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PDBsum entry 3bkz

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protein dna_rna ligands metals links
DNA repair,oxidoreductase/DNA PDB id
3bkz
Jmol
Contents
Protein chain
201 a.a. *
DNA/RNA
Ligands
AKG
Metals
_MN
Waters ×292
* Residue conservation analysis
PDB id:
3bkz
Name: DNA repair,oxidoreductase/DNA
Title: X-ray structure of e coli alkb crosslinked to dsdna in the a
Structure: Alpha-ketoglutarate-dependent dioxygenase alkb. Chain: a. Synonym: alkylated DNA repair protein alkb. Engineered: yes. Mutation: yes. DNA (5'- d( Dtp Dap Dgp Dgp Dtp Dap Dap Dcp Dap Dtp Dcp Dgp Dt)-3'). Chain: b. Engineered: yes.
Source: Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: alkb, aidd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic: yes
Resolution:
1.65Å     R-factor:   0.189     R-free:   0.212
Authors: C.Yi,C.-G.Yang,C.He
Key ref:
C.G.Yang et al. (2008). Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature, 452, 961-965. PubMed id: 18432238 DOI: 10.1038/nature06889
Date:
09-Dec-07     Release date:   22-Apr-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam  
P05050  (ALKB_ECOLI) -  Alpha-ketoglutarate-dependent dioxygenase AlkB
Seq:
Struc:
216 a.a.
201 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.14.11.33  - Dna oxidative demethylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA-base-CH3 + 2-oxoglutarate + O2 = DNA-base + formaldehyde + succinate + CO2
DNA-base-CH(3)
+
2-oxoglutarate
Bound ligand (Het Group name = AKG)
corresponds exactly
+ O(2)
= DNA-base
+ formaldehyde
+ succinate
+ CO(2)
      Cofactor: Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidative single-stranded DNA demethylation   9 terms 
  Biochemical function     oxidative RNA demethylase activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nature06889 Nature 452:961-965 (2008)
PubMed id: 18432238  
 
 
Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
C.G.Yang, C.Yi, E.M.Duguid, C.T.Sullivan, X.Jian, P.A.Rice, C.He.
 
  ABSTRACT  
 
Escherichia coli AlkB and its human homologues ABH2 and ABH3 repair DNA/RNA base lesions by using a direct oxidative dealkylation mechanism. ABH2 has the primary role of guarding mammalian genomes against 1-meA damage by repairing this lesion in double-stranded DNA (dsDNA), whereas AlkB and ABH3 preferentially repair single-stranded DNA (ssDNA) lesions and can repair damaged bases in RNA. Here we show the first crystal structures of AlkB-dsDNA and ABH2-dsDNA complexes, stabilized by a chemical cross-linking strategy. This study reveals that AlkB uses an unprecedented base-flipping mechanism to access the damaged base: it squeezes together the two bases flanking the flipped-out one to maintain the base stack, explaining the preference of AlkB for repairing ssDNA lesions over dsDNA ones. In addition, the first crystal structure of ABH2, presented here, provides a structural basis for designing inhibitors of this human DNA repair protein.
 
  Selected figure(s)  
 
Figure 4.
Figure 4: Crystal structure of the ABH2–DNA6 complex with 1-meA recognized by an intact active site. a, Cartoon trace of the ABH2–DNA6 complex with 1-meA recognized in the active site of ABH2 and a disulphide cross-link (Cys 169 to C9*) installed two base pairs away from the flipped base. The same colour scheme is used as in Fig. 1b. b, View of the active site of ABH2 with manganese(II) (orange), 2KG (blue) and 1-meA (light magenta). N6 of 1-meA is within hydrogen-bond distance to Tyr 122 (3.3 Å) and Glu 175 (2.8 Å). N7 forms a hydrogen bond to a water (3.0 Å) which also interacts with Asp 174 (2.6 Å) and Glu 175 (2.6 Å).
Figure 5.
Figure 5: Structural comparison of AlkB, ABH2 and ABH3 (stereo view). Least-squares superposition of structures of AlkB (in magenta, from AlkB–DNA1 without showing DNA1), ABH2–DNA2 (protein in green and DNA backbone in orange) and ABH3 (in blue, from Protein Data Bank 2IUW). The hairpin and flexible long-loop motifs are shaded, and the finger residue Phe 102 from ABH2 is labelled in green.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 452, 961-965) copyright 2008.  
  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
21279661 E.R.Farquhar, J.P.Emerson, K.D.Koehntop, M.F.Reynolds, M.Trmčić, and L.Que (2011).
In vivo self-hydroxylation of an iron-substituted manganese-dependent extradiol cleaving catechol dioxygenase.
  J Biol Inorg Chem, 16, 589-597.  
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
21278781 S.S.Wu, W.Xu, S.Liu, B.Chen, X.L.Wang, Y.Wang, S.F.Liu, and J.Q.Wu (2011).
Down-regulation of ALKBH2 increases cisplatin sensitivity in H1299 lung cancer cells.
  Acta Pharmacol Sin, 32, 393-398.  
20714506 B.Chen, H.Liu, X.Sun, and C.G.Yang (2010).
Mechanistic insight into the recognition of single-stranded and double-stranded DNA substrates by ABH2 and ABH3.
  Mol Biosyst, 6, 2143-2149.  
21068844 C.Yi, G.Jia, G.Hou, Q.Dai, W.Zhang, G.Zheng, X.Jian, C.G.Yang, Q.Cui, and C.He (2010).
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.
  Nature, 468, 330-333.
PDB codes: 3o1m 3o1o 3o1p 3o1r 3o1s 3o1t 3o1u 3o1v
20927102 E.H.Rubinson, A.S.Gowda, T.E.Spratt, B.Gold, and B.F.Eichman (2010).
An unprecedented nucleic acid capture mechanism for excision of DNA damage.
  Nature, 468, 406-411.
PDB codes: 3jx7 3jxy 3jxz 3jy1
  20725618 G.Lenglet, and M.H.David-Cordonnier (2010).
DNA-Destabilizing Agents as an Alternative Approach for Targeting DNA: Mechanisms of Action and Cellular Consequences.
  J Nucleic Acids, 2010, 0.  
20042601 H.Chen, N.C.Giri, R.Zhang, K.Yamane, Y.Zhang, M.Maroney, and M.Costa (2010).
Nickel ions inhibit histone demethylase JMJD1A and DNA repair enzyme ABH2 by replacing the ferrous iron in the catalytic centers.
  J Biol Chem, 285, 7374-7383.  
20223766 L.Lu, C.Yi, X.Jian, G.Zheng, and C.He (2010).
Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system.
  Nucleic Acids Res, 38, 4415-4425.
PDB codes: 3h8o 3h8r 3h8x
20123966 L.Songe-Møller, E.van den Born, V.Leihne, C.B.Vågbø, T.Kristoffersen, H.E.Krokan, F.Kirpekar, P...Falnes, and A.Klungland (2010).
Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding.
  Mol Cell Biol, 30, 1814-1827.  
20084272 P.J.Holland, and T.Hollis (2010).
Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching.
  PLoS One, 5, e8680.
PDB codes: 3khb 3khc
19959401 T.A.Müller, K.Meek, and R.P.Hausinger (2010).
Human AlkB homologue 1 (ABH1) exhibits DNA lyase activity at abasic sites.
  DNA Repair (Amst), 9, 58-65.  
20482798 T.Norambuena, and F.Melo (2010).
The Protein-DNA Interface database.
  BMC Bioinformatics, 11, 262.  
20525795 V.T.Monsen, O.Sundheim, P.A.Aas, M.P.Westbye, M.M.Sousa, G.Slupphaug, and H.E.Krokan (2010).
Divergent ß-hairpins determine double-strand versus single-strand substrate recognition of human AlkB-homologues 2 and 3.
  Nucleic Acids Res, 38, 6447-6455.  
19889642 Y.Qi, M.C.Spong, K.Nam, M.Karplus, and G.L.Verdine (2010).
Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.
  J Biol Chem, 285, 1468-1478.
PDB codes: 3jr4 3jr5
20376003 Z.Han, T.Niu, J.Chang, X.Lei, M.Zhao, Q.Wang, W.Cheng, J.Wang, Y.Feng, and J.Chai (2010).
Crystal structure of the FTO protein reveals basis for its substrate specificity.
  Nature, 464, 1205-1209.
PDB code: 3lfm
19452522 A.Ruggiero, A.Di Maro, V.Severino, A.Chambery, and R.Berisio (2009).
Crystal structure of PD-L1, a ribosome inactivating protein from Phytolacca dioica L. Leaves with the property to induce DNA cleavage.
  Biopolymers, 91, 1135-1142.
PDB code: 3h5k
19706517 B.Yu, and J.F.Hunt (2009).
Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB.
  Proc Natl Acad Sci U S A, 106, 14315-14320.
PDB codes: 3i2o 3i3m 3i3q 3i49
19145606 C.G.Yang, K.Garcia, and C.He (2009).
Damage detection and base flipping in direct DNA alkylation repair.
  Chembiochem, 10, 417-423.  
19852088 C.Yi, C.G.Yang, and C.He (2009).
A non-heme iron-mediated chemical demethylation in DNA and RNA.
  Acc Chem Res, 42, 519-529.  
19089684 E.J.Wurtmann, and S.L.Wolin (2009).
RNA under attack: cellular handling of RNA damage.
  Crit Rev Biochem Mol Biol, 44, 34-49.  
19786499 E.van den Born, A.Bekkelund, M.N.Moen, M.V.Omelchenko, A.Klungland, and P...Falnes (2009).
Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria.
  Nucleic Acids Res, 37, 7124-7136.  
19096759 H.Chen, and M.Costa (2009).
Iron- and 2-oxoglutarate-dependent dioxygenases: an emerging group of molecular targets for nickel toxicity and carcinogenicity.
  Biometals, 22, 191-196.  
19077538 H.Hashimoto, J.R.Horton, X.Zhang, and X.Cheng (2009).
UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
  Epigenetics, 4, 8.
PDB codes: 3f8i 3f8j 3fde
19508394 J.Mandl, A.Szarka, and G.Bánhegyi (2009).
Vitamin C: update on physiology and pharmacology.
  Br J Pharmacol, 157, 1097-1110.  
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.  
18775698 G.Jia, C.G.Yang, S.Yang, X.Jian, C.Yi, Z.Zhou, and C.He (2008).
Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO.
  FEBS Lett, 582, 3313-3319.  
18772888 H.Hashimoto, J.R.Horton, X.Zhang, M.Bostick, S.E.Jacobsen, and X.Cheng (2008).
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
  Nature, 455, 826-829.
PDB codes: 2zo0 2zo1 2zo2
18813363 J.M.Simmons, T.A.Müller, and R.P.Hausinger (2008).
Fe(II)/alpha-ketoglutarate hydroxylases involved in nucleobase, nucleoside, nucleotide, and chromatin metabolism.
  Dalton Trans, (), 5132-5142.  
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.