EzCatDB: M00175
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DB codeM00175
RLCP classification3.103.90020.1141 : Transfer
CATH domainDomain 13.40.50.1010 : Rossmann foldCatalytic domain
Domain 21.10.150.20 : DNA polymerase; domain 1
Domain 33.30.420.10 : Nucleotidyltransferase; domain 5
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.3.1.11.3,2.7.7.7

CATH domainRelated DB codes (homologues)
1.10.150.20 : DNA polymerase; domain 1M00055,M00104,M00173,M00208,D00158
1.10.473.10M00055
1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4M00055,M00173
3.30.420.10 : Nucleotidyltransferase; domain 5M00206,T00252,M00019,M00020,M00055,M00135,M00146,M00166,M00173,M00186
3.30.70.370 : Alpha-Beta PlaitsM00055,M00104,M00173
3.40.50.1010 : Rossmann foldM00055,D00158

Enzyme Name
UniProtKBKEGG

P19821P52026Q04957
Protein nameDNA polymerase I, thermostableDNA polymerase IDNA 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)

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)

SynonymsEC 2.7.7.7
Taq polymerase 1
POL I
EC 2.7.7.7
POL I
EC 2.7.7.7
PfamPF01367 (5_3_exonuc)
PF02739 (5_3_exonuc_N)
PF00476 (DNA_pol_A)
PF09281 (Taq-exonuc)
[Graphical view]
PF01367 (5_3_exonuc)
PF02739 (5_3_exonuc_N)
PF00476 (DNA_pol_A)
[Graphical view]
PF01367 (5_3_exonuc)
PF02739 (5_3_exonuc_N)
PF00476 (DNA_pol_A)
[Graphical view]

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

UniProtKB:Accession NumberP19821P52026Q04957
Entry nameDPO1_THEAQDPO1_BACSTDPO1_BACCA
ActivityDeoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Subunit
Single-chain monomer with multiple functions.Single-chain monomer with multiple functions.
Subcellular location


Cofactor



Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC02148C00677C00039C00039C00001C00013C00039C00039C01150
E.C.3.1.11.3,2.7.7.72.7.7.72.7.7.73.1.11.33.1.11.32.7.7.72.7.7.73.1.11.33.1.11.3
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



                 
1bgxT01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1cmwA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1taqA01Bound:_ZNUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1tauA01Bound:_ZNUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1bgxT02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1cmwA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1taqA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1tauA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1bgxT03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1cmwA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1taqA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1tauA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1jxeA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1ktqA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qssA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qsyA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qtmA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2ktqA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
3ktqA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
4ktqA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
5ktqA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l3sA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l3tA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l3uA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l3vA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l5uA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1lv5A01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1lv5B01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1xwlA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2bdpA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
3bdpA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
4bdpA01UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1bgxT04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1cmwA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1taqA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1tauA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1jxeA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1ktqA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qssA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qsyA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qtmA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2ktqA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
3ktqA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
4ktqA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
5ktqA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l3sA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l3tA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l3uA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l3vA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l5uA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1lv5A02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1lv5B02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1xwlA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2bdpA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
3bdpA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
4bdpA02UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1bgxT05UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1cmwA05UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1taqA05UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1tauA05UnboundUnboundBound:C-G-G-A-T-C-G-C(chain P)Unbound UnboundUnboundUnboundUnbound
1jxeA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1ktqA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qssA03Bound:2x_MGAnalogue:DG3Analogue:G-A-C-C-A-C-G-G-C-G-C-DDG(chain B)Unbound UnboundUnboundUnboundUnbound
1qsyA03Bound:2x_MGAnalogue:DADAnalogue:G-A-C-C-A-C-G-G-C-G-C-2DA(chain B)Unbound UnboundUnboundUnboundUnbound
1qtmA03Bound:2x_MGBound:TTPAnalogue:G-A-C-C-A-C-G-G-C-G-C-2DT(chain B)Unbound UnboundUnboundUnboundUnbound
2ktqA03Bound:_MGAnalogue:DCTAnalogue:G-A-C-C-A-C-G-G-C-G-C-DOC(chain B)Unbound UnboundUnboundUnboundUnbound
3ktqA03Bound:2x_MGAnalogue:DCTAnalogue:G-A-C-C-A-C-G-G-C-G-C-DOC(chain B)Unbound UnboundUnboundUnboundUnbound
4ktqA03UnboundUnboundAnalogue:G-A-C-C-A-C-G-G-C-G-C-DOC(chain B)Unbound UnboundUnboundUnboundUnbound
5ktqA03UnboundBound:DCPUnboundUnbound UnboundUnboundUnboundUnbound
1l3sA03Bound:_MGUnboundBound:G-C-G-A-T-C-A-C-G(chain B)Unbound UnboundUnboundUnboundUnbound
1l3tA03Bound:_MGUnboundBound:G-C-G-A-T-C-A-C-G-T(chain B)Unbound UnboundUnboundUnboundUnbound
1l3uA03Bound:_MGUnboundBound:G-C-G-A-T-C-A-C-G-T-A(chain B)Unbound UnboundUnboundUnboundUnbound
1l3vA03Bound:_MGUnboundBound:G-C-G-A-T-C-A-C-G-T-A-C-G-T-C(chain B)Unbound UnboundUnboundUnboundUnbound
1l5uA03Bound:_MGUnboundBound:G-C-G-A-T-C-A-C-G-T-A-C(chain B)Unbound UnboundUnboundUnboundUnbound
1lv5A03Bound:_MG,_MNBound:DCPAnalogue:G-G-A-T-C-A-G-C-G-A(chain C)Unbound UnboundUnboundUnboundUnbound
1lv5B03Bound:_MNBound:DCPAnalogue:G-G-A-T-C-A-G-C-G-A(chain E)Unbound UnboundUnboundUnboundUnbound
1xwlA03UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2bdpA03Bound:_MGUnboundBound:G-C-A-T-G-A-T-G-C(chain P)Unbound UnboundUnboundUnboundUnbound
3bdpA03UnboundUnboundAnalogue:G-C-A-T-G-A-T-G-C-2DT(chain P)Unbound UnboundUnboundUnboundUnbound
4bdpA03Bound:_MGUnboundBound:G-C-A-T-C-A-T-G-C-A-A(chain P)Unbound UnboundUnboundUnboundUnbound
1bgxT06UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1cmwA06UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1taqA06UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1tauA06UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1jxeA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1ktqA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qssA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qsyA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1qtmA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2ktqA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
3ktqA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
4ktqA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
5ktqA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1l3sA04UnboundUnboundUnboundUnbound Analogue:SO4 910UnboundUnboundUnbound
1l3tA04UnboundUnboundUnboundUnbound Analogue:SO4 910UnboundUnboundUnbound
1l3uA04UnboundUnboundUnboundUnbound Analogue:SO4 910UnboundUnboundUnbound
1l3vA04UnboundUnboundUnboundUnbound Analogue:SO4 910UnboundUnboundUnbound
1l5uA04UnboundUnboundUnboundUnbound Analogue:SO4 910UnboundUnboundUnbound
1lv5A04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1lv5B04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
1xwlA04UnboundUnboundUnboundUnbound UnboundUnboundUnboundUnbound
2bdpA04UnboundUnboundUnboundUnbound Analogue:SO4 910UnboundUnboundUnbound
3bdpA04UnboundUnboundUnboundUnbound Analogue:SO4 910UnboundUnboundUnbound
4bdpA04UnboundUnboundUnboundUnbound Analogue:SO4 910UnboundUnboundUnbound

Active-site residues
resource
literature [12] & [16]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1bgxT01 
ASP 18;ASP 119(divalent metal-1);ASP 142(divalent metal-1 & -2);ASP 144(divalent metal-2);GLU 117;ASP 120(divalent metal-3)
 
 
1cmwA01 
ASP 18;ASP 119(divalent metal-1);ASP 142(divalent metal-1 & -2);ASP 144(divalent metal-2);GLU 117;ASP 120(divalent metal-3)
 
 
1taqA01 
ASP 18;ASP 119(divalent metal-1);ASP 142(divalent metal-1 & -2);ASP 144(divalent metal-2);GLU 117;ASP 120(divalent metal-3)
 
 
1tauA01 
ASP 18;ASP 119(divalent metal-1);ASP 142(divalent metal-1 & -2);ASP 144(divalent metal-2);GLU 117;ASP 120(divalent metal-3)
 
 
1bgxT02 
 
 
 
1cmwA02 
 
 
 
1taqA02 
 
 
 
1tauA02 
 
 
 
1bgxT03 
 
 
 
1cmwA03 
 
 
 
1taqA03 
 
 
 
1tauA03 
 
 
 
1jxeA01 
 
 
 
1ktqA01 
 
 
 
1qssA01 
 
 
 
1qsyA01 
 
 
 
1qtmA01 
 
 
 
2ktqA01 
 
 
 
3ktqA01 
 
 
 
4ktqA01 
 
 
 
5ktqA01 
 
 
 
1l3sA01 
 
 
 
1l3tA01 
 
 
 
1l3uA01 
 
 
 
1l3vA01 
 
 
 
1l5uA01 
 
 
 
1lv5A01 
 
 
 
1lv5B01 
 
 
 
1xwlA01 
 
 
 
2bdpA01 
 
 
 
3bdpA01 
 
 
 
4bdpA01 
 
 
 
1bgxT04 
 
 
 
1cmwA04 
 
 
 
1taqA04 
 
 
 
1tauA04 
 
 
 
1jxeA02 
 
 
 
1ktqA02 
 
 
 
1qssA02 
 
 
 
1qsyA02 
 
 
 
1qtmA02 
 
 
 
2ktqA02 
 
 
 
3ktqA02 
 
 
 
4ktqA02 
 
 
 
5ktqA02 
 
 
 
1l3sA02 
 
 
 
1l3tA02 
 
 
 
1l3uA02 
 
 
 
1l3vA02 
 
 
 
1l5uA02 
 
 
 
1lv5A02 
 
 
 
1lv5B02 
 
 
 
1xwlA02 
 
 
 
2bdpA02 
 
 
 
3bdpA02 
 
 
 
4bdpA02 
 
 
 
1bgxT05ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
1cmwA05ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
1taqA05ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
mutant S575C, S576C, S577C
1tauA05ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
1jxeA03ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
1ktqA03ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
1qssA03ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
1qsyA03ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
1qtmA03ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
2ktqA03ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
3ktqA03ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
4ktqA03ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
5ktqA03ARG 587
ASP 610;TYR 611(divalent metal-2);ASP 785(divalent metal-1 & -2);GLU 786(divalent metal-1)
GLN 613
 
1l3sA03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
1l3tA03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
1l3uA03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
1l3vA03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
1l5uA03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
1lv5A03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
1lv5B03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
1xwlA03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
2bdpA03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
3bdpA03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
4bdpA03ARG 629
ASP 653;TYR 654(divalent metal-2);ASP 830(divalent metal-1 & -2);GLU 831(divalent metal-1)
GLN 656
 
1bgxT06HIS 639;ARG 659;LYS 663
 
ILE 614
 
1cmwA06HIS 639;ARG 659;LYS 663
 
ILE 614
 
1taqA06HIS 639;ARG 659;LYS 663
 
ILE 614
 
1tauA06HIS 639;ARG 659;LYS 663
 
ILE 614
 
1jxeA04HIS 639;ARG 659;LYS 663
 
ILE 614
 
1ktqA04HIS 639;ARG 659;LYS 663
 
ILE 614
 
1qssA04HIS 639;ARG 659;LYS 663
 
ILE 614
 
1qsyA04HIS 639;ARG 659;LYS 663
 
ILE 614
 
1qtmA04HIS 639;ARG 659;LYS 663
 
ILE 614
 
2ktqA04HIS 639;ARG 659;LYS 663
 
ILE 614
 
3ktqA04HIS 639;ARG 659;LYS 663
 
ILE 614
 
4ktqA04HIS 639;ARG 659;LYS 663
 
ILE 614
 
5ktqA04HIS 639;ARG 659;LYS 663
 
ILE 614
 
1l3sA04HIS 682;ARG 702;LYS 706
 
ILE 657
 
1l3tA04HIS 682;ARG 702;LYS 706
 
ILE 657
 
1l3uA04HIS 682;ARG 702;LYS 706
 
ILE 657
 
1l3vA04HIS 682;ARG 702;LYS 706
 
ILE 657
 
1l5uA04HIS 682;ARG 702;LYS 706
 
ILE 657
 
1lv5A04HIS 682;ARG 702;LYS 706
 
ILE 657
 
1lv5B04HIS 682;ARG 702;LYS 706
 
ILE 657
 
1xwlA04HIS 682;ARG 702;LYS 706
 
ILE 657
 
2bdpA04HIS 682;ARG 702;LYS 706
 
ILE 657
 
3bdpA04HIS 682;ARG 702;LYS 706
 
ILE 657
 
4bdpA04HIS 682;ARG 702;LYS 706
 
ILE 657
 

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 polymerase (E.C. 2.7.7.7) domains. However, the active site of the 3'-5' exonucleae is obsolete, unlike its conterpart from E. coli (M00055 in EzCatDB). The DNA polymerase belongs to the type-A family.
The mechanism of 5'-3' exonuclease has not been elucidated yet.
According to the literature [6] & [12], the mechanisms of this enzyme is as follows:
(A) Transfer of phosphoryl group from NTP to DNA.
(A1) Divalent metal-1, which is bound to Asp785 and Glu786, 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.
(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 Gln613 and Ile 614, sidechain of Arg682, His639, Arg659 and Lys663.

createdupdated
2004-03-032009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
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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