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PDBsum entry 9icv
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protein dna_rna ligands metals links
Transferase/DNA PDB id
9icv

 

 

 

 

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JSmol PyMol  
Contents
Protein chain
327 a.a. *
DNA/RNA
Ligands
DTP
Metals
_ZN ×3
_NA ×2
Waters ×142
* Residue conservation analysis
PDB id:
9icv
Name: Transferase/DNA
Title: DNA polymerase beta (E.C.2.7.7.7)/DNA complex + 2'-deoxyadenosine-5'- triphosphate, soaked in the presence of datp and zncl2
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 Gp A)-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
Resolution:
2.70Å     R-factor:   0.178    
Authors: H.Pelletier,M.R.Sawaya
Key ref:
H.Pelletier et al. (1996). A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. Biochemistry, 35, 12762-12777. PubMed id: 8841119 DOI: 10.1021/bi9529566
Date:
16-Dec-95     Release date:   15-Nov-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P06746  (DPOLB_HUMAN) -  DNA polymerase beta from Homo sapiens
Seq:
Struc: 		335 a.a.
327 a.a.
Key:    Secondary structure  CATH domain

DNA/RNA chains
  C-A-T-T-A-G-A-A 8 bases
  T-C-T-A-A-T-G-A 8 bases

 Enzyme reactions 
   Enzyme class 1: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
DNA(n)
 + 2'-deoxyribonucleoside 5'-triphosphate
 = DNA(n+1)
Bound ligand (Het Group name = DTP)
corresponds exactly 		+ diphosphate
   Enzyme class 2: E.C.4.2.99.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 3: E.C.4.2.99.18  - DNA-(apurinic or apyrimidinic site) lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H+
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1021/bi9529566 Biochemistry 35:12762-12777 (1996)
PubMed id: 8841119  
 
 
A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut.
 
  ABSTRACT  
 
When crystals of human DNA polymerase beta (pol beta) complexed with DNA [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996) Biochemistry 35, 12742-12761] are soaked in the presence of dATP and Mn2+, X-ray structural analysis shows that nucleotidyl transfer to the primer 3'-OH takes place directly in the crystals, even though the DNA is blunt-ended at the active site. Under similar crystal-soaking conditions, there is no evidence for a reaction when Mn2+ is replaced by Mg2+, which is thought to be the divalent metal ion utilized by most polymerases in vivo. These results suggest that one way Mn2+ may manifest its mutagenic effect on polymerases is by promoting greater reactivity than Mg2+ at the catalytic site, thereby allowing the nucleotidyl transfer reaction to take place with little or no regard to instructions from a template. Non-template-directed nucleotidyl transfer is also observed when pol beta-DNA cocrystals are soaked in the presence of dATP and Zn2+, but the reaction products differ in that the sugar moiety of the incorporated nucleotide appears distorted or otherwise cleaved, in agreement with reports that Zn2+ may act as a polymerase inhibitor rather than as a mutagen [Sirover, M. A., & Loeb, L. A. (1976) Science 194, 1434-1436]. Although no reaction is observed when crystals are soaked in the presence of dATP and other metal ions such as Ca2+, Co2+, Cr3+, or Ni2+, X-ray structural analyses show that these metal ions coordinate the triphosphate moiety of the nucleotide in a manner that differs from that observed with Mg2+. In addition, all metal ions tested, with the exception of Mg2+, promote a change in the side-chain position of aspartic acid 192, which is one of three highly conserved active-site carboxylate residues. Soaking experiments with nucleotides other than dATP (namely, dCTP, dGTP, dTTP, ATP, ddATP, ddCTP, AZT-TP, and dATP alpha S) reveal a non-base-specific binding site on pol beta for the triphosphate and sugar moieties of a nucleotide, suggesting a possible mechanism for nucleotide selectivity whereby triphosphate-sugar binding precedes a check for correct base pairing with the template.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21377475 P.Xie (2011).
A model for the dynamics of mammalian family X DNA polymerases.
  J Theor Biol, 277, 111-122.  
20523923 A.Fernández-Botello, B.P.Operschall, A.Holy, V.Moreno, and H.Sigel (2010).
Metal ion-binding properties of 9-[(2-phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), an isomer of the antiviral nucleotide analogue 9-[(2-phosphonomethoxy)ethyl]adenine (PMEA). Steric guiding of metal ion-coordination by the purine-amino group.
  Dalton Trans, 39, 6344-6354.  
19969000 H.Zhang, and F.P.Guengerich (2010).
Effect of N2-guanyl modifications on early steps in catalysis of polymerization by Sulfolobus solfataricus P2 DNA polymerase Dpo4 T239W.
  J Mol Biol, 395, 1007-1018.  
20079883 K.A.Johnson (2010).
The kinetic and chemical mechanism of high-fidelity DNA polymerases.
  Biochim Biophys Acta, 1804, 1041-1048.  
20351257 M.J.Cuneo, and R.E.London (2010).
Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity.
  Proc Natl Acad Sci U S A, 107, 6805-6810.
PDB codes: 3k75 3k77 3lqc
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.  
19502493 F.Romain, I.Barbosa, J.Gouge, F.Rougeon, and M.Delarue (2009).
Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region.
  Nucleic Acids Res, 37, 4642-4656.  
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
18400846 L.Lin, F.Wan, and J.Hu (2008).
Functional and structural dynamics of hepadnavirus reverse transcriptase during protein-primed initiation of reverse transcription: effects of metal ions.
  J Virol, 82, 5703-5714.  
18446195 S.J.Garforth, M.A.Parniak, and V.R.Prasad (2008).
Utilization of a deoxynucleoside diphosphate substrate by HIV reverse transcriptase.
  PLoS ONE, 3, e2074.  
17609217 E.G.Frank, and R.Woodgate (2007).
Increased catalytic activity and altered fidelity of human DNA polymerase iota in the presence of manganese.
  J Biol Chem, 282, 24689-24696.  
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.  
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
16043633 E.Crespan, S.Zanoli, A.Khandazhinskaya, I.Shevelev, M.Jasko, L.Alexandrova, M.Kukhanova, G.Blanca, G.Villani, U.Hübscher, S.Spadari, and G.Maga (2005).
Incorporation of non-nucleoside triphosphate analogues opposite to an abasic site by human DNA polymerases beta and lambda.
  Nucleic Acids Res, 33, 4117-4127.  
16172677 H.Sigel, and R.Griesser (2005).
Nucleoside 5'-triphosphates: self-association, acid-base, and metal ion-binding properties in solution.
  Chem Soc Rev, 34, 875-900.  
15863620 J.Florián, M.F.Goodman, and A.Warshel (2005).
Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases.
  Proc Natl Acad Sci U S A, 102, 6819-6824.  
16283524 J.L.Fornsaglio, T.J.O'Brien, and S.R.Patierno (2005).
Differential impact of ionic and coordinate covalent chromium (Cr)-DNA binding on DNA replication.
  Mol Cell Biochem, 279, 149-155.  
15701045 N.A.Lebedeva, T.A.Seredina, V.N.Silnikov, T.V.Abramova, A.S.Levina, S.N.Khodyreva, N.I.Rechkunova, and O.I.Lavrik (2005).
Analysis of interactions of DNA polymerase beta and reverse transcriptases of human immunodeficiency and mouse leukemia viruses with dNTP analogs containing a modified sugar residue.
  Biochemistry (Mosc), 70, 1-7.  
15994230 N.F.Lue, D.Bosoy, T.J.Moriarty, C.Autexier, B.Altman, and S.Leng (2005).
Telomerase can act as a template- and RNA-independent terminal transferase.
  Proc Natl Acad Sci U S A, 102, 9778-9783.  
16216572 T.M.Hall (2005).
Structure and function of argonaute proteins.
  Structure, 13, 1403-1408.  
15122879 J.J.Arnold, D.W.Gohara, and C.E.Cameron (2004).
Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mn2+.
  Biochemistry, 43, 5138-5148.  
15189842 L.Yang, W.A.Beard, S.H.Wilson, S.Broyde, and T.Schlick (2004).
Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.
  Biophys J, 86, 3392-3408.  
15503234 R.B.Gómez-Coca, L.E.Kapinos, A.Holý, R.A.Vilaplana, F.González-Vílchez, and H.Sigel (2004).
Quantification of isomeric equilibria formed by metal ion complexes of 8-[2-(phosphonomethoxy)ethyl]-8-azaadenine (8,8aPMEA) and 9-[2-(phosphonomethoxy)ethyl]-8-azaadenine (9,8aPMEA). Derivatives of the antiviral nucleotide analogue 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA).
  J Biol Inorg Chem, 9, 961-972.  
15388871 S.Gopalakrishna, V.Gusti, S.Nair, S.Sahar, and R.K.Gaur (2004).
Template-dependent incorporation of 8-N3AMP into RNA with bacteriophage T7 RNA polymerase.
  RNA, 10, 1820-1830.  
14627824 I.Shevelev, G.Blanca, G.Villani, K.Ramadan, S.Spadari, U.Hübscher, and G.Maga (2003).
Mutagenesis of human DNA polymerase lambda: essential roles of Tyr505 and Phe506 for both DNA polymerase and terminal transferase activities.
  Nucleic Acids Res, 31, 6916-6925.  
14529299 M.J.Jezewska, R.Galletto, and W.Bujalowski (2003).
Tertiary conformation of the template-primer and gapped DNA substrates in complexes with rat polymerase beta. Fluorescence energy transfer studies using the multiple donor-acceptor approach.
  Biochemistry, 42, 11864-11878.  
14579358 R.C.Rittenhouse, W.K.Apostoluk, J.H.Miller, and T.P.Straatsma (2003).
Characterization of the active site of DNA polymerase beta by molecular dynamics and quantum chemical calculation.
  Proteins, 53, 667-682.  
12140316 G.Villani, N.Tanguy Le Gac, L.Wasungu, D.Burnouf, R.P.Fuchs, and P.E.Boehmer (2002).
Effect of manganese on in vitro replication of damaged DNA catalyzed by the herpes simplex virus type-1 DNA polymerase.
  Nucleic Acids Res, 30, 3323-3332.  
11863453 M.Boudvillain, A.Schwartz, and A.R.Rahmouni (2002).
Limited topological alteration of the T7 RNA polymerase active center at intrinsic termination sites.
  Biochemistry, 41, 3137-3146.  
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.  
11912205 M.J.Jezewska, R.Galletto, and W.Bujalowski (2002).
Dynamics of gapped DNA recognition by human polymerase beta.
  J Biol Chem, 277, 20316-20327.  
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.  
11756435 W.A.Beard, D.D.Shock, X.P.Yang, S.F.DeLauder, and S.H.Wilson (2002).
Loss of DNA polymerase beta stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity.
  J Biol Chem, 277, 8235-8242.  
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.  
11376161 A.Skandalis, and L.A.Loeb (2001).
Enzymatic properties of rat DNA polymerase beta mutants obtained by randomized mutagenesis.
  Nucleic Acids Res, 29, 2418-2426.  
11205337 J.F.Ruiz, O.Domínguez, T.Laín de Lera, M.Garcia-Díaz, A.Bernad, and L.Blanco (2001).
DNA polymerase mu, a candidate hypermutase?
  Philos Trans R Soc Lond B Biol Sci, 356, 99.  
11258949 M.J.Jezewska, S.Rajendran, and W.Bujalowski (2001).
Interactions of the 8-kDa domain of rat DNA polymerase beta with DNA.
  Biochemistry, 40, 3295-3307.  
10747040 O.Domínguez, J.F.Ruiz, T.Laín de Lera, M.García-Díaz, M.A.González, T.Kirchhoff, C.Martínez-A, A.Bernad, and L.Blanco (2000).
DNA polymerase mu (Pol mu), homologous to TdT, could act as a DNA mutator in eukaryotic cells.
  EMBO J, 19, 1731-1742.  
11027140 Y.Mizushina, T.Ohkubo, F.Sugawara, and K.Sakaguchi (2000).
Structure of lithocholic acid binding to the N-terminal 8-kDa domain of DNA polymerase beta.
  Biochemistry, 39, 12606-12613.  
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.  
10387012 B.W.Kirk, and R.D.Kuchta (1999).
Arg304 of human DNA primase is a key contributor to catalysis and NTP binding: primase and the family X polymerases share significant sequence homology.
  Biochemistry, 38, 7727-7736.  
10531375 C.Méplan, K.Mann, and P.Hainaut (1999).
Cadmium induces conformational modifications of wild-type p53 and suppresses p53 response to DNA damage in cultured cells.
  J Biol Chem, 274, 31663-31670.  
10427002 J.J.Tesmer, R.K.Sunahara, R.A.Johnson, G.Gosselin, A.G.Gilman, and S.R.Sprang (1999).
Two-metal-Ion catalysis in adenylyl cyclase.
  Science, 285, 756-760.
PDB codes: 1cjk 1cjt 1cju 1cjv
9920940 J.L.Kosa, and J.B.Sweasy (1999).
3'-Azido-3'-deoxythymidine-resistant mutants of DNA polymerase beta identified by in vivo selection.
  J Biol Chem, 274, 3851-3858.  
10464295 Y.Mizushina, T.Ohkubo, T.Date, T.Yamaguchi, M.Saneyoshi, F.Sugawara, and K.Sakaguchi (1999).
Mode analysis of a fatty acid molecule binding to the N-terminal 8-kDa domain of DNA polymerase beta. A 1:1 complex and binding surface.
  J Biol Chem, 274, 25599-25607.  
9519297 C.A.Brautigam, and T.A.Steitz (1998).
Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.
  Curr Opin Struct Biol, 8, 54-63.  
9649318 J.Singh, and E.T.Snow (1998).
Chromium(III) decreases the fidelity of human DNA polymerase beta.
  Biochemistry, 37, 9371-9378.  
9715904 M.B.Berry, and G.N.Phillips (1998).
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+.
  Proteins, 32, 276-288.
PDB codes: 1zin 1zio 1zip
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
9305982 X.Zhong, S.S.Patel, B.G.Werneburg, and M.D.Tsai (1997).
DNA polymerase beta: multiple conformational changes in the mechanism of catalysis.
  Biochemistry, 36, 11891-11900.  
9354643 Y.Huang, A.Beaudry, J.McSwiggen, and R.Sousa (1997).
Determinants of ribose specificity in RNA polymerization: effects of Mn2+ and deoxynucleoside monophosphate incorporation into transcripts.
  Biochemistry, 36, 13718-13728.  
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
8841120 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.
PDB codes: 1nom 1zqa 1zqb 1zqc 1zqd 1zqe 1zqf 1zqg 1zqh 1zqi 1zqj 1zqk 1zql 1zqm 1zqn 1zqo 1zqp 1zqq 1zqr 1zqs 1zqu 1zqv 1zqw 1zqx 1zqy 1zqz 8ica 8icb 8icc 8ice 8icf 8icg 8ich 8ici 8icz 9ica 9icb 9icc 9ice 9icg 9ich 9ici 9icj 9icl
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.

 

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