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(-) Description

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 :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (2x)
Biol. Unit 2:  B,E,F  (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:  E  (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

(-) Compounds

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
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: DEOXYINOSINE 3'ENDONUCLEASE, DEOXYRIBONUCLEASE V, DNASE V
 
Molecule 2 - 5'-D(*GP*CP*BRUP*AP*CP*IP*GP*AP*BRUP*CP*GP)-3'
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*AP*TP*CP*TP*GP*TP*AP*GP*CP)-3'
    Chains: D, F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): A CD  
Biological Unit 2 (2x):  B  EF
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):     E 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1BRU4Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1BRU4Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1BRU4Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1BRU-1Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1BRU-1Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1BRU2Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1BRU-1Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 7 (0, 0)
No.NameCountTypeFull Name
1BRU-1Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 8 (1, 2)
No.NameCountTypeFull Name
1BRU2Mod. Nucleotide5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 2W36)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W36)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W36)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W36)

(-) Exons   (0, 0)

(no "Exon" information available for 2W36)

(-) Sequences/Alignments

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.........hhhhhhhhhhhhhh.......eeeee..........hhhhhhhhhhh..eeeee.................eeeeee..eeeeeee........eeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w36 A   1 MDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVALSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLYGTFKMPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLMDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLKKGL 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_5-2w36B01 B:19-217                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) ------------------Endonuclease_5-2w36B02 B:19-217                                                                                                                                                                        ------- Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhhhhhh..........eeeeeeeeeee..eeeeeeeeee....eeeeeeeeeee.........hhhhhhhhhhhhhhhh.....eeeee..........hhhhhhhhhhh..eeeee................eeeeeee..eeeeeeee.......eeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w36 B   1 MDYRQLHRWDLPPEEAIKVQNELRKKIKLTPYEGEPEYVAGVALSFPGKEEGLAVIVVLEYPSFKILEVVSERGEITFPYIPGLLAFREGPLFLKAWEKLRTKPDVVVFDGQGLAHPRKLGIASHMGLFIEIPTIGVAKSRLYGTFKMPEDKRCSWSYLYDGEEIIGCVIRTKEGSAPIFVSPGHLMDVESSKRLIKAFTLPGRRIPEPTRLAHIYTQRLKKGL 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:11
                                           
                 2w36 C   1 GCuACIGAuCG  11
                              |     10 
                              3-BRU 9-BRU


Chain D from PDB  Type:DNA  Length:5
                                     
                 2w36 D  18 GTAGC  22


Chain E from PDB  Type:DNA  Length:11
                                           
                 2w36 E   1 GCuACIGAuCG  11
                              |     10 
                              3-BRU 9-BRU


Chain F from PDB  Type:DNA  Length:5
                                     
                 2w36 F  18 GTAGC  22
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2W36)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W36)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Endonuclease (8)

(-) Gene Ontology  (10, 10)

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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NFI_THEMA | Q9X2H9: 2w35 3hd0 4b20

(-) Related Entries Specified in the PDB File

2w35 STRUCTURES OF ENDONUCLEASE V WITH DNA REVEAL INITIATION OF DEAMINATED ADENINE REPAIR