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PDBsum entry 2fmq

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protein dna_rna ligands metals links
Transferase/DNA PDB id
2fmq
Jmol
Contents
Protein chain
326 a.a. *
DNA/RNA
Ligands
DUP
Metals
_MG
_NA ×3
Waters ×321
* Residue conservation analysis
PDB id:
2fmq
Name: Transferase/DNA
Title: Sodium in active site of DNA polymerase beta
Structure: 5'- d( Cp Cp Gp Ap Cp Ap Gp Cp Gp Cp Ap Tp Cp Ap Gp C)-3'. Chain: b. Engineered: yes. 5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp C)-3'. Chain: c. Engineered: yes. 5'-d(p Gp Tp Cp Gp G)-3'. Chain: d.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.20Å     R-factor:   0.190     R-free:   0.242
Authors: V.K.Batra,W.A.Beard,D.D.Shock,J.M.Krahn,L.C.Pedersen, S.H.Wilson
Key ref:
V.K.Batra et al. (2006). Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure, 14, 757-766. PubMed id: 16615916 DOI: 10.1016/j.str.2006.01.011
Date:
09-Jan-06     Release date:   25-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06746  (DPOLB_HUMAN) -  DNA polymerase beta
Seq:
Struc:
335 a.a.
326 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   5 terms 
  Biological process     DNA biosynthetic process   12 terms 
  Biochemical function     protein binding     11 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2006.01.011 Structure 14:757-766 (2006)
PubMed id: 16615916  
 
 
Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
V.K.Batra, W.A.Beard, D.D.Shock, J.M.Krahn, L.C.Pedersen, S.H.Wilson.
 
  ABSTRACT  
 
The molecular details of the nucleotidyl transferase reaction have remained speculative, as strategies to trap catalytic intermediates for structure determination utilize substrates lacking the primer terminus 3'-OH and catalytic Mg2+, resulting in an incomplete and distorted active site geometry. Since the geometric arrangement of these essential atoms will impact chemistry, structural insight into fidelity strategies has been hampered. Here, we present a crystal structure of a precatalytic complex of a DNA polymerase with bound substrates that include the primer 3'-OH and catalytic Mg2+. This catalytic intermediate was trapped with a nonhydrolyzable deoxynucleotide analog. Comparison with two new structures of DNA polymerase beta lacking the 3'-OH or catalytic Mg2+ is described. These structures provide direct evidence that both atoms are required to achieve a proper geometry necessary for an in-line nucleophilic attack of O3' on the alphaP of the incoming nucleotide.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Stereoview of the Pol b Active Site
Superimposed structures of pol b with either Na^+ (light blue) or Mg2+ (yellow) in the catalytic metal site A. Residues that hydrogen bond (green) to the triphosphate moiety of the incoming nucleotide and the active site aspartates are shown. When Na^+ occupies the catalytic metal site, O3' of the primer terminus is 3.5 and 4.7 from the catalytic metal and aP of the incoming nucleotide, respectively. In contrast, with Mg2+ in the catalytic metal site, an altered sugar pucker positions O3' of the primer terminus 2.2 and 3.4 from the catalytic metal and Pa of the incoming nucleotide, respectively.
 
  The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 757-766) copyright 2006.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22785315 T.Nakamura, Y.Zhao, Y.Yamagata, Y.J.Hua, and W.Yang (2012).
Watching DNA polymerase η make a phosphodiester bond.
  Nature, 487, 196-201.
PDB codes: 4ecq 4ecr 4ecs 4ect 4ecu 4ecv 4ecw 4ecx 4ecy 4ecz 4ed0 4ed1 4ed2 4ed3 4ed6 4ed7 4ed8
21337527 D.L.Ma, D.S.Chan, B.Y.Man, and C.H.Leung (2011).
Oligonucleotide-based luminescent detection of metal ions.
  Chem Asian J, 6, 986.  
20724659 G.K.Surya Prakash, M.Zibinsky, T.G.Upton, B.A.Kashemirov, C.E.McKenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, D.D.Shock, S.H.Wilson, and G.A.Olah (2010).
Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid.
  Proc Natl Acad Sci U S A, 107, 15693-15698.
PDB code: 3lk9
20734113 G.L.Butterfoss, E.F.DeRose, S.A.Gabel, L.Perera, J.M.Krahn, G.A.Mueller, X.Zheng, and R.E.London (2010).
Conformational dependence of 13C shielding and coupling constants for methionine methyl groups.
  J Biomol NMR, 48, 31-47.  
  19842163 R.Rucker, P.Oelschlaeger, and A.Warshel (2010).
A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases.
  Proteins, 78, 671-680.  
20844920 S.H.Wilson, W.A.Beard, D.D.Shock, V.K.Batra, N.A.Cavanaugh, R.Prasad, E.W.Hou, Y.Liu, K.Asagoshi, J.K.Horton, D.F.Stefanick, P.S.Kedar, M.J.Carrozza, A.Masaoka, and M.L.Heacock (2010).
Base excision repair and design of small molecule inhibitors of human DNA polymerase β.
  Cell Mol Life Sci, 67, 3633-3647.  
20526335 V.K.Batra, W.A.Beard, E.W.Hou, L.C.Pedersen, R.Prasad, and S.H.Wilson (2010).
Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site.
  Nat Struct Mol Biol, 17, 889-890.
PDB code: 3mby
19542228 A.Irimia, R.L.Eoff, F.P.Guengerich, and M.Egli (2009).
Structural and functional elucidation of the mechanism promoting error-prone synthesis by human DNA polymerase kappa opposite the 7,8-dihydro-8-oxo-2'-deoxyguanosine adduct.
  J Biol Chem, 284, 22467-22480.
PDB codes: 2w7o 2w7p
19072536 K.Donny-Clark, R.Shapiro, and S.Broyde (2009).
Accommodation of an N-(deoxyguanosin-8-yl)-2-acetylaminofluorene adduct in the active site of human DNA polymerase iota: Hoogsteen or Watson-Crick base pairing?
  Biochemistry, 48, 7.  
19767609 K.Donny-Clark, and S.Broyde (2009).
Influence of local sequence context on damaged base conformation in human DNA polymerase iota: molecular dynamics studies of nucleotide incorporation opposite a benzo[a]pyrene-derived adenine lesion.
  Nucleic Acids Res, 37, 7095-7109.  
19389406 L.Wang, S.Broyde, and Y.Zhang (2009).
Polymerase-tailored variations in the water-mediated and substrate-assisted mechanism for nucleotidyl transfer: insights from a study of T7 DNA polymerase.
  J Mol Biol, 389, 787-796.  
20004168 M.Morar, K.Bhullar, D.W.Hughes, M.Junop, and G.D.Wright (2009).
Structure and mechanism of the lincosamide antibiotic adenylyltransferase LinB.
  Structure, 17, 1649-1659.
PDB codes: 3jyy 3jz0
19364137 P.Xu, L.Oum, Y.C.Lee, N.E.Geacintov, and S.Broyde (2009).
Visualizing sequence-governed nucleotide selectivities and mutagenic consequences through a replicative cycle: processing of a bulky carcinogen N2-dG lesion in a Y-family DNA polymerase.
  Biochemistry, 48, 4677-4690.  
19391628 S.C.Kamerlin, C.E.McKenna, M.F.Goodman, M.F.Goondman, and A.Warshel (2009).
A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases.
  Biochemistry, 48, 5963-5971.  
19124465 S.M.Sherrer, J.A.Brown, L.R.Pack, V.P.Jasti, J.D.Fowler, A.K.Basu, and Z.Suo (2009).
Mechanistic Studies of the Bypass of a Bulky Single-base Lesion Catalyzed by a Y-family DNA Polymerase.
  J Biol Chem, 284, 6379-6388.  
19211662 S.Nakane, N.Nakagawa, S.Kuramitsu, and R.Masui (2009).
Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3'-5' exonuclease activity.
  Nucleic Acids Res, 37, 2037-2052.  
19351147 T.G.Upton, B.A.Kashemirov, C.E.McKenna, M.F.Goodman, G.K.Prakash, R.Kultyshev, V.K.Batra, D.D.Shock, L.C.Pedersen, W.A.Beard, and S.H.Wilson (2009).
Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function.
  Org Lett, 11, 1883-1886.
PDB code: 3gdx
19759017 W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, and S.H.Wilson (2009).
DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".
  J Biol Chem, 284, 31680-31689.
PDB codes: 3isb 3isc 3isd
18437203 A.Abyzov, A.Uzun, P.R.Strauss, and V.A.Ilyin (2008).
An AP endonuclease 1-DNA polymerase beta complex: theoretical prediction of interacting surfaces.
  PLoS Comput Biol, 4, e1000066.  
18184655 D.F.Zamyatkin, F.Parra, J.M.Alonso, D.A.Harki, B.R.Peterson, P.Grochulski, and K.K.Ng (2008).
Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase.
  J Biol Chem, 283, 7705-7712.
PDB codes: 3bsn 3bso
18616290 D.L.Murphy, J.Kosa, J.Jaeger, and J.B.Sweasy (2008).
The Asp285 variant of DNA polymerase beta extends mispaired primer termini via increased nucleotide binding.
  Biochemistry, 47, 8048-8057.  
18177750 G.Martin, S.Doublié, and W.Keller (2008).
Determinants of substrate specificity in RNA-dependent nucleotidyl transferases.
  Biochim Biophys Acta, 1779, 206-216.  
17963236 J.Mendieta, C.E.Cases-González, T.Matamoros, G.Ramírez, and L.Menéndez-Arias (2008).
A Mg2+-induced conformational switch rendering a competent DNA polymerase catalytic complex.
  Proteins, 71, 565-574.  
18931375 L.Jia, N.E.Geacintov, and S.Broyde (2008).
The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions.
  Nucleic Acids Res, 36, 6571-6584.  
18167548 M.Pandey, S.S.Patel, and A.Gabriel (2008).
Kinetic pathway of pyrophosphorolysis by a retrotransposon reverse transcriptase.
  PLoS ONE, 3, e1389.  
18391201 P.Lin, V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, and L.G.Pedersen (2008).
Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta.
  Proc Natl Acad Sci U S A, 105, 5670-5674.  
18471977 V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, and S.H.Wilson (2008).
Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.
  Mol Cell, 30, 315-324.
PDB codes: 3c2k 3c2l 3c2m
18953336 W.Yang (2008).
An equivalent metal ion in one- and two-metal-ion catalysis.
  Nat Struct Mol Biol, 15, 1228-1231.  
17159995 A.F.Moon, M.Garcia-Diaz, K.Bebenek, B.J.Davis, X.Zhong, D.A.Ramsden, T.A.Kunkel, and L.C.Pedersen (2007).
Structural insight into the substrate specificity of DNA Polymerase mu.
  Nat Struct Mol Biol, 14, 45-53.
PDB code: 2ihm
17631059 A.F.Moon, M.Garcia-Diaz, V.K.Batra, W.A.Beard, K.Bebenek, T.A.Kunkel, S.H.Wilson, and L.C.Pedersen (2007).
The X family portrait: structural insights into biological functions of X family polymerases.
  DNA Repair (Amst), 6, 1709-1725.  
18031037 C.E.McKenna, B.A.Kashemirov, T.G.Upton, V.K.Batra, M.F.Goodman, L.C.Pedersen, W.A.Beard, and S.H.Wilson (2007).
(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta.
  J Am Chem Soc, 129, 15412-15413.
PDB code: 2pxi
17439962 G.C.Lin, J.Jaeger, and J.B.Sweasy (2007).
Loop II of DNA polymerase beta is important for polymerization activity and fidelity.
  Nucleic Acids Res, 35, 2924-2935.  
17210571 K.A.Fiala, C.D.Hypes, and Z.Suo (2007).
Mechanism of abasic lesion bypass catalyzed by a Y-family DNA polymerase.
  J Biol Chem, 282, 8188-8198.  
17095011 K.A.Fiala, J.A.Brown, H.Ling, A.K.Kshetry, J.Zhang, J.S.Taylor, W.Yang, and Z.Suo (2007).
Mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent DNA polymerase.
  J Mol Biol, 365, 590-602.
PDB code: 2imw
17375926 L.Wang, X.Yu, P.Hu, S.Broyde, and Y.Zhang (2007).
A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.
  J Am Chem Soc, 129, 4731-4737.  
17475573 M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, and T.A.Kunkel (2007).
Role of the catalytic metal during polymerization by DNA polymerase lambda.
  DNA Repair (Amst), 6, 1333-1340.
PDB codes: 2pfn 2pfo 2pfp 2pfq
18496613 M.Garcia-Diaz, and K.Bebenek (2007).
Multiple functions of DNA polymerases.
  CRC Crit Rev Plant Sci, 26, 105-122.  
17850751 P.B.Balbo, and A.Bohm (2007).
Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis.
  Structure, 15, 1117-1131.
PDB code: 2q66
17174326 P.Oelschlaeger, M.Klahn, W.A.Beard, S.H.Wilson, and A.Warshel (2007).
Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects.
  J Mol Biol, 366, 687-701.  
17576677 P.Xu, L.Oum, L.S.Beese, N.E.Geacintov, and S.Broyde (2007).
Following an environmental carcinogen N2-dG adduct through replication: elucidating blockage and bypass in a high-fidelity DNA polymerase.
  Nucleic Acids Res, 35, 4275-4288.  
17293403 Y.Wang, S.Reddy, W.A.Beard, S.H.Wilson, and T.Schlick (2007).
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta.
  Biophys J, 92, 3063-3070.  
16820532 L.Zhang, O.Rechkoblit, L.Wang, D.J.Patel, R.Shapiro, and S.Broyde (2006).
Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies.
  Nucleic Acids Res, 34, 3326-3337.  
16920835 M.C.Foley, K.Arora, and T.Schlick (2006).
Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda.
  Biophys J, 91, 3182-3195.  
17176036 R.Radhakrishnan, K.Arora, Y.Wang, W.A.Beard, S.H.Wilson, and T.Schlick (2006).
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection.
  Biochemistry, 45, 15142-15156.  
17005572 W.W.Duym, K.A.Fiala, N.Bhatt, and Z.Suo (2006).
Kinetic effect of a downstream strand and its 5'-terminal moieties on single nucleotide gap-filling synthesis catalyzed by human DNA polymerase lambda.
  J Biol Chem, 281, 35649-35655.  
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.