PDBsum entry 8icm

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protein dna_rna ligands metals links
Transferase/DNA PDB id
Jmol PyMol
Protein chain
327 a.a. *
_NA ×2
Waters ×138
* Residue conservation analysis
PDB id:
Name: Transferase/DNA
Title: DNA polymerase beta (pol b) (E.C. complexed with seven base pairs of dna; soaked in the presence of datp (1 millimolar), mncl2 (5 millimolar), and ammonium sulfate (75 millimolar)
Structure: DNA (5'-d( Cp Ap Tp Tp Ap Gp Ap A)-3'). Chain: t. Engineered: yes. DNA (5'-d( Tp Cp Tp Ap Ap Tp G)-3'). Chain: p. Engineered: yes. Protein (DNA polymerase beta . Chain: a. Engineered: yes
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
2.90Å     R-factor:   0.176    
Authors: H.Pelletier,M.R.Sawaya
Key ref:
H.Pelletier and M.R.Sawaya (1996). Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry, 35, 12778-12787. PubMed id: 8841120 DOI: 10.1021/bi960790i
04-Jan-96     Release date:   15-Nov-96    
Go to PROCHECK summary

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

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   6 terms 
  Biological process     immunoglobulin heavy chain V-D-J recombination   27 terms 
  Biochemical function     protein binding     12 terms  


DOI no: 10.1021/bi960790i Biochemistry 35:12778-12787 (1996)
PubMed id: 8841120  
Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.
H.Pelletier, M.R.Sawaya.
X-ray crystallographic studies have shown that DNA binding by human polymerase beta (pol beta) occurs primarily through two structurally and sequentially homologous helix-hairpin-helix (HhH) motifs, one in the fingers subdomain and the other in the 8-kDa domain [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996a) Biochemistry 35, 12742-12761]. In that DNA binding by each HhH motif is facilitated by a metal ion, we set out to determine the identity of the metal ion that most likely binds to the HhH motif in vivo. Crystal soaking experiments were performed on human pol beta-DNA cocrystals with Mg2+, Ca2+, Na+, and K+, the four most prevalent metal ions in the cell, and in each case a data set was collected and the resulting structure was refined. Under the conditions tested, the HhH motifs of pol beta have an affinity for these biologically prevalent metal ions in the order Mg2+ < Ca2+ < Na+ < K+, with K+ displaying the strongest binding. Crystals soaked in the presence of Tl+, a commonly used spectroscopic probe for K+, were too X-ray-sensitive to establish the binding behavior of Tl+, but soaking experiments with Ba2+ and Cs+ resulted in relatively stable crystals that gave evidence of metal ion binding in both HhH motifs, confirming that larger monovalent and divalent metal ions are capable of binding to the HhH metal sites. Although Mn2+, which has been categorized as a potent polymerase mutagen, binds to the HhH motifs with a greater affinity than Mg2+, Mn2+ does not bind to the HhH motifs in the presence of equimolar concentrations of Na+. These results suggest that in vivo, where Mn2+ is present only in trace amounts, Mn2+ probably does not have a large effect on DNA binding and may instead manifest a mutagenic effect on pol beta primarily by distorting nucleotide binding or by directly affecting the catalytic step [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996b) Biochemistry 35, 12762-12777]. Crystal soaking experiments with 31-kDa apoenzyme crystals show that, in the absence of DNA, the HhH motif in the fingers subdomain binds metal ions with either much lower occupancy or not at all, indicating that metal ion binding is dependent on the presence of the DNA substrate.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20083120 F.Faucher, S.S.Wallace, and S.Doublié (2010).
The C-terminal lysine of Ogg2 DNA glycosylases is a major molecular determinant for guanine/8-oxoguanine distinction.
  J Mol Biol, 397, 46-56.
PDB code: 3knt
19747886 F.Faucher, S.S.Wallace, and S.Doublié (2009).
Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase.
  DNA Repair (Amst), 8, 1283-1289.
PDB codes: 3i0w 3i0x
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.  
18662849 A.S.Jaiswal, and S.Narayan (2008).
A novel function of adenomatous polyposis coli (APC) in regulating DNA repair.
  Cancer Lett, 271, 272-280.  
18416825 C.Hazan, F.Boudsocq, V.Gervais, O.Saurel, M.Ciais, C.Cazaux, J.Czaplicki, and A.Milon (2008).
Structural insights on the pamoic acid and the 8 kDa domain of DNA polymerase beta complex: towards the design of higher-affinity inhibitors.
  BMC Struct Biol, 8, 22.  
18084022 K.H.Tang, M.Niebuhr, A.Aulabaugh, and M.D.Tsai (2008).
Solution structures of 2 : 1 and 1 : 1 DNA polymerase-DNA complexes probed by ultracentrifugation and small-angle X-ray scattering.
  Nucleic Acids Res, 36, 849-860.  
18385153 K.H.Tang, M.Niebuhr, C.S.Tung, H.C.Chan, C.C.Chou, and M.D.Tsai (2008).
Mismatched dNTP incorporation by DNA polymerase beta does not proceed via globally different conformational pathways.
  Nucleic Acids Res, 36, 2948-2957.
PDB code: 2van
17586771 J.J.Petkowski, M.Chruszcz, M.D.Zimmerman, H.Zheng, T.Skarina, O.Onopriyenko, M.T.Cymborowski, K.D.Koclega, A.Savchenko, A.Edwards, and W.Minor (2007).
Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit.
  Protein Sci, 16, 1360-1367.
PDB codes: 2fgc 2pc6
17189640 J.Stagno, I.Aphasizheva, A.Rosengarth, H.Luecke, and R.Aphasizhev (2007).
UTP-bound and Apo structures of a minimal RNA uridylyltransferase.
  J Mol Biol, 366, 882-899.
PDB codes: 2ikf 2nom
17353264 O.S.Rissland, A.Mikulasova, and C.J.Norbury (2007).
Efficient RNA polyuridylation by noncanonical poly(A) polymerases.
  Mol Cell Biol, 27, 3612-3624.  
17701034 S.Beetz, D.Diekhoff, and L.A.Steiner (2007).
Characterization of terminal deoxynucleotidyl transferase and polymerase mu in zebrafish.
  Immunogenetics, 59, 735-744.  
16306039 H.Zang, A.Irimia, J.Y.Choi, K.C.Angel, L.V.Loukachevitch, M.Egli, and F.P.Guengerich (2006).
Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4.
  J Biol Chem, 281, 2358-2372.
PDB codes: 2c22 2c28 2c2d 2c2e 2c2r
15078879 D.Wong, and B.Demple (2004).
Modulation of the 5'-deoxyribose-5-phosphate lyase and DNA synthesis activities of mammalian DNA polymerase beta by apurinic/apyrimidinic endonuclease 1.
  J Biol Chem, 279, 25268-25275.  
14992725 M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.Blanco, T.A.Kunkel, and L.C.Pedersen (2004).
A structural solution for the DNA polymerase lambda-dependent repair of DNA gaps with minimal homology.
  Mol Cell, 13, 561-572.
PDB code: 1rzt
12458221 S.J.Kim, W.A.Beard, J.Harvey, D.D.Shock, J.R.Knutson, and S.H.Wilson (2003).
Rapid segmental and subdomain motions of DNA polymerase beta.
  J Biol Chem, 278, 5072-5081.  
14654694 S.Jones, H.P.Shanahan, H.M.Berman, and J.M.Thornton (2003).
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins.
  Nucleic Acids Res, 31, 7189-7198.  
11823435 M.Delarue, J.B.Boulé, J.Lescar, N.Expert-Bezançon, N.Jourdan, N.Sukumar, F.Rougeon, and C.Papanicolaou (2002).
Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase.
  EMBO J, 21, 427-439.
PDB codes: 1jms 1kdh 1kej
11821417 M.García-Díaz, K.Bebenek, R.Sabariegos, O.Domínguez, J.Rodríguez, T.Kirchhoff, E.García-Palomero, A.J.Picher, R.Juárez, J.F.Ruiz, T.A.Kunkel, and L.Blanco (2002).
DNA polymerase lambda, a novel DNA repair enzyme in human cells.
  J Biol Chem, 277, 13184-13191.  
12121998 M.Maitra, A.Gudzelak, S.X.Li, Y.Matsumoto, K.A.Eckert, J.Jager, and J.B.Sweasy (2002).
Threonine 79 is a hinge residue that governs the fidelity of DNA polymerase beta by helping to position the DNA within the active site.
  J Biol Chem, 277, 35550-35560.  
12081642 N.Shimazaki, K.Yoshida, T.Kobayashi, S.Toji, K.Tamai, and O.Koiwai (2002).
Over-expression of human DNA polymerase lambda in E. coli and characterization of the recombinant enzyme.
  Genes Cells, 7, 639-651.  
12426397 S.Singh, G.E.Folkers, A.M.Bonvin, R.Boelens, R.Wechselberger, A.Niztayev, and R.Kaptein (2002).
Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.
  EMBO J, 21, 6257-6266.
PDB code: 1kft
11677229 Y.Mizushina, S.Kamisuki, N.Kasai, N.Shimazaki, M.Takemura, H.Asahara, S.Linn, S.Yoshida, A.Matsukage, O.Koiwai, F.Sugawara, H.Yoshida, and K.Sakaguchi (2002).
A plant phytotoxin, solanapyrone A, is an inhibitor of DNA polymerase beta and lambda.
  J Biol Chem, 277, 630-638.  
11562470 M.Machius, J.L.Chuang, R.M.Wynn, D.R.Tomchick, and D.T.Chuang (2001).
Structure of rat BCKD kinase: nucleotide-induced domain communication in a mitochondrial protein kinase.
  Proc Natl Acad Sci U S A, 98, 11218-11223.
PDB codes: 1gjv 1gkx 1gkz
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
10675345 T.Hollis, Y.Ichikawa, and T.Ellenberger (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.
PDB code: 1diz
10908318 X.Shao, and N.V.Grishin (2000).
Common fold in helix-hairpin-helix proteins.
  Nucleic Acids Res, 28, 2643-2650.  
11042381 Y.Mizushina, T.Ueno, M.Oda, T.Yamaguchi, M.Saneyoshi, and K.Sakaguchi (2000).
The biochemical mode of inhibition of DNA polymerase beta by alpha-rubromycin.
  Biochim Biophys Acta, 1523, 172-181.  
10487755 Y.Fujii, T.Shimizu, M.Kusumoto, Y.Kyogoku, T.Taniguchi, and T.Hakoshima (1999).
Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences.
  EMBO J, 18, 5028-5041.
PDB code: 2irf
9649318 J.Singh, and E.T.Snow (1998).
Chromium(III) decreases the fidelity of human DNA polymerase beta.
  Biochemistry, 37, 9371-9378.  
9388236 M.Oliveros, R.J.Yáñez, M.L.Salas, J.Salas, E.Viñuela, and L.Blanco (1997).
Characterization of an African swine fever virus 20-kDa DNA polymerase involved in DNA repair.
  J Biol Chem, 272, 30899-30910.  
9287163 M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, and H.Pelletier (1997).
Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
  Biochemistry, 36, 11205-11215.
PDB codes: 1bpx 1bpy 1bpz
8841118 H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, and J.Kraut (1996).
Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity.
  Biochemistry, 35, 12742-12761.
PDB codes: 9icm 9icw 9icx 9icy
8841119 H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, and J.Kraut (1996).
A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
  Biochemistry, 35, 12762-12777.
PDB codes: 1zqt 7ice 7icf 7icg 7ich 7ici 7icj 7ick 7icl 7icm 7icn 7ico 7icp 7icq 7icr 7ics 7ict 7icu 7icv 8icj 8ick 8icl 8icm 8icn 8ico 8icp 8icq 8icr 8ics 8ict 8icu 8icv 8icw 8icx 8icy 9icf 9ick 9icn 9ico 9icp 9icq 9icr 9ics 9ict 9icu 9icv
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