M00019
type: Enzyme
rlcp: p1131
cath: http://ezcatdb.cbrc.jp/EzCatDB/cath/3.30.-.-
cath: Nucleotidyltransferase; domain 5
cath: Alpha-Beta Plaits
cath: Helix Hairpins
cath: http://ezcatdb.cbrc.jp/EzCatDB/cath/3.90.710.10
ec: https://purl.uniprot.org/enzyme/2.7.7.7
uniprot: P56689
uniprot: Q56366
uniprot: Q7SIG7
kegg enzyme: DNA-directed DNA polymerase
kegg enzyme: DNA polymerase I
kegg enzyme: DNA polymerase II
kegg enzyme: DNA polymerase III
kegg enzyme: DNA polymerase alpha
kegg enzyme: DNA polymerase beta
kegg enzyme: DNA polymerase gamma
kegg enzyme: DNA nucleotidyltransferase (DNA-directed)
kegg enzyme: deoxyribonucleate nucleotidyltransferase
kegg enzyme: deoxynucleate polymerase
kegg enzyme: deoxyribonucleic acid duplicase
kegg pathway: Purine metabolism
kegg pathway: Pyrimidine metabolism
kegg cofactor: Magnesium
kegg substrate: Deoxynucleoside triphosphate
kegg substrate: DNA(n)
kegg product: Pyrophosphate
kegg product: DNA(n)
pdb: 1tgoA01
pdb: 1qhtA01
pdb: 1qqcA01
pdb: 1d5aA01
pdb: 1gcxA01
pdb: 1tgoA02
pdb: 1qhtA02
pdb: 1qqcA02
pdb: 1d5aA02
pdb: 1gcxA02
pdb: 1tgoA03
pdb: 1qhtA03
pdb: 1qqcA03
pdb: 1d5aA03
pdb: 1gcxA03
pdb: 1tgoA04
pdb: 1qhtA04
pdb: 1qqcA04
pdb: 1d5aA04
pdb: 1gcxA04
pdb: 1tgoA05
pdb: 1qhtA05
pdb: 1qqcA05
pdb: 1d5aA05
pdb: 1gcxA05
active site residues resources: PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif.
active site residues resources: Poxviruses and the origin of the eukaryotic nucleus.
references: Crystallization and preliminary diffraction analysis of a hyperthermostable DNA polymerase from a Thermococcus archaeon.
references: Phosphoesterase domains associated with DNA polymerases of diverse origins.
references: Archaeal DNA replication: identifying the pieces to solve a puzzle.
references: Crystallographic studies on a family B DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1.
references: DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history.
references: Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.
references: Crystal structure of an archaebacterial DNA polymerase.
references: The PCNA from Thermococcus fumicolans functionally interacts with DNA polymerase delta.
references: Sequence analysis of three family B DNA polymerases from the thermoacidophilic crenarchaeon Sulfurisphaera ohwakuensis.
references: RNA template-dependent 5' nuclease activity of Thermus aquaticus and Thermus thermophilus DNA polymerases.
references: Phage phi 29 DNA polymerase residues involved in the proper stabilisation of the primer-terminus at the 3'-5' exonuclease active site.
references: Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7.
references: PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif.
references: The thy pol-2 intein of Thermococcus hydrothermalis is an isoschizomer of PI-TliI and PI-TfuII endonucleases.
references: The archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus.
references: Invariant Asp-1122 and Asp-1124 are essential residues for polymerization catalysis of family D DNA polymerase from Pyrococcus horikoshii.
references: Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1.
references: Poxviruses and the origin of the eukaryotic nucleus.
references: Clamp loaders and sliding clamps.
references: PCR performance of the highly thermostable proof-reading B-type DNA polymerase from Pyrococcus abyssi.
references: Motors and switches: AAA+ machines within the replisome.
references: Structural basis for uracil recognition by archaeal family B DNA polymerases.
references: A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.
comment: 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).

Nucleotidyltransferase; domain 5
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.30.420.10

Alpha-Beta Plaits
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.30.70.270
catalytic domain: index.html

Helix Hairpins
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/1.10.287.280
catalytic domain: index.html

Purine metabolism
type: KeggPathway
references: KEGG:MAP00230

Pyrimidine metabolism
type: KeggPathway
references: KEGG:MAP00240

Magnesium
type: KeggCofactor
references: KEGG:C00305
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:18420
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

Deoxynucleoside triphosphate
type: KeggSubstrate
references: KEGG:C00677
compound type: nucleotide

DNA(n)
type: KeggSubstrate
references: KEGG:C00039
compound type: nucleic acids
type: KeggProduct
label: DNA(n+1)

Pyrophosphate
type: KeggProduct
references: KEGG:C00013
compound type: phosphate group/phosphate ion
references: CHEBI:29888
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1tgoA03
type: Pdb
references: 1tgo
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1tgo
cofactor binding residue: ASP 404;ASP 542(Magnesium binding)

1qhtA03
type: Pdb
references: 1qht
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qht
cofactor binding residue: ASP 404;ASP 542(Magnesium binding)

1qqcA03
type: Pdb
references: 1qqc
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qqc
cofactor binding residue: ASP 404;ASP 542(Magnesium binding)

1d5aA03
type: Pdb
references: 1d5a
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d5a
cofactor binding residue: ASP 404;ASP 542(Magnesium binding)

1gcxA03
type: Pdb
references: 1gcx
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1gcx
cofactor binding residue: ASP 404;ASP 542(Magnesium binding)

1tgoA04
type: Pdb
references: 1tgo
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1tgo
catalytic residue: ARG 460;LYS 464;LYS 487;ASN 491

1qhtA04
type: Pdb
references: 1qht
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qht
catalytic residue: ARG 460;LYS 464;LYS 487;ASN 491

1qqcA04
type: Pdb
references: 1qqc
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1qqc
catalytic residue: ARG 460;LYS 464;LYS 487;ASN 491

1d5aA04
type: Pdb
references: 1d5a
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1d5a
catalytic residue: ARG 460;LYS 464;LYS 487;ASN 491

1gcxA04
type: Pdb
references: 1gcx
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1gcx
catalytic residue: ARG 460;LYS 464;LYS 487;ASN 491

Crystallization and preliminary diffraction analysis of a hyperthermostable DNA polymerase from a Thermococcus archaeon.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9757117
journal: Acta Crystallogr D Biol Crystallogr
volume: 54
pages: 994-5
published year: 1998
authors:
  item: Zhou M
  item: Mao C
  item: Rodriguez AC
  item: Kiefer JR
  item: Kucera RB
  item: Beese LS

Phosphoesterase domains associated with DNA polymerases of diverse origins.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9685491
journal: Nucleic Acids Res
volume: 26
pages: 3746-52
published year: 1998
authors:
  item: Aravind L
  item: Koonin EV

Archaeal DNA replication: identifying the pieces to solve a puzzle.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10430556
journal: Genetics
volume: 152
pages: 1249-67
published year: 1999
authors:
  item: Cann IK
  item: Ishino Y

Crystallographic studies on a family B DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10348896
journal: J Biochem (Tokyo)
volume: 125
pages: 983-6
published year: 1999
authors:
  item: Hashimoto H
  item: Matsumoto T
  item: Nishioka M
  item: Yuasa T
  item: Takeuchi S
  item: Inoue T
  item: Fujiwara S
  item: Takagi M
  item: Imanaka T
  item: Kai Y

DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10075991
journal: Nucleic Acids Res
volume: 27
pages: 1609-18
published year: 1999
authors:
  item: Aravind L
  item: Koonin EV

Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
medline id: 99199230
references: http://www.ncbi.nlm.nih.gov/pubmed/10097083
journal: Proc Natl Acad Sci U S A
volume: 96
pages: 3600-5
published year: 1999
authors:
  item: Hopfner KP
  item: Eichinger A
  item: Engh RA
  item: Laue F
  item: Ankenbauer W
  item: Huber R
  item: Angerer B
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P56689

Crystal structure of an archaebacterial DNA polymerase.
type: BibliographicResource
comment: X|ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/10545321
journal: Structure Fold Des
volume: 7
pages: 1189-99
published year: 1999
authors:
  item: Zhao Y
  item: Jeruzalmi D
  item: Moarefi I
  item: Leighton L
  item: Lasken R
  item: Kuriyan J
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

The PCNA from Thermococcus fumicolans functionally interacts with DNA polymerase delta.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11027519
journal: Biochem Biophys Res Commun
volume: 276
pages: 600-6
published year: 2000
authors:
  item: Henneke G
  item: Raffin JP
  item: Ferrari E
  item: Jonsson ZO
  item: Dietrich J
  item: Hubscher U

Sequence analysis of three family B DNA polymerases from the thermoacidophilic crenarchaeon Sulfurisphaera ohwakuensis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10997874
journal: DNA Res
volume: 7
pages: 243-51
published year: 2000
authors:
  item: Iwai T
  item: Kurosawa N
  item: Itoh YH
  item: Kimura N
  item: Horiuchi T

RNA template-dependent 5' nuclease activity of Thermus aquaticus and Thermus thermophilus DNA polymerases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10827184
journal: J Biol Chem
volume: 275
pages: 24693-700
published year: 2000
authors:
  item: Ma WP
  item: Kaiser MW
  item: Lyamicheva N
  item: Schaefer JJ
  item: Allawi HT
  item: Takova T
  item: Neri BP
  item: Lyamichev VI

Phage phi 29 DNA polymerase residues involved in the proper stabilisation of the primer-terminus at the 3'-5' exonuclease active site.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11071805
journal: J Mol Biol
volume: 304
pages: 1-9
published year: 2000
authors:
  item: de Vega M
  item: Lazaro JM
  item: Salas M

Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7.
type: BibliographicResource
comment: X|ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/10860752
journal: J Mol Biol
volume: 299
pages: 447-62
published year: 2000
authors:
  item: Rodriguez AC
  item: Park HW
  item: Mao C
  item: Beese LS
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11024170
journal: Nucleic Acids Res
volume: 28
pages: 3910-7
published year: 2000
authors:
  item: Bohlke K
  item: Pisani FM
  item: Vorgias CE
  item: Frey B
  item: Sobek H
  item: Rossi M
  item: Antranikian G

The thy pol-2 intein of Thermococcus hydrothermalis is an isoschizomer of PI-TliI and PI-TfuII endonucleases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11058140
journal: Nucleic Acids Res
volume: 28
pages: 4391-6
published year: 2000
authors:
  item: Saves I
  item: Eleaume H
  item: Dietrich J
  item: Masson JM

The archaeal DNA primase: biochemical characterization of the p41-p46 complex from Pyrococcus furiosus.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11584001
journal: J Biol Chem
volume: 276
pages: 45484-90
published year: 2001
authors:
  item: Liu L
  item: Komori K
  item: Ishino S
  item: Bocquier AA
  item: Cann IK
  item: Kohda D
  item: Ishino Y

Invariant Asp-1122 and Asp-1124 are essential residues for polymerization catalysis of family D DNA polymerase from Pyrococcus horikoshii.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11319225
journal: J Biol Chem
volume: 276
pages: 27376-83
published year: 2001
authors:
  item: Shen Y
  item: Musti K
  item: Hiramoto M
  item: Kikuchi H
  item: Kawarabayashi Y
  item: Matsui I

Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1.
type: BibliographicResource
comment: X|ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/11178906
journal: J Mol Biol
volume: 306
pages: 469-77
published year: 2001
authors:
  item: Hashimoto H
  item: Nishioka M
  item: Fujiwara S
  item: Takagi M
  item: Imanaka T
  item: Inoue T
  item: Kai Y
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Poxviruses and the origin of the eukaryotic nucleus.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11443345
journal: J Mol Evol
volume: 52
pages: 419-25
published year: 2001
authors:
  item: Takemura M

Clamp loaders and sliding clamps.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11959500
journal: Curr Opin Struct Biol
volume: 12
pages: 217-24
published year: 2002
authors:
  item: Jeruzalmi D
  item: O'Donnell M
  item: Kuriyan J

PCR performance of the highly thermostable proof-reading B-type DNA polymerase from Pyrococcus abyssi.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12445650
journal: FEMS Microbiol Lett
volume: 217
pages: 89-94
published year: 2002
authors:
  item: Dietrich J
  item: Schmitt P
  item: Zieger M
  item: Preve B
  item: Rolland JL
  item: Chaabihi H
  item: Gueguen Y

Motors and switches: AAA+ machines within the replisome.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12415300
journal: Nat Rev Mol Cell Biol
volume: 3
pages: 826-35
published year: 2002
authors:
  item: Davey MJ
  item: Jeruzalmi D
  item: Kuriyan J
  item: O'Donnell M

Structural basis for uracil recognition by archaeal family B DNA polymerases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12415291
journal: Nat Struct Biol
volume: 9
pages: 922-7
published year: 2002
authors:
  item: Fogg MJ
  item: Pearl LH
  item: Connolly BA

A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11788711
journal: Nucleic Acids Res
volume: 30
pages: 482-96
published year: 2002
authors:
  item: Makarova KS
  item: Aravind L
  item: Grishin NV
  item: Rogozin IB
  item: Koonin EV

deoxyribonucleic acid polymerase
type: KeggEnzyme

deoxyribonucleic duplicase
type: KeggEnzyme

deoxyribonucleic polymerase
type: KeggEnzyme

deoxyribonucleic polymerase I
type: KeggEnzyme

DNA duplicase
type: KeggEnzyme

DNA nucleotidyltransferase
type: KeggEnzyme

DNA polymerase
type: KeggEnzyme

DNA replicase
type: KeggEnzyme

DNA-dependent DNA polymerase
type: KeggEnzyme

duplicase
type: KeggEnzyme

Klenow fragment
type: KeggEnzyme

sequenase
type: KeggEnzyme

Taq DNA polymerase
type: KeggEnzyme

Taq Pol I
type: KeggEnzyme

Tca DNA polymerase
type: KeggEnzyme

ReferenceForCatalyticMechanism
reference index: 12
reference section: p.453-456

ReferenceForCatalyticMechanism
reference index: 17
reference section: p.471-473