:						G

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 7 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 8 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:43 , ASP A:110 , HOH A:2024 , DG C:9 , HOH C:2007 , HOH C:2009	BINDING SITE FOR RESIDUE MG A1224
2	AC2	SOFTWARE	ASP B:43 , ASP B:110 , HOH B:2041 , DG F:9 , HOH F:2004 , HOH F:2005	BINDING SITE FOR RESIDUE MG B1224

(no "SS Bond" information available for 2W35)

Asymmetric Unit

No.	Residues
1	Tyr A:61	-	Pro A:62
2	Tyr B:61	-	Pro B:62

(no "SAP(SNP)/Variant" information available for 2W35)

(no "PROSITE Motif" information available for 2W35)

(no "Exon" information available for 2W35)

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:224
 aligned with NFI_THEMA | Q9X2H9 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
            NFI_THEMA     1 MDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLYGTFKMPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLMDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLKKGL 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh..........eeeeeeeeeee..eeeeeeeeee....eeeeeeeeeee........hhhhhhhhhhhhhhh.......eeee...........hhhhhhhhhhh..eeeee.................eeeeee..eeeeeee........eeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w35 A   1 MDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLYGTFKMPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLMDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLKKGL 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with NFI_THEMA | Q9X2H9 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
            NFI_THEMA     1 MDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLYGTFKMPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLMDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLKKGL 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------Endonuclease_5-2w35B01 B:19-217                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) ------------------Endonuclease_5-2w35B02 B:19-217                                                                                                                                                                        ------- Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhhhhhh..........eeeeeeeeeee..eeeeeeeeee....eeeeeeeeeee.........hhhhhhhhhhhhhh.......eeeee..........hhhhhhhhhhh..eeeee.................eeeeee..eeeeeee........eeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w35 B   1 MDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVDLSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLYGTFKMPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLMDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLKKGL 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:DNA  Length:4
                                    
                 2w35 C   6 ACIG   9

Chain D from PDB  Type:DNA  Length:4
                                    
                 2w35 D  10 AGCC  13

Chain F from PDB  Type:DNA  Length:7
                                       
                 2w35 F   3 GCGACIG   9

Chain G from PDB  Type:DNA  Length:6
                                      
                 2w35 G  10 AGCCGT  15

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 '\|'

(no "SCOP Domain" information available for 2W35)

(no "CATH Domain" information available for 2W35)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Endonuclease (8)

Family: Endonuclease_5 (2)

Thermotoga maritima (2)

1a	Endonuclease_5-2w35B01	B:19-217
1b	Endonuclease_5-2w35B02	B:19-217

Asymmetric Unit(hide GO term definitions)

Chain A,B (NFI_THEMA | Q9X2H9)

molecular function
	GO:0043737	deoxyribonuclease V activity	Catalysis of the endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	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:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
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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		Tyr A:61 - Pro A:62	[ RasMol ]
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	NFI_THEMA \| Q9X2H9	:	2w36 3hd0 4b20

2w36	STRUCTURES OF ENDONUCLEASE V WITH DNA REVEAL INITIATION OF DEAMINATED ADENINE REPAIR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (10, 10)

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