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PDBsum entry 1diz

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protein dna_rna metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
1diz
Jmol
Contents
Protein chains
282 a.a. *
DNA/RNA
Metals
_NA ×2
Waters ×207
* Residue conservation analysis
PDB id:
1diz
Name: Hydrolase/DNA
Title: Crystal structure of e. Coli 3-methyladenine DNA glycosylase (alka) complexed with DNA
Structure: DNA (5'-d( Gp Ap Cp Ap Tp Gp Ap (Nri) p Tp Gp Cp Cp T)-3'). Chain: c, e. Engineered: yes. DNA (5'- d( Gp Gp Cp Ap Ap Tp Cp Ap Tp Gp Tp Cp A)-3'). Chain: d, f. Engineered: yes. 3-methyladenine DNA glycosylase ii.
Source: Synthetic: yes. Other_details: this sequence occurs naturally in e. Coli. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PQS)
Resolution:
2.50Å     R-factor:   0.250     R-free:   0.290
Authors: T.Hollis,Y.Ichikawa,T.E.Ellenberger
Key ref:
T.Hollis et al. (2000). DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA. EMBO J, 19, 758-766. PubMed id: 10675345 DOI: 10.1093/emboj/19.4.758
Date:
30-Nov-99     Release date:   20-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04395  (3MG2_ECOLI) -  DNA-3-methyladenine glycosylase 2
Seq:
Struc:
282 a.a.
282 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.2.21  - DNA-3-methyladenine glycosylase Ii.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine, and 7-methyladenine.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to DNA damage stimulus   4 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
DOI no: 10.1093/emboj/19.4.758 EMBO J 19:758-766 (2000)
PubMed id: 10675345  
 
 
DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
T.Hollis, Y.Ichikawa, T.Ellenberger.
 
  ABSTRACT  
 
The Escherichia coli AlkA protein is a base excision repair glycosylase that removes a variety of alkylated bases from DNA. The 2.5 A crystal structure of AlkA complexed to DNA shows a large distortion in the bound DNA. The enzyme flips a 1-azaribose abasic nucleotide out of DNA and induces a 66 degrees bend in the DNA with a marked widening of the minor groove. The position of the 1-azaribose in the enzyme active site suggests an S(N)1-type mechanism for the glycosylase reaction, in which the essential catalytic Asp238 provides direct assistance for base removal. Catalytic selectivity might result from the enhanced stacking of positively charged, alkylated bases against the aromatic side chain of Trp272 in conjunction with the relative ease of cleaving the weakened glycosylic bond of these modified nucleotides. The structure of the AlkA-DNA complex offers the first glimpse of a helix-hairpin-helix (HhH) glycosylase complexed to DNA. Modeling studies suggest that other HhH glycosylases can bind to DNA in a similar manner.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 A 3-methyladenine substrate modeled in AlkA's active site. 3-methyladenine (pink) was superimposed on the 1-azaribose moiety in the crystal structure of the AlkA–DNA complex. In the resulting model, the 3-methyladenine base stacks face-to-face against Trp272 and makes edge-on contacts with Tyr222. The open architecture of AlkA's substrate-binding pocket would accommodate many types of modified bases. Trp218 is located behind the ribose of the flipped out nucleotide, leaving no room for a water nucleophile (cf. Figure 6).
Figure 6.
Figure 6 Mechanistic implications of the AlkA active site. The closely interacting van der Waals surfaces of the protein (green) and the DNA (yellow) leave no room between the deoxyribose of a flipped out nucleotide and Trp218 to position a water molecule (red) for an attack on the back of the glycosylic bond. This is strong evidence against a direct displacement (S[N]2) mechanism of glycosylic bond cleavage (see text for details).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 758-766) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22659876 C.Yi, B.Chen, B.Qi, W.Zhang, G.Jia, L.Zhang, C.J.Li, A.R.Dinner, C.G.Yang, and C.He (2012).
Duplex interrogation by a direct DNA repair protein in search of base damage.
  Nat Struct Mol Biol, 19, 671-676.
PDB codes: 3rzg 3rzh 3rzj 3rzk 3rzl 3rzm 3s57 3s5a
21267490 A.Ebrahimi, M.Habibi-Khorassani, and S.Bazzi (2011).
The impact of protonation and deprotonation of 3-methyl-2'-deoxyadenosine on N-glycosidic bond cleavage.
  Phys Chem Chem Phys, 13, 3334-3343.  
21036872 M.I.Ponferrada-Marín, J.T.Parrilla-Doblas, T.Roldán-Arjona, and R.R.Ariza (2011).
A discontinuous DNA glycosylase domain in a family of enzymes that excise 5-methylcytosine.
  Nucleic Acids Res, 39, 1473-1484.  
20005182 I.D.Odell, K.Newick, N.H.Heintz, S.S.Wallace, and D.S.Pederson (2010).
Non-specific DNA binding interferes with the efficient excision of oxidative lesions from chromatin by the human DNA glycosylase, NEIL1.
  DNA Repair (Amst), 9, 134-143.  
19446526 F.Faucher, S.Duclos, V.Bandaru, S.S.Wallace, and S.Doublié (2009).
Crystal structures of two archaeal 8-oxoguanine DNA glycosylases provide structural insight into guanine/8-oxoguanine distinction.
  Structure, 17, 703-712.
PDB codes: 3fhf 3fhg
19361427 F.Faucher, S.M.Robey-Bond, S.S.Wallace, and S.Doublié (2009).
Structural characterization of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase in its apo form and in complex with 8-oxodeoxyguanosine.
  J Mol Biol, 387, 669-679.
PDB codes: 3f0z 3f10
19200715 S.Schneider, S.Schorr, and T.Carell (2009).
Crystal structure analysis of DNA lesion repair and tolerance mechanisms.
  Curr Opin Struct Biol, 19, 87-95.  
18682218 B.R.Bowman, S.Lee, S.Wang, and G.L.Verdine (2008).
Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA.
  Structure, 16, 1166-1174.
PDB codes: 3cvs 3cvt 3cw7 3cwa 3cws 3cwt 3cwu
18472311 G.M.Lingaraju, M.Kartalou, L.B.Meira, and L.D.Samson (2008).
Substrate specificity and sequence-dependent activity of the Saccharomyces cerevisiae 3-methyladenine DNA glycosylase (Mag).
  DNA Repair (Amst), 7, 970-982.  
18072751 J.C.Delaney, and J.M.Essigmann (2008).
Biological properties of single chemical-DNA adducts: a twenty year perspective.
  Chem Res Toxicol, 21, 232-252.  
18191596 Z.Y.Sun, K.J.Oh, M.Kim, J.Yu, V.Brusic, L.Song, Z.Qiao, J.H.Wang, G.Wagner, and E.L.Reinherz (2008).
HIV-1 broadly neutralizing antibody extracts its epitope from a kinked gp41 ectodomain region on the viral membrane.
  Immunity, 28, 52-63.
PDB code: 2pv6
17410210 A.H.Metz, T.Hollis, and B.F.Eichman (2007).
DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
  EMBO J, 26, 2411-2420.
PDB codes: 2ofi 2ofk
17395642 B.Dalhus, I.H.Helle, P.H.Backe, I.Alseth, T.Rognes, M.Bjørås, and J.K.Laerdahl (2007).
Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats.
  Nucleic Acids Res, 35, 2451-2459.  
17617640 G.Tamulaitis, M.Zaremba, R.H.Szczepanowski, M.Bochtler, and V.Siksnys (2007).
Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.
  Nucleic Acids Res, 35, 4792-4799.  
17396151 I.Leiros, M.P.Nabong, K.Grøsvik, J.Ringvoll, G.T.Haugland, L.Uldal, K.Reite, I.K.Olsbu, I.Knaevelsrud, E.Moe, O.A.Andersen, N.K.Birkeland, P.Ruoff, A.Klungland, and S.Bjelland (2007).
Structural basis for enzymatic excision of N1-methyladenine and N3-methylcytosine from DNA.
  EMBO J, 26, 2206-2217.
PDB codes: 2jhj 2jhn
17412704 J.Bischerour, and R.Chalmers (2007).
Base-flipping dynamics in a DNA hairpin processing reaction.
  Nucleic Acids Res, 35, 2584-2595.  
17485252 J.L.Tubbs, A.E.Pegg, and J.A.Tainer (2007).
DNA binding, nucleotide flipping, and the helix-turn-helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy.
  DNA Repair (Amst), 6, 1100-1115.  
17848989 L.T.Chen, T.P.Ko, Y.W.Chang, K.A.Lin, A.H.Wang, and T.F.Wang (2007).
Structural and functional analyses of five conserved positively charged residues in the L1 and N-terminal DNA binding motifs of archaeal RADA protein.
  PLoS ONE, 2, e858.
PDB code: 2z43
16395333 B.Taneja, A.Patel, A.Slesarev, and A.Mondragón (2006).
Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases.
  EMBO J, 25, 398-408.
PDB codes: 2csb 2csd
16155580 C.M.Bradley, D.R.Ronning, R.Ghirlando, R.Craigie, and F.Dyda (2005).
Structural basis for DNA bridging by barrier-to-autointegration factor.
  Nat Struct Mol Biol, 12, 935-936.
PDB code: 2bzf
15642264 G.M.Lingaraju, A.A.Sartori, D.Kostrewa, A.E.Prota, J.Jiricny, and F.K.Winkler (2005).
A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure.
  Structure, 13, 87-98.
PDB codes: 1xqo 1xqp
15456766 C.Y.Lee, H.Bai, R.Houle, G.M.Wilson, and A.L.Lu (2004).
An Escherichia coli MutY mutant without the six-helix barrel domain is a dimer in solution and assembles cooperatively into multisubunit complexes with DNA.
  J Biol Chem, 279, 52653-52663.  
15221026 D.S.Daniels, T.T.Woo, K.X.Luu, D.M.Noll, N.D.Clarke, A.E.Pegg, and J.A.Tainer (2004).
DNA binding and nucleotide flipping by the human DNA repair protein AGT.
  Nat Struct Mol Biol, 11, 714-720.
PDB codes: 1t38 1t39
14990576 H.J.Lee, H.M.Lim, and S.Adhya (2004).
An unsubstituted C2 hydrogen of adenine is critical and sufficient at the -11 position of a promoter to signal base pair deformation.
  J Biol Chem, 279, 16899-16902.  
15102448 J.C.Fromme, A.Banerjee, and G.L.Verdine (2004).
DNA glycosylase recognition and catalysis.
  Curr Opin Struct Biol, 14, 43-49.  
14961129 J.C.Fromme, A.Banerjee, S.J.Huang, and G.L.Verdine (2004).
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase.
  Nature, 427, 652-656.
PDB codes: 1rrq 1rrs 1rrt 1vrl
15494448 K.Hashiguchi, J.A.Stuart, N.C.de Souza-Pinto, and V.A.Bohr (2004).
The C-terminal alphaO helix of human Ogg1 is essential for 8-oxoguanine DNA glycosylase activity: the mitochondrial beta-Ogg1 lacks this domain and does not have glycosylase activity.
  Nucleic Acids Res, 32, 5596-5608.  
15178685 L.Larivière, and S.Moréra (2004).
Structural evidence of a passive base-flipping mechanism for beta-glucosyltransferase.
  J Biol Chem, 279, 34715-34720.
PDB codes: 1sxp 1sxq
15126496 P.J.O'Brien, and T.Ellenberger (2004).
The Escherichia coli 3-methyladenine DNA glycosylase AlkA has a remarkably versatile active site.
  J Biol Chem, 279, 26876-26884.  
15143064 R.A.Estabrook, R.Lipson, B.Hopkins, and N.Reich (2004).
The coupling of tight DNA binding and base flipping: identification of a conserved structural motif in base flipping enzymes.
  J Biol Chem, 279, 31419-31428.  
15326180 R.C.Manuel, K.Hitomi, A.S.Arvai, P.G.House, A.J.Kurtz, M.L.Dodson, A.K.McCullough, J.A.Tainer, and R.S.Lloyd (2004).
Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase.
  J Biol Chem, 279, 46930-46939.
PDB codes: 1wef 1weg 1wei
14769949 V.V.Koval, N.A.Kuznetsov, D.O.Zharkov, A.A.Ishchenko, K.T.Douglas, G.A.Nevinsky, and O.S.Fedorova (2004).
Pre-steady-state kinetics shows differences in processing of various DNA lesions by Escherichia coli formamidopyrimidine-DNA glycosylase.
  Nucleic Acids Res, 32, 926-935.  
14661275 A.David, N.Bleimling, C.Beuck, J.M.Lehn, E.Weinhold, and M.P.Teulade-Fichou (2003).
DNA mismatch-specific base flipping by a bisacridine macrocycle.
  Chembiochem, 4, 1326-1331.  
14517230 B.F.Eichman, E.J.O'Rourke, J.P.Radicella, and T.Ellenberger (2003).
Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases.
  EMBO J, 22, 4898-4909.
PDB codes: 1pu6 1pu7 1pu8
12600940 B.R.Szymczyna, J.Bowman, S.McCracken, A.Pineda-Lucena, Y.Lu, B.Cox, M.Lambermon, B.R.Graveley, C.H.Arrowsmith, and B.J.Blencowe (2003).
Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing.
  Genes Dev, 17, 461-475.
PDB code: 1mp1
13129925 C.Cao, K.Kwon, Y.L.Jiang, A.C.Drohat, and J.T.Stivers (2003).
Solution structure and base perturbation studies reveal a novel mode of alkylated base recognition by 3-methyladenine DNA glycosylase I.
  J Biol Chem, 278, 48012-48020.
PDB code: 1p7m
12601164 E.J.O'Rourke, C.Chevalier, A.V.Pinto, J.M.Thiberge, L.Ielpi, A.Labigne, and J.P.Radicella (2003).
Pathogen DNA as target for host-generated oxidative stress: role for repair of bacterial DNA damage in Helicobacter pylori colonization.
  Proc Natl Acad Sci U S A, 100, 2789-2794.  
12840008 J.C.Fromme, and G.L.Verdine (2003).
Structure of a trapped endonuclease III-DNA covalent intermediate.
  EMBO J, 22, 3461-3471.
PDB codes: 1orn 1orp 1p59
12592398 J.C.Fromme, S.D.Bruner, W.Yang, M.Karplus, and G.L.Verdine (2003).
Product-assisted catalysis in base-excision DNA repair.
  Nat Struct Biol, 10, 204-211.
PDB codes: 1hu0 1lwv 1lww 1lwy
12799430 L.Li, and A.L.Lu (2003).
The C-terminal domain of Escherichia coli MutY is involved in DNA binding and glycosylase activities.
  Nucleic Acids Res, 31, 3038-3049.  
12456671 P.Wu, C.Qiu, A.Sohail, X.Zhang, A.S.Bhagwat, and X.Cheng (2003).
Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4.
  J Biol Chem, 278, 5285-5291.
PDB code: 1ngn
12517755 R.W.Welford, I.Schlemminger, L.A.McNeill, K.S.Hewitson, and C.J.Schofield (2003).
The selectivity and inhibition of AlkB.
  J Biol Chem, 278, 10157-10161.  
12719419 T.Nakano, H.Terato, K.Asagoshi, A.Masaoka, M.Mukuta, Y.Ohyama, T.Suzuki, K.Makino, and H.Ide (2003).
DNA-protein cross-link formation mediated by oxanine. A novel genotoxic mechanism of nitric oxide-induced DNA damage.
  J Biol Chem, 278, 25264-25272.  
12161745 A.C.Drohat, K.Kwon, D.J.Krosky, and J.T.Stivers (2002).
3-Methyladenine DNA glycosylase I is an unexpected helix-hairpin-helix superfamily member.
  Nat Struct Biol, 9, 659-664.
PDB code: 1lmz
12057763 D.O.Zharkov, and A.P.Grollman (2002).
Combining structural and bioinformatics methods for the analysis of functionally important residues in DNA glycosylases.
  Free Radic Biol Med, 32, 1254-1263.  
11847126 D.O.Zharkov, G.Golan, R.Gilboa, A.S.Fernandes, S.E.Gerchman, J.H.Kycia, R.A.Rieger, A.P.Grollman, and G.Shoham (2002).
Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.
  EMBO J, 21, 789-800.
PDB codes: 1k3w 1k3x
12034838 E.E.Verhoeven, M.van Kesteren, J.J.Turner, G.A.van der Marel, J.H.van Boom, G.F.Moolenaar, and N.Goosen (2002).
The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system.
  Nucleic Acids Res, 30, 2492-2500.  
12434002 H.Terato, A.Masaoka, K.Asagoshi, A.Honsho, Y.Ohyama, T.Suzuki, M.Yamada, K.Makino, K.Yamamoto, and H.Ide (2002).
Novel repair activities of AlkA (3-methyladenine DNA glycosylase II) and endonuclease VIII for xanthine and oxanine, guanine lesions induced by nitric oxide and nitrous acid.
  Nucleic Acids Res, 30, 4975-4984.  
12198481 K.S.Yan, and M.M.Zhou (2002).
TAGging the target for damage control.
  Nat Struct Biol, 9, 638-640.  
12065399 L.Serre, K.Pereira de Jésus, S.Boiteux, C.Zelwer, and B.Castaing (2002).
Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.
  EMBO J, 21, 2854-2865.
PDB codes: 1kfv 7abc
11912217 R.Gilboa, D.O.Zharkov, G.Golan, A.S.Fernandes, S.E.Gerchman, E.Matz, J.H.Kycia, A.P.Grollman, and G.Shoham (2002).
Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA.
  J Biol Chem, 277, 19811-19816.
PDB code: 1k82
12000829 V.Starkuviene, and H.J.Fritz (2002).
A novel type of uracil-DNA glycosylase mediating repair of hydrolytic DNA damage in the extremely thermophilic eubacterium Thermus thermophilus.
  Nucleic Acids Res, 30, 2097-2102.  
11788726 Y.N.Fondufe-Mittendorf, C.Härer, W.Kramer, and H.J.Fritz (2002).
Two amino acid replacements change the substrate preference of DNA mismatch glycosylase Mig.MthI from T/G to A/G.
  Nucleic Acids Res, 30, 614-621.  
11170417 E.L.Rachofsky, E.Seibert, J.T.Stivers, R.Osman, and J.B.Ross (2001).
Conformation and dynamics of abasic sites in DNA investigated by time-resolved fluorescence of 2-aminopurine.
  Biochemistry, 40, 957-967.  
11160880 H.Yang, I.T.Phan, S.Fitz-Gibbon, M.K.Shivji, R.D.Wood, W.M.Clendenin, E.C.Hyman, and J.H.Miller (2001).
A thermostable endonuclease III homolog from the archaeon Pyrobaculum aerophilum.
  Nucleic Acids Res, 29, 604-613.  
11389598 K.S.Tanaka, X.Y.Chen, Y.Ichikawa, P.C.Tyler, R.H.Furneaux, and V.L.Schramm (2001).
Ricin A-chain inhibitors resembling the oxacarbenium ion transition state.
  Biochemistry, 40, 6845-6851.  
11223884 O.D.Schärer, and J.Jiricny (2001).
Recent progress in the biology, chemistry and structural biology of DNA glycosylases.
  Bioessays, 23, 270-281.  
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
11551943 Y.L.Jiang, K.Kwon, and J.T.Stivers (2001).
Turning On uracil-DNA glycosylase using a pyrene nucleotide switch.
  J Biol Chem, 276, 42347-42354.  
11087375 C.V.Privezentzev, M.Saparbaev, A.Sambandam, M.M.Greenberg, and J.Laval (2000).
AlkA protein is the third Escherichia coli DNA repair protein excising a ring fragmentation product of thymine.
  Biochemistry, 39, 14263-14268.  
12760026 K.P.Hopfner, S.S.Parikh, and J.A.Tainer (2000).
Envisioning the fourth dimension of the genetic code: the structural biology of macromolecular recognition and conformational switching in DNA repair.
  Cold Spring Harb Symp Quant Biol, 65, 113-126.  
10921868 M.Sugahara, T.Mikawa, T.Kumasaka, M.Yamamoto, R.Kato, K.Fukuyama, Y.Inoue, and S.Kuramitsu (2000).
Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8.
  EMBO J, 19, 3857-3869.
PDB code: 1ee8
12760025 S.D.Bruner, D.P.Norman, J.C.Fromme, and G.L.Verdine (2000).
Structural and mechanistic studies on repair of 8-oxoguanine in mammalian cells.
  Cold Spring Harb Symp Quant Biol, 65, 103-111.  
10924106 T.C.Umland, S.Q.Wei, R.Craigie, and D.R.Davies (2000).
Structural basis of DNA bridging by barrier-to-autointegration factor.
  Biochemistry, 39, 9130-9138.
PDB code: 1ci4
11040219 T.F.Mah, K.Kuznedelov, A.Mushegian, K.Severinov, and J.Greenblatt (2000).
The alpha subunit of E. coli RNA polymerase activates RNA binding by NusA.
  Genes Dev, 14, 2664-2675.  
11095667 X.Li, and A.L.Lu (2000).
Intact MutY and its catalytic domain differentially contact with A/8-oxoG-containing DNA.
  Nucleic Acids Res, 28, 4593-4603.  
10908318 X.Shao, and N.V.Grishin (2000).
Common fold in helix-hairpin-helix proteins.
  Nucleic Acids Res, 28, 2643-2650.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.