EzCatDB: M00019
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DB codeM00019
RLCP classification3.103.90020.1131 : Transfer
CATH domainDomain 13.30.-.-
Domain 23.30.420.10 : Nucleotidyltransferase; domain 5
Domain 33.30.70.270 : Alpha-Beta PlaitsCatalytic domain
Domain 41.10.287.280 : Helix HairpinsCatalytic domain
Domain 53.90.710.10
E.C.2.7.7.7

CATH domainRelated DB codes (homologues)
1.10.287.280 : Helix HairpinsM00104
3.30.420.10 : Nucleotidyltransferase; domain 5M00206,T00252,M00020,M00055,M00135,M00146,M00166,M00173,M00175,M00186
3.30.70.270 : Alpha-Beta PlaitsM00206,M00135,M00146,M00166,M00209

Enzyme Name
UniProtKBKEGG

P56689Q56366Q7SIG7
Protein nameDNA polymeraseDNA polymeraseDNA polymeraseDNA-directed DNA polymerase
DNA polymerase I
DNA polymerase II
DNA polymerase III
DNA polymerase alpha
DNA polymerase beta
DNA polymerase gamma
DNA nucleotidyltransferase (DNA-directed)
DNA nucleotidyltransferase (DNA-directed)
deoxyribonucleate nucleotidyltransferase
deoxynucleate polymerase
deoxyribonucleic acid duplicase
deoxyribonucleic acid polymerase
deoxyribonucleic duplicase
deoxyribonucleic polymerase
deoxyribonucleic polymerase I
DNA duplicase
DNA nucleotidyltransferase
DNA polymerase
DNA replicase
DNA-dependent DNA polymerase
duplicase
Klenow fragment
sequenase
Taq DNA polymerase
Taq Pol I
Tca DNA polymerase
SynonymsEC 2.7.7.7
TO POL
EC 2.7.7.7
EC 2.7.7.7
D Tok Pol
PfamPF00136 (DNA_pol_B)
PF03104 (DNA_pol_B_exo1)
[Graphical view]
PF00136 (DNA_pol_B)
PF03104 (DNA_pol_B_exo1)
[Graphical view]
PF00136 (DNA_pol_B)
PF03104 (DNA_pol_B_exo1)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00240Pyrimidine metabolism

UniProtKB:Accession NumberP56689Q56366Q7SIG7
Entry nameDPOL_THEGODPOL_THES9DPOL_DESST
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


Subcellular location


Cofactor

Binds 2 magnesium ions.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00677C00039C00013C00039
CompoundMagnesiumDeoxynucleoside triphosphateDNA(n)PyrophosphateDNA(n+1)
Typedivalent metal (Ca2+, Mg2+)nucleotidenucleic acidsphosphate group/phosphate ionnucleic acids
ChEBI18420


29888

PubChem888


21961011
1023

             
1tgoA01UnboundUnboundUnboundUnboundUnbound
1qhtA01UnboundUnboundUnboundUnboundUnbound
1qqcA01UnboundUnboundUnboundUnboundUnbound
1d5aA01UnboundUnboundUnboundUnboundUnbound
1gcxA01UnboundUnboundUnboundUnboundUnbound
1tgoA02UnboundUnboundUnboundUnboundUnbound
1qhtA02UnboundUnboundUnboundUnboundUnbound
1qqcA02Bound:2x_MGUnboundUnboundUnboundUnbound
1d5aA02Bound:2x_MGUnboundUnboundUnboundUnbound
1gcxA02UnboundUnboundUnboundUnboundUnbound
1tgoA03UnboundUnboundUnboundUnboundUnbound
1qhtA03UnboundUnboundUnboundUnboundUnbound
1qqcA03UnboundUnboundUnboundUnboundUnbound
1d5aA03UnboundUnboundUnboundUnboundUnbound
1gcxA03UnboundUnboundUnboundUnboundUnbound
1tgoA04UnboundUnboundUnboundUnboundUnbound
1qhtA04UnboundUnboundUnboundUnboundUnbound
1qqcA04UnboundUnboundUnboundUnboundUnbound
1d5aA04UnboundUnboundUnboundUnboundUnbound
1gcxA04UnboundUnboundUnboundUnboundUnbound
1tgoA05UnboundUnboundUnboundUnboundUnbound
1qhtA05UnboundUnboundUnboundUnboundUnbound
1qqcA05UnboundUnboundUnboundUnboundUnbound
1d5aA05UnboundUnboundUnboundUnboundUnbound
1gcxA05UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [12] & [17]
pdbCatalytic residuesCofactor-binding residues
          
1tgoA01 
 
1qhtA01 
 
1qqcA01 
 
1d5aA01 
 
1gcxA01 
 
1tgoA02 
 
1qhtA02 
 
1qqcA02 
 
1d5aA02 
 
1gcxA02 
 
1tgoA03 
ASP 404;ASP 542(Magnesium binding)
1qhtA03 
ASP 404;ASP 542(Magnesium binding)
1qqcA03 
ASP 404;ASP 542(Magnesium binding)
1d5aA03 
ASP 404;ASP 542(Magnesium binding)
1gcxA03 
ASP 404;ASP 542(Magnesium binding)
1tgoA04ARG 460;LYS 464;LYS 487;ASN 491
 
1qhtA04ARG 460;LYS 464;LYS 487;ASN 491
 
1qqcA04ARG 460;LYS 464;LYS 487;ASN 491
 
1d5aA04ARG 460;LYS 464;LYS 487;ASN 491
 
1gcxA04ARG 460;LYS 464;LYS 487;ASN 491
 
1tgoA05 
 
1qhtA05 
 
1qqcA05 
 
1d5aA05 
 
1gcxA05 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[12]p.453-456
[17]p.471-473

references
[1]
PubMed ID9757117
JournalActa Crystallogr D Biol Crystallogr
Year1998
Volume54
Pages994-5
AuthorsZhou M, Mao C, Rodriguez AC, Kiefer JR, Kucera RB, Beese LS
TitleCrystallization and preliminary diffraction analysis of a hyperthermostable DNA polymerase from a Thermococcus archaeon.
[2]
PubMed ID9685491
JournalNucleic Acids Res
Year1998
Volume26
Pages3746-52
AuthorsAravind L, Koonin EV
TitlePhosphoesterase domains associated with DNA polymerases of diverse origins.
[3]
PubMed ID10430556
JournalGenetics
Year1999
Volume152
Pages1249-67
AuthorsCann IK, Ishino Y
TitleArchaeal DNA replication: identifying the pieces to solve a puzzle.
[4]
PubMed ID10348896
JournalJ Biochem (Tokyo)
Year1999
Volume125
Pages983-6
AuthorsHashimoto H, Matsumoto T, Nishioka M, Yuasa T, Takeuchi S, Inoue T, Fujiwara S, Takagi M, Imanaka T, Kai Y
TitleCrystallographic studies on a family B DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1.
[5]
PubMed ID10075991
JournalNucleic Acids Res
Year1999
Volume27
Pages1609-18
AuthorsAravind L, Koonin EV
TitleDNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID99199230
PubMed ID10097083
JournalProc Natl Acad Sci U S A
Year1999
Volume96
Pages3600-5
AuthorsHopfner KP, Eichinger A, Engh RA, Laue F, Ankenbauer W, Huber R, Angerer B
TitleCrystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.
Related PDB1tgo
Related UniProtKBP56689
[7]
CommentsX|ray crystallography
PubMed ID10545321
JournalStructure Fold Des
Year1999
Volume7
Pages1189-99
AuthorsZhao Y, Jeruzalmi D, Moarefi I, Leighton L, Lasken R, Kuriyan J
TitleCrystal structure of an archaebacterial DNA polymerase.
Related PDB1d5a,1qqc
[8]
PubMed ID11027519
JournalBiochem Biophys Res Commun
Year2000
Volume276
Pages600-6
AuthorsHenneke G, Raffin JP, Ferrari E, Jonsson ZO, Dietrich J, Hubscher U
TitleThe PCNA from Thermococcus fumicolans functionally interacts with DNA polymerase delta.
[9]
PubMed ID10997874
JournalDNA Res
Year2000
Volume7
Pages243-51
AuthorsIwai T, Kurosawa N, Itoh YH, Kimura N, Horiuchi T
TitleSequence analysis of three family B DNA polymerases from the thermoacidophilic crenarchaeon Sulfurisphaera ohwakuensis.
[10]
PubMed ID10827184
JournalJ Biol Chem
Year2000
Volume275
Pages24693-700
AuthorsMa WP, Kaiser MW, Lyamicheva N, Schaefer JJ, Allawi HT, Takova T, Neri BP, Lyamichev VI
TitleRNA template-dependent 5' nuclease activity of Thermus aquaticus and Thermus thermophilus DNA polymerases.
[11]
PubMed ID11071805
JournalJ Mol Biol
Year2000
Volume304
Pages1-9
Authorsde Vega M, Lazaro JM, Salas M
TitlePhage phi 29 DNA polymerase residues involved in the proper stabilisation of the primer-terminus at the 3'-5' exonuclease active site.
[12]
CommentsX|ray crystallography
PubMed ID10860752
JournalJ Mol Biol
Year2000
Volume299
Pages447-62
AuthorsRodriguez AC, Park HW, Mao C, Beese LS
TitleCrystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7.
Related PDB1qht
[13]
PubMed ID11024170
JournalNucleic Acids Res
Year2000
Volume28
Pages3910-7
AuthorsBohlke K, Pisani FM, Vorgias CE, Frey B, Sobek H, Rossi M, Antranikian G
TitlePCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif.
[14]
PubMed ID11058140
JournalNucleic Acids Res
Year2000
Volume28
Pages4391-6
AuthorsSaves I, Eleaume H, Dietrich J, Masson JM
TitleThe thy pol-2 intein of Thermococcus hydrothermalis is an isoschizomer of PI-TliI and PI-TfuII endonucleases.
[15]
PubMed ID11584001
JournalJ Biol Chem
Year2001
Volume276
Pages45484-90
AuthorsLiu L, Komori K, Ishino S, Bocquier AA, Cann IK, Kohda D, Ishino Y
TitleThe archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus.
[16]
PubMed ID11319225
JournalJ Biol Chem
Year2001
Volume276
Pages27376-83
AuthorsShen Y, Musti K, Hiramoto M, Kikuchi H, Kawarabayashi Y, Matsui I
TitleInvariant Asp-1122 and Asp-1124 are essential residues for polymerization catalysis of family D DNA polymerase from Pyrococcus horikoshii.
[17]
CommentsX|ray crystallography
PubMed ID11178906
JournalJ Mol Biol
Year2001
Volume306
Pages469-77
AuthorsHashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, Kai Y
TitleCrystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1.
Related PDB1gcx
[18]
PubMed ID11443345
JournalJ Mol Evol
Year2001
Volume52
Pages419-25
AuthorsTakemura M
TitlePoxviruses and the origin of the eukaryotic nucleus.
[19]
PubMed ID11959500
JournalCurr Opin Struct Biol
Year2002
Volume12
Pages217-24
AuthorsJeruzalmi D, O'Donnell M, Kuriyan J
TitleClamp loaders and sliding clamps.
[20]
PubMed ID12445650
JournalFEMS Microbiol Lett
Year2002
Volume217
Pages89-94
AuthorsDietrich J, Schmitt P, Zieger M, Preve B, Rolland JL, Chaabihi H, Gueguen Y
TitlePCR performance of the highly thermostable proof-reading B-type DNA polymerase from Pyrococcus abyssi.
[21]
PubMed ID12415300
JournalNat Rev Mol Cell Biol
Year2002
Volume3
Pages826-35
AuthorsDavey MJ, Jeruzalmi D, Kuriyan J, O'Donnell M
TitleMotors and switches: AAA+ machines within the replisome.
[22]
PubMed ID12415291
JournalNat Struct Biol
Year2002
Volume9
Pages922-7
AuthorsFogg MJ, Pearl LH, Connolly BA
TitleStructural basis for uracil recognition by archaeal family B DNA polymerases.
[23]
PubMed ID11788711
JournalNucleic Acids Res
Year2002
Volume30
Pages482-96
AuthorsMakarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV
TitleA DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.

comments
This enzyme belongs to the DNA polymerase type-B family.
Although the structure of the C-terminal domain is slightly different from counterparts of bacteriophage, this enzyme shares similar catalytic domains and catalytic residues with the counterparts (M00020 in EzCatDB).
Thus, the catalytic mechanism of DNA polymerase must be similar to that of the counterpart (M00020 in EzCatDB).

createdupdated
2004-03-162009-02-26


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)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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