EzCatDB: M00055
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DB codeM00055
RLCP classification3.103.90020.1141 : Transfer
1.15.10100.1172 : Hydrolysis
CATH domainDomain 13.40.50.1010 : Rossmann fold
Domain 21.10.150.20 : DNA polymerase; domain 1
Domain 33.30.420.10 : Nucleotidyltransferase; domain 5Catalytic domain
Domain 41.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4
Domain 53.30.70.370 : Alpha-Beta PlaitsCatalytic domain
Domain 61.10.473.10Catalytic domain
E.C.3.1.11.3,3.1.11.1,2.7.7.7

CATH domainRelated DB codes (homologues)
1.10.150.20 : DNA polymerase; domain 1M00104,M00173,M00175,M00208,D00158
1.10.473.10M00175
1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4M00173,M00175
3.30.420.10 : Nucleotidyltransferase; domain 5M00206,T00252,M00019,M00020,M00135,M00146,M00166,M00173,M00175,M00186
3.30.70.370 : Alpha-Beta PlaitsM00104,M00173,M00175
3.40.50.1010 : Rossmann foldM00175,D00158

Enzyme Name
UniProtKBKEGG

P00582
Protein nameDNA polymerase Iexodeoxyribonuclease (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)

SynonymsPOL I
EC 2.7.7.7
RefSeqNP_418300.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491586.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF01367 (5_3_exonuc)
PF02739 (5_3_exonuc_N)
PF00476 (DNA_pol_A)
PF01612 (DNA_pol_A_exo1)
[Graphical view]

KEGG pathways
MAP codePathwaysE.C.
MAP00230Purine metabolism2.7.7.7
MAP00240Pyrimidine metabolism2.7.7.7

UniProtKB:Accession NumberP00582
Entry nameDPO1_ECOLI
ActivityDeoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
SubunitSingle-chain monomer with multiple functions.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC02148C00677C00039C00039C00001C00013C00039C00039C01150
E.C.3.1.11.3,3.1.11.1,2.7.7.72.7.7.72.7.7.73.1.11.3,3.1.11.13.1.11.3,3.1.11.12.7.7.72.7.7.73.1.11.3,3.1.11.13.1.11.3,3.1.11.1
CompoundDivalent metalDeoxynucleoside triphosphateDNA(n)DNA(n+1)H2OPyrophosphateDNA(n+1)DNA(n)5'-Phosphomononucleotides
Typedivalent metal (Ca2+, Mg2+)nucleotidenucleic acidsnucleic acidsH2Ophosphate group/phosphate ionnucleic acidsnucleic acidsnucleotide
ChEBI



15377
29888



PubChem



962
22247451
21961011
1023



                 
1d8yA01UnboundUnboundUnboundBound:T-T-T-T(chain B) UnboundUnboundUnboundUnbound
1d9dA01Bound:_ZNUnboundUnboundAnalogue:_DA-U31-C31(chain B) UnboundUnboundUnboundUnbound
1d9fA01Bound:_ZNUnboundUnboundAnalogue:_DT-U31-_DT(chain B) UnboundUnboundUnboundUnbound
1kfsA01Bound:_MG,_ZNUnboundUnboundBound:A-C-G(chain B) UnboundUnboundUnboundUnbound
1kfdA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1klnA01Bound:_ZNUnboundUnboundBound:G-C-C-T-C-G-C-G-G-C-G-G-C(chain B) UnboundUnboundUnboundUnbound
1krpA01Bound:2x_ZNUnboundUnboundAnalogue:T-T-PST(chain B) UnboundUnboundUnboundUnbound
1kspA01UnboundUnboundUnboundAnalogue:T-T-PST(chain B) UnboundUnboundUnboundUnbound
1qslA01Analogue:_EUUnboundUnboundBound:A-C-G-C UnboundUnboundUnboundUnbound
2kfnA01Bound:_MN,_ZNUnboundUnboundBound:T-A-US1-G(chain B) UnboundUnboundUnboundUnbound
2kfzA01Bound:2x_ZNUnboundUnboundBound:T-A-US1-G(chain B) UnboundUnboundUnboundUnbound
2kzmA01Bound:_MN,_ZNUnboundUnboundBound:C-G-C(chain B) UnboundUnboundUnboundUnbound
2kzzA01Bound:2x_ZNUnboundUnboundBound:A-C-G(chain B) UnboundUnboundUnboundUnbound
1d8yA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1d9dA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1d9fA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1kfsA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1kfdA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1klnA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1krpA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1kspA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qslA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kfnA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kfzA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kzmA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kzzA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1d8yA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1d9dA03Bound:_ZNUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1d9fA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1kfsA03Bound:_ZNUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1kfdA03UnboundBound:CTPUnboundUnbound UnboundUnboundUnboundUnbound
1klnA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1krpA03Bound:_ZNUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1kspA03Bound:_ZNUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qslA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kfnA03Bound:_ZNUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kfzA03Bound:_ZNUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kzmA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kzzA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1d8yA04UnboundUnboundUnboundUnbound Analogue:SO4 38UnboundUnboundUnbound
1d9dA04UnboundUnboundUnboundUnbound Analogue:SO4 38UnboundUnboundUnbound
1d9fA04UnboundUnboundUnboundUnbound Analogue:SO4 38UnboundUnboundUnbound
1kfsA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1kfdA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1klnA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1krpA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1kspA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qslA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kfnA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kfzA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kzmA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2kzzA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound

Active-site residues
resource
literature [12] & [16]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1d8yA01       ;TYR 497
                              ;       ;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
mutant D355A;E357A
1d9dA01GLU 357;TYR 497
ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
 
1d9fA01GLU 357;TYR 497
ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
 
1kfsA01GLU 357;TYR 497
ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
mutant V324M
1kfdA01GLU 357;TYR 497
ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
 
1klnA01GLU 357;TYR 497
                              ;GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
mutant D355A
1krpA01GLU 357;TYR 497
ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
mutant V324M
1kspA01GLU 357;TYR 497
ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
mutant V324M
1qslA01GLU 357;TYR 497
ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
 
2kfnA01GLU 357;TYR 497
ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
 
2kfzA01GLU 357;TYR 497
ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
 
2kzmA01GLU 357;TYR 497
ASP 355(divalent metal-A & -B);GLU 357;ASP 501(divalent metal-A);ASP 424(divalent metal-B)
 
 
2kzzA01GLU 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 
 
 
 
1d8yA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
1d9dA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
1d9fA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
1kfsA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
1kfdA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
1klnA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
1krpA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
1kspA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
1qslA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
2kfnA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
2kfzA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
2kzmA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
2kzzA03ARG 682
ASP 705;TYR 706(divalent metal-2);ASP 882(divalent metal-1 & -2);GLU 883(divalent metal-1)
GLN 708
 
1d8yA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
1d9dA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
1d9fA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
1kfsA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
1kfdA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
1klnA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
1krpA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
1kspA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
1qslA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
2kfnA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
2kfzA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
2kzmA04HIS 734;ARG 754;LYS 758
 
ILE 709
 
2kzzA04HIS 734;ARG 754;LYS 758
 
ILE 709
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[5]

[6]Fig.10, p.30-312
[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]
PubMed ID7013792
JournalBiochemistry
Year1981
Volume20
Pages1245-52
AuthorsBrody RS, Frey PA
TitleUnambiguous determination of the stereochemistry of nucleotidyl transfer catalyzed by DNA polymerase I from Escherichia coli.
[2]
PubMed ID6343618
JournalJ Mol Biol
Year1983
Volume166
Pages453-6
AuthorsBrick P, Ollis D, Steitz TA
TitleCrystallization and 7 A resolution electron density map of the large fragment of Escherichia coli DNA polymerase I.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID85137890
PubMed ID3883192
JournalNature
Year1985
Volume313
Pages762-6
AuthorsOllis DL, Brick P, Hamlin R, Xuong NG, Steitz TA
TitleStructure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP.
Related UniProtKBP00582
[4]
PubMed ID3323527
JournalJ Mol Biol
Year1987
Volume198
Pages123-7
AuthorsClark JM, Joyce CM, Beardsley GP
TitleNovel blunt-end addition reactions catalyzed by DNA polymerase I of Escherichia coli.
[5]
PubMed ID2832946
JournalScience
Year1988
Volume240
Pages199-201
AuthorsDerbyshire V, Freemont PS, Sanderson MR, Beese L, Friedman JM, Joyce CM, Steitz TA
TitleGenetic and crystallographic studies of the 3',5'-exonucleolytic site of DNA polymerase I.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID91114709
PubMed ID1989886
JournalEMBO J
Year1991
Volume10
Pages25-33
AuthorsBeese LS, Steitz TA
TitleStructural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism.
Related UniProtKBP00582
[7]
PubMed ID1726742
JournalNucleic Acids Symp Ser
Year1991
Volume(24)
Pages185-8
AuthorsLavrik OI
TitleOligonucleotides and their derivatives as tools for investigations of protein-nucleic acid interactions in template biocatalysis.
[8]
PubMed ID1569092
JournalJ Biol Chem
Year1992
Volume267
Pages8417-28
AuthorsPolesky AH, Dahlberg ME, Benkovic SJ, Grindley ND, Joyce CM
TitleSide chains involved in catalysis of the polymerase reaction of DNA polymerase I from Escherichia coli.
[9]
CommentsSTRUCTURE BY NMR OF 728-777.
Medline ID93183012
PubMed ID8442659
JournalArch Biochem Biophys
Year1993
Volume301
Pages174-83
AuthorsMullen GP, Vaughn JB Jr, Mildvan AS
TitleSequential proton NMR resonance assignments, circular dichroism, and structural properties of a 50-residue substrate-binding peptide from DNA polymerase I.
Related UniProtKBP00582
[10]
CommentsX-RAY CRYSTALLOGRAPHY (3.9 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID94083412
PubMed ID8260491
JournalBiochemistry
Year1993
Volume32
Pages14095-101
AuthorsBeese LS, Friedman JM, Steitz TA
TitleCrystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate.
Related PDB1kfd
Related UniProtKBP00582
[11]
CommentsX-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID93227044
PubMed ID8469987
JournalScience
Year1993
Volume260
Pages352-5
AuthorsBeese LS, Derbyshire V, Steitz TA
TitleStructure of DNA polymerase I Klenow fragment bound to duplex DNA.
Related PDB1kln
Related UniProtKBP00582
[12]
CommentsReview
JournalCurr Opin Struct Biol
Year1993
Volume3
Pages31-8
AuthorsSteitz TA
TitleDNA- and RNA-dependent DNA polymerases.
[13]
PubMed ID7528445
JournalScience
Year1994
Volume266
Pages2022-5
AuthorsSteitz TA, Smerdon SJ, Jager J, Joyce CM
TitleA unified polymerase mechanism for nonhomologous DNA and RNA polymerases.
[14]
PubMed ID7801132
JournalScience
Year1994
Volume266
Pages2025-6
AuthorsPelletier H
TitlePolymerase structures and mechanism.
[15]
PubMed ID8594345
JournalMethods Enzymol
Year1995
Volume262
Pages147-71
AuthorsMullen GP
TitleSolution structure of DNA polymerases and DNA polymerase-substrate complexes.
[16]
CommentsX-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
Medline ID95364959
PubMed ID7637814
JournalNature
Year1995
Volume376
Pages612-6
AuthorsKim Y, Eom SH, Wang J, Lee DS, Suh SW, Steitz TA
TitleCrystal structure of Thermus aquaticus DNA polymerase.
Related PDB1taq
Related UniProtKBP19821
[17]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832.
Medline ID96016150
PubMed ID7568114
JournalProc Natl Acad Sci U S A
Year1995
Volume92
Pages9264-8
AuthorsKorolev S, Nayal M, Barnes WM, Di Cera E, Waksman G
TitleCrystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-A resolution: structural basis for thermostability.
Related PDB1ktq
Related UniProtKBP19821
[18]
PubMed ID8679555
JournalBiochemistry
Year1996
Volume35
Pages7256-66
AuthorsKaushik N, Pandey VN, Modak MJ
TitleSignificance of the O-helix residues of Escherichia coli DNA polymerase I in DNA synthesis: dynamics of the dNTP binding pocket.
[19]
CommentsX-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
Medline ID96353982
PubMed ID8717047
JournalNature
Year1996
Volume382
Pages278-81
AuthorsEom SH, Wang J, Steitz TA
TitleStructure of Taq ploymerase with DNA at the polymerase active site.
Related PDB1tau
Related UniProtKBP19821
[20]
PubMed ID9214499
JournalNature
Year1997
Volume388
Pages33-4
AuthorsArtymiuk PJ, Poirrette AR, Rice DW, Willett P
TitleA polymerase I palm in adenylyl cyclase?
[21]
PubMed ID9396823
JournalNucleic Acids Res
Year1997
Volume25
Pages5110-8
AuthorsMoser MJ, Holley WR, Chatterjee A, Mian IS
TitleThe proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains.
[22]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 297-876
Medline ID97169447
PubMed ID9016716
JournalStructure
Year1997
Volume5
Pages95-108
AuthorsKiefer JR, Mao C, Hansen CJ, Basehore SL, Hogrefe HH, Braman JC, Beese LS
TitleCrystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.
Related PDB1xwl
Related UniProtKBP52026
[23]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 295-832.
Medline ID99077817
PubMed ID9857206
JournalEMBO J
Year1998
Volume17
Pages7514-25
AuthorsLi Y, Korolev S, Waksman G
TitleCrystal 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 PDB2ktq,3ktq,4ktq
Related UniProtKBP19821
[24]
PubMed ID9523721
JournalEur J Biochem
Year1998
Volume252
Pages124-32
AuthorsAmblar M, Lopez P
TitlePurification and properties of the 5'-3' exonuclease D190-->a mutant of DNA polymerase I from Streptococcus pneumoniae.
[25]
PubMed ID9571040
JournalJ Mol Biol
Year1998
Volume278
Pages147-65
AuthorsAstatke M, Grindley ND, Joyce CM
TitleHow E. coli DNA polymerase I (Klenow fragment) distinguishes between deoxy- and dideoxynucleotides.
[26]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID98181033
PubMed ID9514742
JournalJ Mol Biol
Year1998
Volume277
Pages363-77
AuthorsBrautigam CA, Steitz TA
TitleStructural principles for the inhibition of the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates.
Related PDB1kfs,1krp,1ksp
Related UniProtKBP00582
[27]
PubMed ID9584195
JournalMol Cell Biol
Year1998
Volume18
Pages3552-62
AuthorsMizuno T, Ito N, Yokoi M, Kobayashi A, Tamai K, Miyazawa H, Hanaoka F
TitleThe 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.
[28]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 297-876
Medline ID98101648
PubMed ID9440698
JournalNature
Year1998
Volume391
Pages304-7
AuthorsKiefer JR, Mao C, Braman JC, Beese LS
TitleVisualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal.
Related PDB2bdp,3bdp,4bdp
Related UniProtKBP52026
[29]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID98445410
PubMed ID9770525
JournalProc Natl Acad Sci U S A
Year1998
Volume95
Pages12562-7
AuthorsMurali R, Sharkey DJ, Daiss JL, Murthy HM
TitleCrystal 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 PDB1bgx
Related UniProtKBP19821
[30]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 290-832.
Medline ID98266352
PubMed ID9605316
JournalProtein Sci
Year1998
Volume7
Pages1116-23
AuthorsLi Y, Kong Y, Korolev S, Waksman G
TitleCrystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates.
Related PDB5ktq
Related UniProtKBP19821
[31]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
Medline ID20133099
PubMed ID10666572
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages1971-7
AuthorsUrs UK, Murali R, Krishna Murthy HM
TitleStructure of taq DNA polymerase shows a new orientation for the structure-specific nuclease domain.
Related PDB1cmw
Related UniProtKBP19821
[32]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID99105820
PubMed ID9888810
JournalBiochemistry
Year1999
Volume38
Pages696-704
AuthorsBrautigam CA, Sun S, Piccirilli JA, Steitz TA
TitleStructures 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 PDB2kfn,2kfz,2kzm,2kzz
Related UniProtKBP00582
[33]
CommentsX-ray crystallography
PubMed ID10631518
JournalChem Biol
Year1999
Volume6
Pages901-8
AuthorsBrautigam CA, Aschheim K, Steitz TA
TitleStructural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment.
Related PDB1qsl
[34]
PubMed ID9915846
JournalJ Biol Chem
Year1999
Volume274
Pages3067-75
AuthorsMinnick DT, Bebenek K, Osheroff WP, Turner RM Jr, Astatke M, Liu L, Kunkel TA, Joyce CM
TitleSide chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment).
[35]
CommentsX-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 293-831.
Medline ID99380545
PubMed ID10449720
JournalProc Natl Acad Sci U S A
Year1999
Volume96
Pages9491-6
AuthorsLi Y, Mitaxov V, Waksman G
TitleStructure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation.
Related PDB1qss,1qsy,1qtm
Related UniProtKBP19821
[36]
CommentsX-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) OF KLENOW FRAGMENT.
Medline ID20056229
PubMed ID10588690
JournalProc Natl Acad Sci U S A
Year1999
Volume96
Pages14240-5
AuthorsTeplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M
TitleStructural origins of the exonuclease resistance of a zwitterionic RNA.
Related PDB1d8y,1d9d,1d9f
Related UniProtKBP00582
[37]
PubMed ID10924147
JournalBiochemistry
Year2000
Volume39
Pages9508-13
AuthorsKamiya H, Maki H, Kasai H
TitleTwo DNA polymerases of Escherichia coli display distinct misinsertion specificities for 2-hydroxy-dATP during DNA synthesis.
[38]
PubMed ID11004506
JournalBiochim Biophys Acta
Year2000
Volume1492
Pages341-52
AuthorsIzumi M, Yokoi M, Nishikawa NS, Miyazawa H, Sugino A, Yamagishi M, Yamaguchi M, Matsukage A, Yatagai F, Hanaoka F
TitleTranscription of the catalytic 180-kDa subunit gene of mouse DNA polymerase alpha is controlled by E2F, an Ets-related transcription factor, and Sp1.
[39]
PubMed ID10779513
JournalJ Biol Chem
Year2000
Volume275
Pages19685-92
AuthorsGangurde R, Kaushik N, Singh K, Modak MJ
TitleA 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.
[40]
PubMed ID10818095
JournalJ Biol Chem
Year2000
Volume275
Pages23759-68
AuthorsTuske S, Singh K, Kaushik N, Modak MJ
TitleThe J-helix of Escherichia coli DNA polymerase I (Klenow fragment) regulates polymerase and 3'- 5'-exonuclease functions.
[41]
PubMed ID11329298
JournalBiochemistry
Year2001
Volume40
Pages2282-90
AuthorsAlekseyev YO, Dzantiev L, Romano LJ
TitleEffects 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.
[42]
PubMed ID11506573
JournalJ Am Chem Soc
Year2001
Volume123
Pages8125-6
AuthorsKuhn U, Warzeska S, Pritzkow H, Kramer R
TitleA bioinspired dicopper(II) catalyst for the transesterification of dimethyl phosphate.
[43]
PubMed ID11278428
JournalJ Biol Chem
Year2001
Volume276
Pages19172-81
AuthorsAmblar M, de Lacoba MG, Corrales MA, Lopez P
TitleBiochemical analysis of point mutations in the 5'-3' exonuclease of DNA polymerase I of Streptococcus pneumoniae. Functional and structural implications.
[44]
PubMed ID11278911
JournalJ Biol Chem
Year2001
Volume276
Pages18836-42
AuthorsShinkai A, Patel PH, Loeb LA
TitleThe conserved active site motif A of Escherichia coli DNA polymerase I is highly mutable.
[45]
PubMed ID11346641
JournalJ Biol Chem
Year2001
Volume276
Pages27562-7
AuthorsTosaka A, Ogawa M, Yoshida S, Suzuki M
TitleO-helix mutant T664P of Thermus aquaticus DNA polymerase I: altered catalytic properties for incorporation of incorrect nucleotides but not correct nucleotides.
[46]
PubMed ID11536367
JournalMol Carcinog
Year2001
Volume31
Pages171-83
AuthorsPopanda O, Flohr C, Dai JC, Hunzicker A, Thielmann HW
TitleA 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.
[47]
PubMed ID11677239
JournalJ Biol Chem
Year2002
Volume277
Pages1653-61
AuthorsArrigo CJ, Singh K, Modak MJ
TitleDNA polymerase I of Mycobacterium tuberculosis: functional role of a conserved aspartate in the hinge joining the M and N helices.
[48]
PubMed ID12364611
JournalNucleic Acids Res
Year2002
Volume30
Pages4314-20
AuthorsYang SW, Astatke M, Potter J, Chatterjee DK
TitleMutant Thermotoga neapolitana DNA polymerase I: altered catalytic properties for non-templated nucleotide addition and incorporation of correct nucleotides.
[49]
PubMed ID12649320
JournalProc Natl Acad Sci U S A
Year2003
Volume100
Pages3895-900
AuthorsJohnson SJ, Taylor JS, Beese LS
TitleProcessive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations.
Related PDB1l3s,1l3t,1l3u,1l3v,1l5u,1lv5

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.

createdupdated
2004-03-032009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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