DB code: M00055

RLCP classification 3.103.90020.1141 : Transfer
1.15.10100.1172 : Hydrolysis
CATH domain 3.40.50.1010 : Rossmann fold
1.10.150.20 : DNA polymerase; domain 1
3.30.420.10 : Nucleotidyltransferase; domain 5 Catalytic domain
1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4
3.30.70.370 : Alpha-Beta Plaits Catalytic domain
1.10.473.10 : Catalytic domain
E.C. 3.1.11.3 3.1.11.1 2.7.7.7
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
1.10.150.20 : DNA polymerase; domain 1 M00104 M00173 M00175 M00208 D00158
1.10.473.10 : M00175
1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4 M00173 M00175
3.30.420.10 : Nucleotidyltransferase; domain 5 M00206 T00252 M00019 M00020 M00135 M00146 M00166 M00173 M00175 M00186
3.30.70.370 : Alpha-Beta Plaits M00104 M00173 M00175
3.40.50.1010 : Rossmann fold M00175 D00158

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P00582 DNA polymerase I
POL I
EC 2.7.7.7
NP_418300.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491586.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01367 (5_3_exonuc)
PF02739 (5_3_exonuc_N)
PF00476 (DNA_pol_A)
PF01612 (DNA_pol_A_exo1)
[Graphical View]

KEGG enzyme name
exodeoxyribonuclease (lambda-induced)
(EC 3.1.11.3 )
lambda exonuclease
(EC 3.1.11.3 )
phage lambda-induced exonuclease
(EC 3.1.11.3 )
Escherichia coli exonuclease IV
(EC 3.1.11.3 )
E. coli exonuclease IV
(EC 3.1.11.3 )
exodeoxyribonuclease IV
(EC 3.1.11.3 )
exonuclease IV
(EC 3.1.11.3 )
exodeoxyribonuclease I
(EC 3.1.11.1 )
Escherichia coli exonuclease I
(EC 3.1.11.1 )
E. coli exonuclease I
(EC 3.1.11.1 )
exonuclease I
(EC 3.1.11.1 )
DNA-directed DNA polymerase
(EC 2.7.7.7 )
DNA polymerase I
(EC 2.7.7.7 )
DNA polymerase II
(EC 2.7.7.7 )
DNA polymerase III
(EC 2.7.7.7 )
DNA polymerase alpha
(EC 2.7.7.7 )
DNA polymerase beta
(EC 2.7.7.7 )
DNA polymerase gamma
(EC 2.7.7.7 )
DNA nucleotidyltransferase (DNA-directed)
(EC 2.7.7.7 )
DNA nucleotidyltransferase (DNA-directed)
(EC 2.7.7.7 )
deoxyribonucleate nucleotidyltransferase
(EC 2.7.7.7 )
deoxynucleate polymerase
(EC 2.7.7.7 )
deoxyribonucleic acid duplicase
(EC 2.7.7.7 )
deoxyribonucleic acid polymerase
(EC 2.7.7.7 )
deoxyribonucleic duplicase
(EC 2.7.7.7 )
deoxyribonucleic polymerase
(EC 2.7.7.7 )
deoxyribonucleic polymerase I
(EC 2.7.7.7 )
DNA duplicase
(EC 2.7.7.7 )
DNA nucleotidyltransferase
(EC 2.7.7.7 )
DNA polymerase
(EC 2.7.7.7 )
DNA replicase
(EC 2.7.7.7 )
DNA-dependent DNA polymerase
(EC 2.7.7.7 )
duplicase
(EC 2.7.7.7 )
Klenow fragment
(EC 2.7.7.7 )
sequenase
(EC 2.7.7.7 )
Taq DNA polymerase
(EC 2.7.7.7 )
Taq Pol I
(EC 2.7.7.7 )
Tca DNA polymerase
(EC 2.7.7.7 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00582 DPO1_ECOLI Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Single-chain monomer with multiple functions.

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism 2.7.7.7
MAP00240 Pyrimidine metabolism 2.7.7.7

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C02148 C00677 C00039 C00039 C00001 C00013 C00039 C00039 C01150
E.C. 3.1.11.3
3.1.11.1
2.7.7.7
2.7.7.7
2.7.7.7
3.1.11.3
3.1.11.1
3.1.11.3
3.1.11.1
2.7.7.7
2.7.7.7
3.1.11.3
3.1.11.1
3.1.11.3
3.1.11.1
Compound Divalent metal Deoxynucleoside triphosphate DNA(n) DNA(n+1) H2O Pyrophosphate DNA(n+1) DNA(n) 5'-Phosphomononucleotides
Type divalent metal (Ca2+, Mg2+) nucleotide nucleic acids nucleic acids H2O phosphate group/phosphate ion nucleic acids nucleic acids nucleotide
ChEBI 15377
 15377
 		29888
 29888
PubChem 22247451
 962
 22247451
 962
 		1023
 21961011
 1023
 21961011
1d8yA01 Unbound Unbound Unbound Bound:T-T-T-T (chain B) Unbound Unbound Unbound Unbound
1d9dA01 Bound:_ZN Unbound Unbound Analogue:_DA-U31-C31 (chain B) Unbound Unbound Unbound Unbound
1d9fA01 Bound:_ZN Unbound Unbound Analogue:_DT-U31-_DT (chain B) Unbound Unbound Unbound Unbound
1kfsA01 Bound:_MG,_ZN Unbound Unbound Bound:A-C-G (chain B) Unbound Unbound Unbound Unbound
1kfdA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1klnA01 Bound:_ZN Unbound Unbound Bound:G-C-C-T-C-G-C-G-G-C-G-G-C (chain B) Unbound Unbound Unbound Unbound
1krpA01 Bound:2x_ZN Unbound Unbound Analogue:T-T-PST (chain B) Unbound Unbound Unbound Unbound
1kspA01 Unbound Unbound Unbound Analogue:T-T-PST (chain B) Unbound Unbound Unbound Unbound
1qslA01 Analogue:_EU Unbound Unbound Bound:A-C-G-C Unbound Unbound Unbound Unbound
2kfnA01 Bound:_MN,_ZN Unbound Unbound Bound:T-A-US1-G (chain B) Unbound Unbound Unbound Unbound
2kfzA01 Bound:2x_ZN Unbound Unbound Bound:T-A-US1-G (chain B) Unbound Unbound Unbound Unbound
2kzmA01 Bound:_MN,_ZN Unbound Unbound Bound:C-G-C (chain B) Unbound Unbound Unbound Unbound
2kzzA01 Bound:2x_ZN Unbound Unbound Bound:A-C-G (chain B) Unbound Unbound Unbound Unbound
1d8yA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d9dA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d9fA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1kfsA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1kfdA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1klnA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1krpA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1kspA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qslA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kfnA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kfzA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kzmA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kzzA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d8yA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d9dA03 Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d9fA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1kfsA03 Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1kfdA03 Unbound Bound:CTP Unbound Unbound Unbound Unbound Unbound Unbound
1klnA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1krpA03 Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1kspA03 Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qslA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kfnA03 Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kfzA03 Bound:_ZN Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kzmA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kzzA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1d8yA04 Unbound Unbound Unbound Unbound Analogue:SO4_38 Unbound Unbound Unbound
1d9dA04 Unbound Unbound Unbound Unbound Analogue:SO4_38 Unbound Unbound Unbound
1d9fA04 Unbound Unbound Unbound Unbound Analogue:SO4_38 Unbound Unbound Unbound
1kfsA04 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1kfdA04 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1klnA04 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1krpA04 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1kspA04 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1qslA04 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kfnA04 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kfzA04 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kzmA04 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2kzzA04 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [12] & [16]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1d8yA01 ;TYR 497 ; ;ASP 501(divalent metal-A);ASP 424(divalent metal-B) mutant D355A;E357A
1d9dA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
1d9fA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
1kfsA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) mutant V324M
1kfdA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
1klnA01 GLU 357;TYR 497 ;GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) mutant D355A
1krpA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) mutant V324M
1kspA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B) mutant V324M
1qslA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
2kfnA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
2kfzA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
2kzmA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
2kzzA01 GLU 357;TYR 497 ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
1d8yA02
1d9dA02
1d9fA02
1kfsA02
1kfdA02
1klnA02
1krpA02
1kspA02
1qslA02
2kfnA02
2kfzA02
2kzmA02
2kzzA02
1d8yA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
1d9dA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
1d9fA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
1kfsA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
1kfdA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
1klnA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
1krpA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
1kspA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
1qslA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
2kfnA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
2kfzA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
2kzmA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
2kzzA03 ARG 682 ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1) GLN 708
1d8yA04 HIS 734;ARG 754;LYS 758 ILE 709
1d9dA04 HIS 734;ARG 754;LYS 758 ILE 709
1d9fA04 HIS 734;ARG 754;LYS 758 ILE 709
1kfsA04 HIS 734;ARG 754;LYS 758 ILE 709
1kfdA04 HIS 734;ARG 754;LYS 758 ILE 709
1klnA04 HIS 734;ARG 754;LYS 758 ILE 709
1krpA04 HIS 734;ARG 754;LYS 758 ILE 709
1kspA04 HIS 734;ARG 754;LYS 758 ILE 709
1qslA04 HIS 734;ARG 754;LYS 758 ILE 709
2kfnA04 HIS 734;ARG 754;LYS 758 ILE 709
2kfzA04 HIS 734;ARG 754;LYS 758 ILE 709
2kzmA04 HIS 734;ARG 754;LYS 758 ILE 709
2kzzA04 HIS 734;ARG 754;LYS 758 ILE 709

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
[6]
Fig.10, p.30-31 2
[8]
[12]
Fig.4, Fig.5, p.34-36
[13]
Fig.3
[14]
p.2026
[16]
p.615-616
[20]
[22]
p.101-102
[23]
p.7521
[26]
p.372
[28]
p.306
[30]
Fig.3
[32]
Fig.1
[33]
Fig.1
[43]

References
[1]
Resource
Comments
Medline ID
PubMed ID 7013792
Journal Biochemistry
Year 1981
Volume 20
Pages 1245-52
Authors Brody RS, Frey PA
Title Unambiguous determination of the stereochemistry of nucleotidyl transfer catalyzed by DNA polymerase I from Escherichia coli.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6343618
Journal J Mol Biol
Year 1983
Volume 166
Pages 453-6
Authors Brick P, Ollis D, Steitz TA
Title Crystallization and 7 A resolution electron density map of the large fragment of Escherichia coli DNA polymerase I.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID 85137890
PubMed ID 3883192
Journal Nature
Year 1985
Volume 313
Pages 762-6
Authors Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA
Title Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP.
Related PDB
Related UniProtKB P00582
[4]
Resource
Comments
Medline ID
PubMed ID 3323527
Journal J Mol Biol
Year 1987
Volume 198
Pages 123-7
Authors Clark JM, Joyce CM, Beardsley GP
Title Novel blunt-end addition reactions catalyzed by DNA polymerase I of Escherichia coli.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 2832946
Journal Science
Year 1988
Volume 240
Pages 199-201
Authors Derbyshire V, Freemont PS, Sanderson MR, Beese L, Friedman JM, Joyce CM, Steitz TA
Title Genetic and crystallographic studies of the 3',5'-exonucleolytic site of DNA polymerase I.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID 91114709
PubMed ID 1989886
Journal EMBO J
Year 1991
Volume 10
Pages 25-33
Authors Beese LS, Steitz TA
Title Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism.
Related PDB
Related UniProtKB P00582
[7]
Resource
Comments
Medline ID
PubMed ID 1726742
Journal Nucleic Acids Symp Ser
Year 1991
Volume (24)
Pages 185-8
Authors Lavrik OI
Title Oligonucleotides and their derivatives as tools for investigations of protein-nucleic acid interactions in template biocatalysis.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 1569092
Journal J Biol Chem
Year 1992
Volume 267
Pages 8417-28
Authors Polesky AH, Dahlberg ME, Benkovic SJ, Grindley ND, Joyce CM
Title Side chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli.
Related PDB
Related UniProtKB
[9]
Resource
Comments STRUCTURE BY NMR OF 728-777.
Medline ID 93183012
PubMed ID 8442659
Journal Arch Biochem Biophys
Year 1993
Volume 301
Pages 174-83
Authors Mullen GP, Vaughn JB Jr, Mildvan AS
Title Sequential proton NMR resonance assignments, circular dichroism, and structural properties of a 50-residue substrate-binding peptide from DNA polymerase I.
Related PDB
Related UniProtKB P00582
[10]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.9 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID 94083412
PubMed ID 8260491
Journal Biochemistry
Year 1993
Volume 32
Pages 14095-101
Authors Beese LS, Friedman JM, Steitz TA
Title Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate.
Related PDB 1kfd
Related UniProtKB P00582
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID 93227044
PubMed ID 8469987
Journal Science
Year 1993
Volume 260
Pages 352-5
Authors Beese LS, Derbyshire V, Steitz TA
Title Structure of DNA polymerase I Klenow fragment bound to duplex DNA.
Related PDB 1kln
Related UniProtKB P00582
[12]
Resource
Comments Review
Medline ID
PubMed ID
Journal Curr Opin Struct Biol
Year 1993
Volume 3
Pages 31-8
Authors Steitz TA
Title DNA- and RNA-dependent DNA polymerases.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 7528445
Journal Science
Year 1994
Volume 266
Pages 2022-5
Authors Steitz TA, Smerdon SJ, Jager J, Joyce CM
Title A unified polymerase mechanism for nonhomologous DNA and RNA polymerases.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 7801132
Journal Science
Year 1994
Volume 266
Pages 2025-6
Authors Pelletier H
Title Polymerase structures and mechanism.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 8594345
Journal Methods Enzymol
Year 1995
Volume 262
Pages 147-71
Authors Mullen GP
Title Solution structure of DNA polymerases and DNA polymerase-substrate complexes.
Related PDB
Related UniProtKB
[16]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
Medline ID 95364959
PubMed ID 7637814
Journal Nature
Year 1995
Volume 376
Pages 612-6
Authors Kim Y, Eom SH, Wang J, Lee DS, Suh SW, Steitz TA
Title Crystal structure of Thermus aquaticus DNA polymerase.
Related PDB 1taq
Related UniProtKB P19821
[17]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832.
Medline ID 96016150
PubMed ID 7568114
Journal Proc Natl Acad Sci U S A
Year 1995
Volume 92
Pages 9264-8
Authors Korolev S, Nayal M, Barnes WM, Di Cera E, Waksman G
Title Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability.
Related PDB 1ktq
Related UniProtKB P19821
[18]
Resource
Comments
Medline ID
PubMed ID 8679555
Journal Biochemistry
Year 1996
Volume 35
Pages 7256-66
Authors Kaushik N, Pandey VN, Modak MJ
Title Significance of the O-helix residues of Escherichia coli DNA polymerase I in DNA synthesis: dynamics of the dNTP binding pocket.
Related PDB
Related UniProtKB
[19]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID 96353982
PubMed ID 8717047
Journal Nature
Year 1996
Volume 382
Pages 278-81
Authors Eom SH, Wang J, Steitz TA
Title Structure of Taq ploymerase with DNA at the polymerase active site.
Related PDB 1tau
Related UniProtKB P19821
[20]
Resource
Comments
Medline ID
PubMed ID 9214499
Journal Nature
Year 1997
Volume 388
Pages 33-4
Authors Artymiuk PJ, Poirrette AR, Rice DW, Willett P
Title A polymerase I palm in adenylyl cyclase?
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 9396823
Journal Nucleic Acids Res
Year 1997
Volume 25
Pages 5110-8
Authors Moser MJ, Holley WR, Chatterjee A, Mian IS
Title The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains.
Related PDB
Related UniProtKB
[22]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 297-876
Medline ID 97169447
PubMed ID 9016716
Journal Structure
Year 1997
Volume 5
Pages 95-108
Authors Kiefer JR, Mao C, Hansen CJ, Basehore SL, Hogrefe HH, Braman JC, Beese LS
Title Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.
Related PDB 1xwl
Related UniProtKB P52026
[23]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 295-832.
Medline ID 99077817
PubMed ID 9857206
Journal EMBO J
Year 1998
Volume 17
Pages 7514-25
Authors Li Y, Korolev S, Waksman G
Title Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.
Related PDB 2ktq 3ktq 4ktq
Related UniProtKB P19821
[24]
Resource
Comments
Medline ID
PubMed ID 9523721
Journal Eur J Biochem
Year 1998
Volume 252
Pages 124-32
Authors Amblar M, Lopez P
Title Purification and properties of the 5'-3' exonuclease D190-->a mutant of DNA polymerase I from Streptococcus pneumoniae.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 9571040
Journal J Mol Biol
Year 1998
Volume 278
Pages 147-65
Authors Astatke M, Grindley ND, Joyce CM
Title How E. coli DNA polymerase I (Klenow fragment) distinguishes between deoxy- and dideoxynucleotides.
Related PDB
Related UniProtKB
[26]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID 98181033
PubMed ID 9514742
Journal J Mol Biol
Year 1998
Volume 277
Pages 363-77
Authors Brautigam CA, Steitz TA
Title Structural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates.
Related PDB 1kfs 1krp 1ksp
Related UniProtKB P00582
[27]
Resource
Comments
Medline ID
PubMed ID 9584195
Journal Mol Cell Biol
Year 1998
Volume 18
Pages 3552-62
Authors Mizuno T, Ito N, Yokoi M, Kobayashi A, Tamai K, Miyazawa H, Hanaoka F
Title The second-largest subunit of the mouse DNA polymerase alpha-primase complex facilitates both production and nuclear translocation of the catalytic subunit of DNA polymerase alpha.
Related PDB
Related UniProtKB
[28]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 297-876
Medline ID 98101648
PubMed ID 9440698
Journal Nature
Year 1998
Volume 391
Pages 304-7
Authors Kiefer JR, Mao C, Braman JC, Beese LS
Title Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal.
Related PDB 2bdp 3bdp 4bdp
Related UniProtKB P52026
[29]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 98445410
PubMed ID 9770525
Journal Proc Natl Acad Sci U S A
Year 1998
Volume 95
Pages 12562-7
Authors Murali R, Sharkey DJ, Daiss JL, Murthy HM
Title Crystal structure of Taq DNA polymerase in complex with an inhibitory Fab: the Fab is directed against an intermediate in the helix-coil dynamics of the enzyme.
Related PDB 1bgx
Related UniProtKB P19821
[30]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832.
Medline ID 98266352
PubMed ID 9605316
Journal Protein Sci
Year 1998
Volume 7
Pages 1116-23
Authors Li Y, Kong Y, Korolev S, Waksman G
Title Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates.
Related PDB 5ktq
Related UniProtKB P19821
[31]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
Medline ID 20133099
PubMed ID 10666572
Journal Acta Crystallogr D Biol Crystallogr
Year 1999
Volume 55
Pages 1971-7
Authors Urs UK, Murali R, Krishna Murthy HM
Title Structure of taq DNA polymerase shows a new orientation for the structure-specific nuclease domain.
Related PDB 1cmw
Related UniProtKB P19821
[32]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID 99105820
PubMed ID 9888810
Journal Biochemistry
Year 1999
Volume 38
Pages 696-704
Authors Brautigam CA, Sun S, Piccirilli JA, Steitz TA
Title Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli.
Related PDB 2kfn 2kfz 2kzm 2kzz
Related UniProtKB P00582
[33]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10631518
Journal Chem Biol
Year 1999
Volume 6
Pages 901-8
Authors Brautigam CA, Aschheim K, Steitz TA
Title Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment.
Related PDB 1qsl
Related UniProtKB
[34]
Resource
Comments
Medline ID
PubMed ID 9915846
Journal J Biol Chem
Year 1999
Volume 274
Pages 3067-75
Authors Minnick DT, Bebenek K, Osheroff WP, Turner RM Jr, Astatke M, Liu L, Kunkel TA, Joyce CM
Title Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment).
Related PDB
Related UniProtKB
[35]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 293-831.
Medline ID 99380545
PubMed ID 10449720
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 9491-6
Authors Li Y, Mitaxov V, Waksman G
Title Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation.
Related PDB 1qss 1qsy 1qtm
Related UniProtKB P19821
[36]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID 20056229
PubMed ID 10588690
Journal Proc Natl Acad Sci U S A
Year 1999
Volume 96
Pages 14240-5
Authors Teplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M
Title Structural origins of the exonuclease resistance of a zwitterionic RNA.
Related PDB 1d8y 1d9d 1d9f
Related UniProtKB P00582
[37]
Resource
Comments
Medline ID
PubMed ID 10924147
Journal Biochemistry
Year 2000
Volume 39
Pages 9508-13
Authors Kamiya H, Maki H, Kasai H
Title Two DNA polymerases of Escherichia coli display distinct misinsertion specificities for 2-hydroxy-dATP during DNA synthesis.
Related PDB
Related UniProtKB
[38]
Resource
Comments
Medline ID
PubMed ID 11004506
Journal Biochim Biophys Acta
Year 2000
Volume 1492
Pages 341-52
Authors Izumi M, Yokoi M, Nishikawa NS, Miyazawa H, Sugino A, Yamagishi M, Yamaguchi M, Matsukage A, Yatagai F, Hanaoka F
Title Transcription of the catalytic 180-kDa subunit gene of mouse DNA polymerase alpha is controlled by E2F, an Ets-related transcription factor, and Sp1.
Related PDB
Related UniProtKB
[39]
Resource
Comments
Medline ID
PubMed ID 10779513
Journal J Biol Chem
Year 2000
Volume 275
Pages 19685-92
Authors Gangurde R, Kaushik N, Singh K, Modak MJ
Title A carboxylate triad is essential for the polymerase activity of Escherichia coli DNA polymerase I (Klenow fragment). Presence of two functional triads at the catalytic center.
Related PDB
Related UniProtKB
[40]
Resource
Comments
Medline ID
PubMed ID 10818095
Journal J Biol Chem
Year 2000
Volume 275
Pages 23759-68
Authors Tuske S, Singh K, Kaushik N, Modak MJ
Title The J-helix of Escherichia coli DNA polymerase I (Klenow fragment) regulates polymerase and 3'- 5'-exonuclease functions.
Related PDB
Related UniProtKB
[41]
Resource
Comments
Medline ID
PubMed ID 11329298
Journal Biochemistry
Year 2001
Volume 40
Pages 2282-90
Authors Alekseyev YO, Dzantiev L, Romano LJ
Title Effects of benzo[a]pyrene DNA adducts on Escherichia coli DNA polymerase I (Klenow fragment) primer-template interactions: evidence for inhibition of the catalytically active ternary complex formation.
Related PDB
Related UniProtKB
[42]
Resource
Comments
Medline ID
PubMed ID 11506573
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 8125-6
Authors Kuhn U, Warzeska S, Pritzkow H, Kramer R
Title A bioinspired dicopper(II) catalyst for the transesterification of dimethyl phosphate.
Related PDB
Related UniProtKB
[43]
Resource
Comments
Medline ID
PubMed ID 11278428
Journal J Biol Chem
Year 2001
Volume 276
Pages 19172-81
Authors Amblar M, de Lacoba MG, Corrales MA, Lopez P
Title Biochemical analysis of point mutations in the 5'-3' exonuclease of DNA polymerase I of Streptococcus pneumoniae. Functional and structural implications.
Related PDB
Related UniProtKB
[44]
Resource
Comments
Medline ID
PubMed ID 11278911
Journal J Biol Chem
Year 2001
Volume 276
Pages 18836-42
Authors Shinkai A, Patel PH, Loeb LA
Title The conserved active site motif A of Escherichia coli DNA polymerase I is highly mutable.
Related PDB
Related UniProtKB
[45]
Resource
Comments
Medline ID
PubMed ID 11346641
Journal J Biol Chem
Year 2001
Volume 276
Pages 27562-7
Authors Tosaka A, Ogawa M, Yoshida S, Suzuki M
Title O-helix mutant T664P of Thermus aquaticus DNA polymerase I: altered catalytic properties for incorporation of incorrect nucleotides but not correct nucleotides.
Related PDB
Related UniProtKB
[46]
Resource
Comments
Medline ID
PubMed ID 11536367
Journal Mol Carcinog
Year 2001
Volume 31
Pages 171-83
Authors Popanda O, Flohr C, Dai JC, Hunzicker A, Thielmann HW
Title A mutation in subunit B of the DNA polymerase alpha-primase complex from Novikoff hepatoma cells concomitant with a conformational change and abnormal catalytic properties of the DNA polymerase alpha-primase complex.
Related PDB
Related UniProtKB
[47]
Resource
Comments
Medline ID
PubMed ID 11677239
Journal J Biol Chem
Year 2002
Volume 277
Pages 1653-61
Authors Arrigo CJ, Singh K, Modak MJ
Title DNA polymerase I of Mycobacterium tuberculosis: functional role of a conserved aspartate in the hinge joining the M and N helices.
Related PDB
Related UniProtKB
[48]
Resource
Comments
Medline ID
PubMed ID 12364611
Journal Nucleic Acids Res
Year 2002
Volume 30
Pages 4314-20
Authors Yang SW, Astatke M, Potter J, Chatterjee DK
Title Mutant Thermotoga neapolitana DNA polymerase I: altered catalytic properties for non-templated nucleotide addition and incorporation of correct nucleotides.
Related PDB
Related UniProtKB
[49]
Resource
Comments
Medline ID
PubMed ID 12649320
Journal Proc Natl Acad Sci U S A
Year 2003
Volume 100
Pages 3895-900
Authors Johnson SJ, Taylor JS, Beese LS
Title Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.
Related PDB 1l3s 1l3t 1l3u 1l3v 1l5u 1lv5
Related UniProtKB

Comments
This enzyme is composed of the N-terminal 5'-3' exonuclease (E.C. 3.1.11.3) domains, 3'-5' exonuclease (E.C. 3.1.11.1) domain, and the C-terminal DNA polymerase (E.C. 2.7.7.7) domains. The DNA polymerase belongs to the type-A family.
The structure and mechanism of 5'-3' exonuclease have not been elucidated yet.
According to the literature [6] & [12], the mechanisms of two active sites are as follows:
(A) Transfer of phosphoryl group from NTP to DNA (This reaction is the same as that of M00175 in EzCatDB.):
(A1) Divalent metal-1, which is bound to Asp882 and Glu883, interacts with acceptor, 3'-OH of DNA and activates it by lowering its pKa.
(A2) The acceptor, 3'-hydroxyl group, makes a nucleophilic attack on the transferred alpha-phosphoryl group of dNTP.
(A3) Divalent metal-1 and metal-2 stabilize the transition state by interacting with the transferred group, whereas the leaving groups, beta- and gamma-phosphate groups, are stabilized by divalent metal-2 along with mainchain amide of Gln708 and Ile 709, sidechain of Arg682, His734, Arg754 and Lys758.
(B) Hydrolysis of phosphoric ester of DNA:
(B1) Divalent metal-A, which is bound to Asp355, Glu357 & Asp501, activates a water moclecule by lowering its pKa. The position of this water is oriented by Glu357 & Tyr497.
(B2) The activated water makes a nucleophilic attack on the phosphoryl atom.
(B3) Divalent metal-A and metal-B stabilize the transition state by interacting with the transferred group, whereas the negative charge on the leaving group, 3'-oxyanion, is stabilized by divalent metal-B.

Created Updated
2004-03-03 2009-02-26